Form and Function of Clostridium thermocellum Biofilms

ABSTRACTThe importance of bacterial adherence has been acknowledged in microbial lignocellulose conversion studies; however, few reports have described the function and structure of biofilms supported by cellulosic substrates. We investigated the organization, dynamic formation, and carbon flow associated with biofilms of the obligately anaerobic cellulolytic bacteriumClostridium thermocellum27405. Using noninvasive,in situfluorescence imaging, we showed biofilms capable of near complete substrate conversion with a characteristic monolayered cell structure without an extracellular polymeric matrix typically seen in biofilms. Cell division at the interface and terminal endospores appeared throughout all stages of biofilm growth. Using continuous-flow reactors with a rate of dilution (2 h−1) 12-fold higher than the bacterium's maximum growth rate, we compared biofilm activity under low (44 g/liter) and high (202 g/liter) initial cellulose loading. The average hydrolysis rate was over 3-fold higher in the latter case, while the proportions of oligomeric cellulose hydrolysis products lost from the biofilm were 13.7% and 29.1% of the total substrate carbon hydrolyzed, respectively. Fermentative catabolism was comparable between the two cellulose loadings, with ca. 4% of metabolized sugar carbon being utilized for cell production, while 75.4% and 66.7% of the two cellulose loadings, respectively, were converted to primary carbon metabolites (ethanol, acetic acid, lactic acid, carbon dioxide). However, there was a notable difference in the ethanol-to-acetic acid ratio (g/g), measured to be 0.91 for the low cellulose loading and 0.41 for the high cellulose loading. The results suggest that substrate availability for cell attachment rather than biofilm colonization rates govern the efficiency of cellulose conversion.

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Expression of 17 Genes in Clostridium thermocellum ATCC 27405 during Fermentation of Cellulose or Cellobiose in Continuous Culture

Applied and Environmental Microbiology ◽

10.1128/aem.71.8.4672-4678.2005 ◽

2005 ◽

Vol 71 (8) ◽

pp. 4672-4678 ◽

Cited By ~ 77

Author(s):

David M. Stevenson ◽

Paul J. Weimer

Keyword(s):

Growth Rate ◽

Acetic Acid ◽

Alcohol Dehydrogenase ◽

Continuous Culture ◽

Clostridium Thermocellum ◽

Product Distribution ◽

Scaffolding Protein ◽

Rrna Gene ◽

Cellulolytic Bacterium ◽

Type Iv

ABSTRACT Clostridium thermocellum is a thermophilic, anaerobic, cellulolytic bacterium that produces ethanol and acetic acid as major fermentation end products. The effect of growth conditions on gene expression in C. thermocellum ATCC 27405 was studied using cells grown in continuous culture under cellobiose or cellulose limitation over a ∼10-fold range of dilution rates (0.013 to 0.16 h−1). Fermentation product distribution displayed similar patterns in cellobiose- or cellulose-grown cultures, including substantial shifts in the proportion of ethanol and acetic acid with changes in growth rate. Expression of 17 genes involved or potentially involved in cellulose degradation, intracellular phosphorylation, catabolite repression, and fermentation end product formation was quantified by real-time PCR, with normalization to two calibrator genes (recA and the 16S rRNA gene) to determine relative expression. Thirteen genes displayed modest (fivefold or less) differences in expression with growth rate or substrate type: sdbA (cellulosomal scaffoldin-dockerin binding protein), cdp (cellodextrin phosphorylase), cbp (cellobiose phosphorylase), hydA (hydrogenase), ldh (lactate dehydrogenase), ack (acetate kinase), one putative type IV alcohol dehydrogenase, two putative cyclic AMP binding proteins, three putative Hpr-like proteins, and a putative Hpr serine kinase. By contrast, four genes displayed >10-fold-reduced levels of expression when grown on cellobiose at dilution rates of >0.05 h−1: cipA (cellulosomal scaffolding protein), celS (exoglucanase), manA (mannanase), and a second type IV alcohol dehydrogenase. The data suggest that at least some cellulosomal components are transcriptionally regulated but that differences in expression with growth rate or among substrates do not directly account for observed changes in fermentation end product distribution.

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Agent-Based Modeling Demonstrates How Local Chemotactic Behavior Can Shape Biofilm Architecture

mSphere ◽

10.1128/msphere.00285-19 ◽

2019 ◽

Vol 4 (3) ◽

Cited By ~ 4

Author(s):

Emily G. Sweeney ◽

Andrew Nishida ◽

Alexandra Weston ◽

Maria S. Bañuelos ◽

Kristin Potter ◽

...

