Biofilms in lab and nature: a molecular geneticist’s voyage to microbial ecology

This article reviews the latest findings on how extracellular signaling controls cell fate determination during the process of biofilm formation by Bacillus subtilis in the artificial setting of the laboratory. To complement molecular genetic approaches, surface-associated communities in settings as diverse as the pitcher plant Sarracenia purpurea and the human lung were investigated. The study of the pitcher plant revealed that the presence or absence of a mosquito larva in the pitcherplant controlled bacterial diversity in the ecosystem inside the pitcher plant. Through the analysis of the respiratory tract microbiota of humans suffering from cystic fibrosis (CF) a correlation between lung function and bacterial community diversity was found. Those that had lungs in good condition had also more diverse communities, whereas patients harboring Pseudomonas aeruginosa—the predominant CF pathogen—in their lungs had less diverse communities. Further studies focused on interspecies and intraspecies relationships at the molecular level in search for signaling molecules that would promote biofilm formation. Two molecules were found that induced biofilm formation in B. subtilis: nystatin—released by other species—and surfactin—released by B. subtilis itself. This is a role not previously known for two molecules that were known for other activities—nystatin as an antifungal and surfactin as a surfactant.  In addition, surfactin was found to also trigger cannibalismunder starvation. This could be a strategy to maintain the population because the cells destroyed serve as nutrientsfor the rest. The path that led the author to the study of microbial biofilms is also described. [Int Microbiol 2010; 13(1):1-7

Histones Join the Fight against Bacteria Inside Cells

Experiments on Drosophila have shown that the histones that are normally bound to lipid droplets inside cells can be released to provide protection against infection

Mutualistic interaction between Salmonella enterica and Aspergillus niger and its effects on Zea mays colonization

Salmonella Typhimurium inhabits a variety of environments and is able to infect a broad range of hosts. Throughout its life cycle, some hosts can act as intermediates in the path to the infection of others. Aspergillus niger is a ubiquitous fungus that can often be found in soil or associated to plants and microbial consortia. Recently, S. Typhimurium was shown to establish biofilms on the hyphae of A. niger. In this work, we have found that this interaction is stable for weeks without a noticeable negative effect on either organism. Indeed, bacterial growth is promoted upon the establishment of the interaction. Moreover, bacterial biofilms protect the fungus from external insults such as the effects of the anti-fungal agent cycloheximide. Thus, the Salmonella–Aspergillus interaction can be defined as mutualistic. A tripartite gnotobiotic system involving the bacterium, the fungus and a plant revealed that co-colonization has a greater negative effect on plant growth than colonization by either organism in dividually. Strikingly, co-colonization also causes a reduction in plant invasion by S. Typhimurium. This work demonstrates that S. Typhimurium and A. niger establish a mutualistic interaction that alters bacterial colonization of plants and affects plant physiology

Why are bacteria refractory to antimicrobials?

La incidència de la resistència als antibiòtics en bacteris patògens està augmentant. Aquesta resistència es pot aconseguir mitjançant tres rutes clares: amb la inactivació del medicament, amb la modificació de la diana (target) i amb la disminució de la concentració del medicament que arriba a la diana. Des de fa temps se sap que els mecanismes de resistència a antibiòtics específics es poden adquirir a través de mutacions en el genoma bacterià o mitjançant l'addició de més gens durant el trasllat horitzontal de gens. Recentment, també s'ha descobert la importància dels diferents estats fisiològics per a la supervivència dels bacteris en presència d'antibiòtics. Ara és aparent que els bacteris tenen complexos mecanismes de resistència intrínsecs que sovint no es detecten en les proves estàndards de sensibilitat que es fan als antibiòtics en els laboratoris clínics. Entre aquests mecanismes intrínsecs, és de suma importància el desenvolupament de la resistència en bacteris que es troben en agregats associats a superfícies o biopel·lícules.The incidence of antibiotic resistance in pathogenic bacteria is rising. Antibiotic resistance can be achieved via three distinct routes: inactivation of the drug, modification of the target of action, and decreasing the concentration of drug that can reach the target. It has long been recognized that specific antibiotic resistance mechanisms can be acquired through mutation of the bacterial genome or by the addition of genes through horizontal gene transfer. Recent attention has also brought to light the importance of different physiological states for the survival of bacteria in the presence of antibiotics. It is now apparent that bacteria have complex, intrinsic resistance mechanisms that oftentimes are not detected in the standard antibiotic sensitivity tests performed in clinical laboratories. Paramount among these intrinsic mechanisms is the development of resistance in bacteria found in surface-associated aggregates or biofilms

