Bacteria grow in either planktonic form or as biofilms, which are attached to either inert or biological surfaces. Both growth forms are highly relevant states in nature and of paramount scientific ...focus. However, interchanges between bacteria in these two states have been little explored. We discovered that a subpopulation of planktonic bacilli is propelled by flagella to tunnel deep within a biofilm structure. Swimmers create transient pores that increase macromolecular transfer within the biofilm. Irrigation of the biofilm by swimmer bacteria may improve biofilm bacterial fitness by increasing nutrient flow in the matrix. However, we show that the opposite may also occur (i.e., swimmers can exacerbate killing of biofilm bacteria by facilitating penetration of toxic substances from the environment). We combined these observations with the fact that numerous bacteria produce antimicrobial substances in nature. We hypothesized and proved that motile bacilli expressing a bactericide can also kill a heterologous biofilm population, Staphylococcus aureus in this case, and then occupy the newly created space. These findings identify microbial motility as a determinant of the biofilm landscape and add motility to the complement of traits contributing to rapid alterations in biofilm populations.
Complex regulatory programs control cell adaptation to environmental changes by setting condition‐specific proteomes. In balanced growth, bacterial protein abundances depend on the dilution rate, ...transcript abundances and transcript‐specific translation efficiencies. We revisited the current theory claiming the invariance of bacterial translation efficiency. By integrating genome‐wide transcriptome datasets and datasets from a library of synthetic gfp‐reporter fusions, we demonstrated that translation efficiencies in Bacillus subtilis decreased up to fourfold from slow to fast growth. The translation initiation regions elicited a growth rate‐dependent, differential production of proteins without regulators, hence revealing a unique, hard‐coded, growth rate‐dependent mode of regulation. We combined model‐based data analyses of transcript and protein abundances genome‐wide and revealed that this global regulation is extensively used in B. subtilis. We eventually developed a knowledge‐based, three‐step translation initiation model, experimentally challenged the model predictions and proposed that a growth rate‐dependent drop in free ribosome abundance accounted for the differential protein production.
Synopsis
Genome‐wide transcriptome and proteome data, measurements of translation efficiency in a library of synthetic reporter fusions and a mathematical model of protein production show that translation efficiency is growth rate dependent and transcript specific.
The gene‐specific translation initiation region (TIR) drives a growth‐dependent, differential production of proteins in the absence of regulators.
Bacterial translation efficiency drops with increasing growth rate and is well represented by a Michaelis–Menten‐type rate law as a function of free ribosomes.
The mathematical model of protein production was challenged with transcriptome and proteome data and revealed a large repertoire of differentially translated transcripts as a function of the growth rate.
Genome‐wide transcriptome and proteome data, measurements of translation efficiency in a library of synthetic reporter fusions and a mathematical model of protein production show that translation efficiency is growth rate dependent and transcript specific.
Summary
Almost one‐third of crop yields are lost every year due to microbial alterations and diseases. The main control strategy to limit these losses is the use of an array of chemicals active ...against spoilage and unwanted pathogenic microorganisms. Their massive use has led to extensive environmental pollution, human poisoning and a variety of diseases. An emerging alternative to this chemical approach is the use of microbial biocontrol agents. Biopesticides have been used with success in several fields, but a better understanding of their mode of action is necessary to better control their activity and increase their use. Very few studies have considered that biofilms are the preferred mode of life of microorganisms in the target agricultural biotopes. Increasing evidence shows that the spatial organization of microbial communities on crop surfaces may drive important bioprotection mechanisms. The aim of this review is to summarize the evidence of biofilm formation by biocontrol agents on crops and discuss how this surface‐associated mode of life may influence their biology and interactions with other microorganisms and the host and, finally, their overall beneficial activity.
The aim of this review is to summarize the evidence of biofilm formation by biocontrol agents on crops and discuss how this surface‐associated mode of life may influence their biology and interactions with other microorganisms and the host, and finally, their overall beneficial activity.