Keyword(s):

Helicobacter Pylori ◽

Three Dimensional ◽

Structural Features ◽

Agent Based Modeling ◽

Emergent Properties ◽

Cellular Interactions ◽

Biofilm Growth ◽

Content Type ◽

Agent Based ◽

H Pylori

ABSTRACTBacteria are often found living in aggregated multicellular communities known as biofilms. Biofilms are three-dimensional structures that confer distinct physical and biological properties to the collective of cells living within them. We used agent-based modeling to explore whether local cellular interactions were sufficient to give rise to global structural features of biofilms. Specifically, we asked whether chemorepulsion from a self-produced quorum-sensing molecule, autoinducer-2 (AI-2), was sufficient to recapitulate biofilm growth and cellular organization observed for biofilms ofHelicobacter pylori, a common bacterial resident of human stomachs. To carry out this modeling, we modified an existing platform, Individual-based Dynamics of Microbial Communities Simulator (iDynoMiCS), to incorporate three-dimensional chemotaxis, planktonic cells that could join or leave the biofilm structure, and cellular production of AI-2. We simulated biofilm growth of previously characterizedH. pyloristrains with various AI-2 production and sensing capacities. Using biologically plausible parameters, we were able to recapitulate both the variation in biofilm mass and cellular distributions observed with these strains. Specifically, the strains that were competent to chemotax away from AI-2 produced smaller and more heterogeneously spaced biofilms, whereas the AI-2 chemotaxis-defective strains produced larger and more homogeneously spaced biofilms. The model also provided new insights into the cellular demographics contributing to the biofilm patterning of each strain. Our analysis supports the idea that cellular interactions at small spatial and temporal scales are sufficient to give rise to larger-scale emergent properties of biofilms.IMPORTANCEMost bacteria exist in aggregated, three-dimensional structures called biofilms. Although biofilms play important ecological roles in natural and engineered settings, they can also pose societal problems, for example, when they grow in plumbing systems or on medical implants. Understanding the processes that promote the growth and disassembly of biofilms could lead to better strategies to manage these structures. We had previously shown thatHelicobacter pyloribacteria are repulsed by high concentrations of a self-produced molecule, AI-2, and thatH. pylorimutants deficient in AI-2 sensing form larger and more homogeneously spaced biofilms. Here, we used computer simulations of biofilm formation to show that localH. pyloribehavior of repulsion from high AI-2 could explain the overall architecture ofH. pyloribiofilms. Our findings demonstrate that it is possible to change global biofilm organization by manipulating local cell behaviors, which suggests that simple strategies targeting cells at local scales could be useful for controlling biofilms in industrial and medical settings.

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Biochemical and Genetic Bases of Indole-3-Acetic Acid (Auxin Phytohormone) Degradation by the Plant-Growth-Promoting Rhizobacterium Paraburkholderia phytofirmans PsJN

Applied and Environmental Microbiology ◽

10.1128/aem.01991-16 ◽

2016 ◽

Vol 83 (1) ◽

Cited By ~ 19

Author(s):

Raúl Donoso ◽

Pablo Leiva-Novoa ◽

Ana Zúñiga ◽

Tania Timmermann ◽

Gonzalo Recabarren-Gajardo ◽

...

Keyword(s):

Energy Source ◽

Gene Regulation ◽

Acetic Acid ◽

Plant Growth ◽

Plant Hormone ◽

Content Type ◽

Gene Functions ◽

Plant Growth Promoting ◽

Growth Promoting ◽

Indole 3 Acetic Acid

ABSTRACT Several bacteria use the plant hormone indole-3-acetic acid (IAA) as a sole carbon and energy source. A cluster of genes (named iac) encoding IAA degradation has been reported in Pseudomonas putida 1290, but the functions of these genes are not completely understood. The plant-growth-promoting rhizobacterium Paraburkholderia phytofirmans PsJN harbors iac gene homologues in its genome, but with a different gene organization and context than those of P. putida 1290. The iac gene functions enable P. phytofirmans to use IAA as a sole carbon and energy source. Employing a heterologous expression system approach, P. phytofirmans iac genes with previously undescribed functions were associated with specific biochemical steps. In addition, two uncharacterized genes, previously unreported in P. putida and found to be related to major facilitator and tautomerase superfamilies, are involved in removal of an IAA metabolite called dioxindole-3-acetate. Similar to the case in strain 1290, IAA degradation proceeds through catechol as intermediate, which is subsequently degraded by ortho-ring cleavage. A putative two-component regulatory system and a LysR-type regulator, which apparently respond to IAA and dioxindole-3-acetate, respectively, are involved in iac gene regulation in P. phytofirmans. These results provide new insights about unknown gene functions and complex regulatory mechanisms in IAA bacterial catabolism. IMPORTANCE This study describes indole-3-acetic acid (auxin phytohormone) degradation in the well-known betaproteobacterium P. phytofirmans PsJN and comprises a complete description of genes, some of them with previously unreported functions, and the general basis of their gene regulation. This work contributes to the understanding of how beneficial bacteria interact with plants, helping them to grow and/or to resist environmental stresses, through a complex set of molecular signals, in this case through degradation of a highly relevant plant hormone.

