scholarly journals Development of a Novel Biofilm Continuous Culture Method for Simultaneous Assessment of Architecture and Gaseous Metabolite Production

2008 ◽  
Vol 74 (17) ◽  
pp. 5429-5435 ◽  
Author(s):  
Yutaka Yawata ◽  
Nobuhiko Nomura ◽  
Hiroo Uchiyama
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Flow Reactor ◽  
Culture Method ◽  
Model System ◽  
Metabolite Production ◽  
Biofilm Architecture ◽  
Novel Method ◽  
Architecture Development ◽  
Simultaneous Assessment ◽  
Gaseous Metabolites

ABSTRACT The way that gaseous metabolite production changes along with biofilm architecture development is poorly understood. To address this question, we developed a novel flow reactor biofilm culture method that allows for simultaneous assessment of gaseous metabolite production and architecture visualization. In this report, we establish the utility of this method using denitrification by Pseudomonas aeruginosa biofilms as a model system. Using this method, we were able to collect and analyze gaseous metabolites produced by denitrification and also visualize biofilm architecture in a nondestructive manner. Thus, we propose that this novel method is a powerful tool to investigate potential relationships between biofilm architecture and the gas-producing metabolic activity of biofilms, providing new insights into biofilm ecology.

Effect of nucleic acid stain Syto9 on nascent biofilm architecture of Acinetobacter sp. BD413

2005 ◽  
Vol 52 (7) ◽  
pp. 195-202 ◽  
Author(s):  
R. GrayMerod ◽  
L. Hendrickx ◽  
L.N. Mueller ◽  
J.B. Xavier ◽  
S. Wuertz
Keyword(s):  
Nucleic Acid ◽  
Microbial Population ◽  
Separate Flow ◽  
Flow Cell ◽  
Cellular Level ◽  
Flow Cells ◽  
Biofilm Architecture ◽  
Acinetobacter Sp ◽  
Nucleic Acid Stain ◽  
Architecture Development

Flow cells were utilized to determine the effects of repetitive Syto9 staining on developing Acinetobacter sp. BD413 biofilm and to identify features describing reproducible biofilm architecture at 63× magnification. Syto9 is a general nucleic acid stain employed to visualize the entire microbial population of the biofilm and a component in the LIVE/DEAD® BacLight™ Bacterial Viability kits. CLSM images were quantified with the biofilm analysis software PHLIP to calculate six commonly used biofilm architecture characteristics. The characteristics biovolume and mean thickness were most reproducible when biofilms were grown in separate flow cells under controlled conditions, while roughness, porosity, total spreading and surface area to biovolume ratio exhibited inherent variability. Biovolume was more variable in separate flow cells than in channels of the same flow cell. However, even biofilms grown in channels of the same flow cell did not generate reproducible architectures based on the six characteristics. Results suggest difficulties in differentiating the effect of changes due to treatment from the natural variability of architecture development at the cellular level. Despite this high variability, biofilms only stained once developed into thicker structures containing more biomass than biofilms stained multiple times, suggesting that repeated staining with Syto9 affects architecture development. The application of Syto9 to monitor developing biofilms is not recommended.

scholarly journals Spatial Patterns of Carbonate Biomineralization in Biofilms

2015 ◽  
Vol 81 (21) ◽  
pp. 7403-7410 ◽  
Author(s):  
Xiaobao Li ◽  
David L. Chopp ◽  
William A. Russin ◽  
Paul T. Brannon ◽  
Matthew R. Parsek ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Important Process ◽  
Mineral Precipitation ◽  
Content Type ◽  
Biofilm Architecture ◽  
The Common ◽  
Engineered Systems ◽  
Over Time ◽  
Carbonate Deposits

ABSTRACTMicrobially catalyzed precipitation of carbonate minerals is an important process in diverse biological, geological, and engineered systems. However, the processes that regulate carbonate biomineralization and their impacts on biofilms are largely unexplored, mainly because of the inability of current methods to directly observe biomineralization within biofilms. Here, we present a method forin situ, real-time imaging of biomineralization in biofilms and use it to show thatPseudomonas aeruginosabiofilms produce morphologically distinct carbonate deposits that substantially modify biofilm structures. The patterns of carbonate biomineralization producedin situwere substantially different from those caused by accumulation of particles produced by abiotic precipitation. Contrary to the common expectation that mineral precipitation should occur at the biofilm surface, we found that biomineralization started at the base of the biofilm. The carbonate deposits grew over time, detaching biofilm-resident cells and deforming the biofilm morphology. These findings indicate that biomineralization is a general regulator of biofilm architecture and properties.

scholarly journals An integrated model system to gain mechanistic insights into biofilm formation and antimicrobial resistance development in Pseudomonas aeruginosa MPAO1

2020 ◽  
Author(s):  
Adithi R. Varadarajan ◽  
Raymond N. Allan ◽  
Jules D. P. Valentin ◽  
Olga E. Castañeda Ocampo ◽  
Vincent Somerville ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Biofilm Formation ◽  
Soft Lithography ◽  
Flow Chamber ◽  
Model System ◽  
Secretion Systems ◽  
Phenotypic Data ◽  
Biofilm Growth ◽  
Mutant Collection

AbstractPseudomonas aeruginosa MPAO1 is the parental strain of the widely utilized transposon mutant collection for this important clinical pathogen. Here, we validate a model system to identify genes involved in biofilm growth and antibiotic resistance.Our model employs a genomics-driven workflow to assemble the complete MPAO1 genome, identify unique and conserved genes by comparative genomics with the PAO1 reference strain and missed genes by proteogenomics. Among over 200 unique MPAO1 genes, we identified six general essential genes that were overlooked when mapping public Tn-seq datasets against PAO1, including an antitoxin. Genomic data were integrated with phenotypic data from an experimental workflow using a user-friendly, soft lithography-based microfluidic flow chamber for biofilm growth. Experiments conducted across three laboratories delivered reproducible data on P. aeruginosa biofilms and validated both known and novel genes involved in biofilm growth and antibiotic resistance identified in screens of the mutant collection. Differential protein expression data from planktonic cells versus biofilm confirmed upregulation of candidates known to affect biofilm formation, of structural and secreted proteins of type six secretion systems, and provided proteogenomic evidence for some missed MPAO1 genes. This integrated, broadly applicable model promises to improve the mechanistic understanding of biofilm formation, antimicrobial tolerance and resistance evolution.

Generalized Application of Periodic Symmetry in Molecular Simulations

2003 ◽  
Author(s):  
Li Pan ◽  
Don Metzger ◽  
Marek Niewczas
Keyword(s):  
Molecular Simulations ◽  
Model System ◽  
New Method ◽  
Simulation Algorithm ◽  
Element Analysis ◽  
Kinematic Constraints ◽  
One Dimensional ◽  
Novel Method ◽  
External Forces ◽  
Physical Boundary

Periodic symmetry is widely used in molecular simulations to mimic the presence of an infinite bulk surrounding an N-atom model system. However, the traditional methods of applying periodic symmetry end up enforcing over-restrictive kinematic constraints between the periodic boundaries. After a brief overview of the periodic symmetry, the nature of the constraint is discussed briefly in this paper. Thereafter, the objective is to provide a means to ensure that periodicity is upheld while avoiding unnecessary constraint of the repeating cell boundaries. This paper demonstrates the usual application of periodic symmetry into a molecular simulation algorithm through a typical example. Meanwhile, a novel method is introduced, which uses equivalent external forces applied to physical boundary atoms. Comparisons between the classic treatment and the new method using one-dimensional and two-dimensional models are made. Moreover, the potential application of the new method in regular Finite Element Analysis is discussed.

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