Functional amyloids in bacteria

The term amyloidosis is used to refer to a family of pathologies altering the homeostasis of human organs. Despite having a name that alludes to starch content, the amyloid accumulations are made up of proteins that polymerize as long and rigid fibers. Amyloid proteins vary widely with respect to their amino acid sequences but they share similarities in their quaternary structure; the amyloid fibers are enriched in β-sheets arranged perpendicular to the axis of the fiber. This structural feature provides great robustness, remarkable stability, and insolubility. In addition, amyloid proteins specifically stain with certain dyes such as Congo red and thioflavin-T. The aggregation into amyloid fibers, however, it is not restricted to pathogenic processes, rather it seems to be widely distributed among proteins and polypeptides. Amyloid fibers are present in insects, fungi and bacteria, and they are important in maintaining the homeostasis of the organism. Such findings have motivated the use of the term “functional amyloid” to differentiate these amyloid proteins from their toxic siblings. This review focuses on systems that have evolved in bacteria that control the expression and assembly of amyloid proteins on cell surfaces, such that the robustness of amyloid proteins are used towards a beneficial end. [Int Microbiol 2014; 17(2):65-73]Keywords: Bacillus subtilis · bacterial biofilms · extracellular matrix · TasA amyloid-like fiber

Computational analysis of bacterial sulfatases and their modifying enzymes

AbstractThe sequence analysis of enzymes that might modify bacterial sulfatases should be useful in the task of identifying the human sulfatase-modifying homologs — enzymes that are defective in the rare inherited disease multi-sulfatase deficiency

Selfish and Altruistic Bacterial Populations Maximize Fitness Under Stress by Local Segregation

Landscapes in ecology have a profound influence on the adaption and evolution of competing populations for resources. We are interested in how altruistic populations survive in the presence of selfish individuals in a non-stirred, closed and complex nutrient landscape. Well-stirred (landscape-free) but closed environments have a depressing future when selfish individuals arise in a population, a fate known as the tragedy of the Commons. Over-exploitation of a well-stirred communal habitat by selfish individuals which do not follow rules of communal self-regulation ends up in the elimination (extinction) of both the original altruistic inhabitants and the selfish population. In the context of bacterial population, the Commons tragedy that occurs is the consumption of limited resources by the individuals, resulting in metabolic stressing of the bacteria and growth advantages to be gained by defection from a ``social contract" of altruistic cooperation. There is no avoidance of this tragedy and the collapse of an original altruistic wild-type population by an emergent selfish population in a well-stirred but closed environment is inevitable. However, there is a fundamental difference between resource exploitation in a well-stirred homogenous commons and in a heterogenous landscape of nutrients which is not stirred. We show here using a non-stirred nanofabricated habitat landscape that altruists and selfish bacteria can in fact coexist, that they can maintain phenotype diversity and avoid the tragedy of the Commons. This emergent spatial segregation of competing populations under stress greatly changes, we believe, our perception of the true sophistication of bacterial response to stress and competition, and has broad implications for the adaptive strategies of higher organisms under stress in complex environments

Complete Genome Sequences of Seven Strains Composing a Model Bacterial Community of Maize Roots

ABSTRACT Previously, we assembled a model bacterial community of maize roots. Here, we report the complete genome sequences of the seven strains composing the community

Whole-Genome Sequences of 94 Environmental Isolates of Bacillus cereus Sensu Lato

Bacillus cereus sensu lato is a species complex that includes the anthrax pathogen Bacillus anthracis and other bacterial species of medical, industrial, and ecological importance. Their phenotypes of interest are typically linked to large plasmids that are closely related to the anthrax plasmids pXO1 and pXO2. Here, we present the draft genome sequences of 94 isolates of B. cereus sensu lato, which were chosen for their plasmid content and environmental origins