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Preparation of Sticky Escherichia coli through Surface Display of an Adhesive Catecholamine Moiety

Applied and Environmental Microbiology ◽

10.1128/aem.02223-13 ◽

2013 ◽

Vol 80 (1) ◽

pp. 43-53 ◽

Cited By ~ 18

Author(s):

Joseph P. Park ◽

Min-Jung Choi ◽

Se Hun Kim ◽

Seung Hwan Lee ◽

Haeshin Lee

Keyword(s):

Escherichia Coli ◽

Cell Surface ◽

Communication Systems ◽

Cell Attachment ◽

Surface Display ◽

Content Type ◽

E Coli ◽

Material Surfaces ◽

Mussel Adhesive ◽

Adhesive Proteins

ABSTRACTMussels attach to virtually all types of inorganic and organic surfaces in aqueous environments, and catecholamines composed of 3,4-dihydroxy-l-phenylalanine (DOPA), lysine, and histidine in mussel adhesive proteins play a key role in the robust adhesion. DOPA is an unusual catecholic amino acid, and its side chain is called catechol. In this study, we displayed the adhesive moiety of DOPA-histidine onEscherichia colisurfaces using outer membrane protein W as an anchoring motif for the first time. Localization of catecholamines on the cell surface was confirmed by Western blot and immunofluorescence microscopy. Furthermore, cell-to-cell cohesion (i.e., cellular aggregation) induced by the displayed catecholamine and synthesis of gold nanoparticles on the cell surface support functional display of adhesive catecholamines. The engineeredE. coliexhibited significant adhesion onto various material surfaces, including silica and glass microparticles, gold, titanium, silicon, poly(ethylene terephthalate), poly(urethane), and poly(dimethylsiloxane). The uniqueness of this approach utilizing the engineered stickyE. coliis that no chemistry for cell attachment are necessary, and the ability of spontaneousE. coliattachment allows one to immobilize the cells on challenging material surfaces such as synthetic polymers. Therefore, we envision that mussel-inspired catecholamine yielded stickyE. colithat can be used as a new type of engineered microbe for various emerging fields, such as whole living cell attachment on versatile material surfaces, cell-to-cell communication systems, and many others.

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Microbiological and Physicochemical Characterization of Small-Scale Cocoa Fermentations and Screening of Yeast and Bacterial Strains To Develop a Defined Starter Culture

Applied and Environmental Microbiology ◽

10.1128/aem.01144-12 ◽

2012 ◽

Vol 78 (15) ◽

pp. 5395-5405 ◽

Cited By ~ 86

Author(s):

Gilberto Vinícius de Melo Pereira ◽

Maria Gabriela da Cruz Pedrozo Miguel ◽

Cíntia Lacerda Ramos ◽

Rosane Freitas Schwan

Keyword(s):

Acetic Acid ◽

Lactic Acid ◽

Citric Acid ◽

Dominant Species ◽

Starter Culture ◽

Physicochemical Characterization ◽

Cocoa Bean ◽

Small Scale ◽

Content Type ◽

Cocoa Bean Fermentation

ABSTRACTSpontaneous cocoa bean fermentations performed under bench- and pilot-scale conditions were studied using an integrated microbiological approach with culture-dependent and culture-independent techniques, as well as analyses of target metabolites from both cocoa pulp and cotyledons. Both fermentation ecosystems reached equilibrium through a two-phase process, starting with the simultaneous growth of the yeasts (withSaccharomyces cerevisiaeas the dominant species) and lactic acid bacteria (LAB) (Lactobacillus fermentumandLactobacillus plantarumwere the dominant species), which were gradually replaced by the acetic acid bacteria (AAB) (Acetobacter tropicaliswas the dominant species). In both processes, a sequence of substrate consumption (sucrose, glucose, fructose, and citric acid) and metabolite production kinetics (ethanol, lactic acid, and acetic acid) similar to that of previous, larger-scale fermentation experiments was observed. The technological potential of yeast, LAB, and AAB isolates was evaluated using a polyphasic study that included the measurement of stress-tolerant growth and fermentation kinetic parameters in cocoa pulp media. Overall, strainsL. fermentumUFLA CHBE8.12 (citric acid fermenting, lactic acid producing, and tolerant to heat, acid, lactic acid, and ethanol),S. cerevisiaeUFLA CHYC7.04 (ethanol producing and tolerant to acid, heat, and ethanol), andAcetobacter tropicalisUFLA CHBE16.01 (ethanol and lactic acid oxidizing, acetic acid producing, and tolerant to acid, heat, acetic acid, and ethanol) were selected to form a cocktail starter culture that should lead to better-controlled and more-reliable cocoa bean fermentation processes.