•Bacillus velezensis QST713 strongly protects Agaricus bisporus crops against Trichoderma aggressivum in France.•The complete genome of this commercial biofungicide was sequenced and described.•It ...encodes at least 15 secondary metabolite gene clusters including two potential new antimicrobials.•It forms robust and highly complex 3D structured biofilm.•The availability of the genome data provides information for further exploration and understanding of biocontrol mechanisms.
Bacillus subtilis QST713 is extensively used as a biological control agent in agricultural fields including in the button mushroom culture, Agaricus bisporus. This last use exploits its inhibitory activity against microbial pathogens such as Trichoderma aggressivum f. europaeum, the main button mushroom green mould competitor. Here, we report the complete genome sequence of this bacterium with a genome size of 4 233 757 bp, 4263 predicted genes and an average GC content of 45.9%. Based on phylogenomic analyses, strain QST713 is finally designated as Bacillus velezensis. Genomic analyses revealed two clusters encoding potential new antimicrobials with NRPS and TransATPKS synthetase. B. velezensis QST713 genome also harbours several genes previously described as being involved in surface colonization and biofilm formation. This strain shows a strong ability to form in vitro spatially organized biofilm and to antagonize T. aggressivum. The availability of this genome sequence could bring new elements to understand the interactions with micro or/and macroorganisms in crops.
Biofilm formation by 102 Bacillus cereus and B. thuringiensis strains was determined. Strains isolated from soil or involved in digestive tract infections were efficient biofilm formers, whereas ...strains isolated from other diseases were poor biofilm formers. Cell surface hydrophobicity, the presence of an S layer, and adhesion to epithelial cells were also examined.
Predicting resource allocation between cell processes is the primary step towards decoding the evolutionary constraints governing bacterial growth under various conditions. Quantitative prediction at ...genome-scale remains a computational challenge as current methods are limited by the tractability of the problem or by simplifying hypotheses. Here, we show that the constraint-based modeling method Resource Balance Analysis (RBA), calibrated using genome-wide absolute protein quantification data, accurately predicts resource allocation in the model bacterium Bacillus subtilis for a wide range of growth conditions. The regulation of most cellular processes is consistent with the objective of growth rate maximization except for a few suboptimal processes which likely integrate more complex objectives such as coping with stressful conditions and survival. As a proof of principle by using simulations, we illustrated how calibrated RBA could aid rational design of strains for maximizing protein production, offering new opportunities to investigate design principles in prokaryotes and to exploit them for biotechnological applications.
•We introduced the constraint-based modeling method Resource Balance Analysis (RBA).•We measured absolute abundances of most of cytosolic proteins in 5 conditions.•We identified the apparent catalytic rates of cytosolic proteins.•We accurately predicted the resource allocation of B. subtilis using RBA.•RBA performs realistic simulations of protein excretion.
Many organisms coordinate cell growth and division through size control mechanisms: cells must reach a critical size to trigger a cell cycle event. Bacterial division is often assumed to be ...controlled in this way, but experimental evidence to support this assumption is still lacking. Theoretical arguments show that size control is required to maintain size homeostasis in the case of exponential growth of individual cells. Nevertheless, if the growth law deviates slightly from exponential for very small cells, homeostasis can be maintained with a simple 'timer' triggering division. Therefore, deciding whether division control in bacteria relies on a 'timer' or 'sizer' mechanism requires quantitative comparisons between models and data.
The timer and sizer hypotheses find a natural expression in models based on partial differential equations. Here we test these models with recent data on single-cell growth of Escherichia coli. We demonstrate that a size-independent timer mechanism for division control, though theoretically possible, is quantitatively incompatible with the data and extremely sensitive to slight variations in the growth law. In contrast, a sizer model is robust and fits the data well. In addition, we tested the effect of variability in individual growth rates and noise in septum positioning and found that size control is robust to this phenotypic noise.
Confrontations between cell cycle models and data usually suffer from a lack of high-quality data and suitable statistical estimation techniques. Here we overcome these limitations by using high precision measurements of tens of thousands of single bacterial cells combined with recent statistical inference methods to estimate the division rate within the models. We therefore provide the first precise quantitative assessment of different cell cycle models.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
In eukaryotes, RNA species originating from pervasive transcription are regulators of various cellular processes, from the expression of individual genes to the control of cellular development and ...oncogenesis. In prokaryotes, the function of pervasive transcription and its output on cell physiology is still unknown. Most bacteria possess termination factor Rho, which represses pervasive, mostly antisense, transcription. Here, we investigate the biological significance of Rho-controlled transcription in the Gram-positive model bacterium Bacillus subtilis. Rho inactivation strongly affected gene expression in B. subtilis, as assessed by transcriptome and proteome analysis of a rho-null mutant during exponential growth in rich medium. Subsequent physiological analyses demonstrated that a considerable part of Rho-controlled transcription is connected to balanced regulation of three mutually exclusive differentiation programs: cell motility, biofilm formation, and sporulation. In the absence of Rho, several up-regulated sense and antisense transcripts affect key structural and regulatory elements of these differentiation programs, thereby suppressing motility and biofilm formation and stimulating sporulation. We dissected how Rho is involved in the activity of the cell fate decision-making network, centered on the master regulator Spo0A. We also revealed a novel regulatory mechanism of Spo0A activation through Rho-dependent intragenic transcription termination of the protein kinase kinB gene. Altogether, our findings indicate that distinct Rho-controlled transcripts are functional and constitute a previously unknown built-in module for the control of cell differentiation in B. subtilis. In a broader context, our results highlight the recruitment of the termination factor Rho, for which the conserved biological role is probably to repress pervasive transcription, in highly integrated, bacterium-specific, regulatory networks.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The development of a biofilm constitutes a survival strategy by providing bacteria a protective environment safe from stresses such as microbicide action and can thus lead to important health-care ...problems. In this study, biofilm resistance of a Bacillus subtilis strain (called hereafter ND(medical)) recently isolated from endoscope washer-disinfectors to peracetic acid was investigated and its ability to protect the pathogen Staphylococcus aureus in mixed biofilms was evaluated. Biocide action within Bacillus subtilis biofilms was visualised in real time using a non-invasive 4D confocal imaging method. The resistance of single species and mixed biofilms to peracetic acid was quantified using standard plate counting methods and their architecture was explored using confocal imaging and electronic microscopy. The results showed that the ND(medical) strain demonstrates the ability to make very large amount of biofilm together with hyper-resistance to the concentration of PAA used in many formulations (3500 ppm). Evidences strongly suggest that the enhanced resistance of the ND(medical) strain was related to the specific three-dimensional structure of the biofilm and the large amount of the extracellular matrix produced which can hinder the penetration of peracetic acid. When grown in mixed biofilm with Staphylococcus aureus, the ND(medical) strain demonstrated the ability to protect the pathogen from PAA action, thus enabling its persistence in the environment. This work points out the ability of bacteria to adapt to an extremely hostile environment, and the necessity of considering multi-organism ecosystems instead of single species model to decipher the mechanisms of biofilm resistance to antimicrobials agents.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Biofilms constitute the prevalent way of life for microorganisms in both natural and man-made environments. Biofilm-dwelling cells display greater tolerance to antimicrobial agents than those that ...are free-living, and the mechanisms by which this occurs have been investigated extensively using single-strain axenic models. However, there is growing evidence that interspecies interactions may profoundly alter the response of the community to such toxic exposure. In this paper, we propose an overview of the studies dealing with multispecies biofilms resistance to biocides, with particular reference to the protection of pathogenic species by resident surface flora when subjected to disinfectants treatments. The mechanisms involved in such protection include interspecies signaling, interference between biocides molecules and public goods in the matrix, or the physiology and genetic plasticity associated with a structural spatial arrangement. After describing these different mechanisms, we will discuss the experimental methods available for their analysis in the context of complex multispecies biofilms.
PDF