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Additive manufacturing of elastomeric foam with cell unit design for broadening compressive stress plateau

Rapid Prototyping Journal ◽

10.1108/rpj-09-2017-0172 ◽

2018 ◽

Vol 24 (9) ◽

pp. 1579-1585 ◽

Cited By ~ 3

Author(s):

Xiaowei Zhu ◽

Yanqiu Chen ◽

Yu Liu ◽

Yongqiang Deng ◽

Changyu Tang ◽

...

Keyword(s):

Additive Manufacturing ◽

Compressive Stress ◽

Foam Cell ◽

Cell Structure ◽

Performance Testing ◽

Elastic Buckling ◽

Stress Plateau ◽

Content Type ◽

Direct Ink Writing ◽

Unit Design

Purpose The purpose of this paper is to provide additive manufacturing-based solutions for preparation of elastomeric foam with broaden compressive stress plateau. Design/methodology/approach Mechanic models are developed for obtaining designs of foam cell units with enhanced elastic buckling. An experimental approach is taken to fabricate the foams based on direct ink writing technique. Experimental and simulation data are collected to assist understanding of our proposals and solutions. Findings A simple tetragonal structured elastomeric foam is proposed and fabricated by direct ink writing, in which its cell unit is theoretically designed by repeating every four filament layers. The foam exhibits a broader stress plateau, because of the pronounced elastic buckling under compressive loading as predicted by the authors’ mechanic modeling. A two-stage stress plateaus as observed in the foam, being attributed to the dual elastic buckling of the cell units along two lateral directions of the XY plane during compression. Research limitations/implications Future work should incorporate more microscopic parameters to tune the elastomeric foam for mechanic performance testing on linear elastic deformation and densification of polymer matrix. Practical implications Additive manufacturing offers an alternative to fabricate elastomeric foam with controlled cell unit design and therefore mechanics. Our results comment on its broad space for development such superior cushioning or damping material in the fields of vibration and energy absorption. Originality/value This work has contributed to new knowledge on preparation of high performance elastomeric foam by providing a better understanding on its cell structure, being printed using direct ink writing machines.

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Decoding Antibacterial and Antibiofilm Properties of Cinnamon and Cardamom Essential Oils: A Combined Molecular Docking and Experimental Study

10.21203/rs.3.rs-955241/v1 ◽

2021 ◽

Author(s):

Elahe Pourkhosravani ◽

fatemeh dehghan nayeri ◽

Mitra Mohammadi Bazargani

Keyword(s):

Cell Attachment ◽

Antibacterial Properties ◽

Binding Mode ◽

Dilution Method ◽

Antibiofilm Activity ◽

Bacterial Strains ◽

Biofilm Growth ◽

Computational Docking ◽

E Coli ◽

Industrial Strains

Abstract This study sets out to compare the antibacterial and antibiofilm profiles of Ci/Ca EOs alone and in combination together against infectious bacterial strains. MIC assay was carried out to survey the effectiveness of prepared EOs by two-fold serial dilution method and MTT evaluation. Synergic antibacterial properties of EOs against target strains were studied by using checkerboard titration method. Biofilm growth and development were evaluated using CV and XTT reduction assays. Antibacterial activity was observed for EOs against both bacterial strains with stronger activity for CiEO against both bacteria. The synergistic antibacterial effect was observed only against B. subtilis. Based on the FIC index, combinations could not inhibit the growth of E. coli. The pure EOs and their combination inhibited cell attachment for both studied bacteria with stronger effect on E. coli. CV and XTT reduction assays results showed that Ci EO and its combination with CaEO had the highest antibiofilm activity at lowest MIC value 0.08% and 0.04/0.02% against biofilm formed by E. coli and B. subtilis respectively, indicating a high antibiofilm potential. Computational docking analyses also postulated that the active constituents of evaluated EOs have the potential to interact with different bacterial targets, suggested binding mode of action of EOs metabolites. By and large, synergistic anti-biofilm properties of EOs may provide further options for developing novel formula to inhibit a variety of infectious clinical and industrial strains without (or less) toxicity effects on human body.

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Effects of Biofilm Growth on Plasmid Copy Number and Expression of Antibiotic Resistance Genes in Enterococcus faecalis

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02010-12 ◽

2013 ◽

Vol 57 (4) ◽

pp. 1850-1856 ◽

Cited By ~ 17

Author(s):

L. C. Cook ◽

G. M. Dunny

Keyword(s):

Antibiotic Resistance ◽

Enterococcus Faecalis ◽

Resistance Genes ◽

Copy Number ◽

Antibiotic Resistance Genes ◽

Plasmid Copy Number ◽

Plasmid Copy ◽

Rapid Reduction ◽

Biofilm Growth ◽

Content Type

ABSTRACTBiofilm growth causes increased average plasmid copy number as well as increased copy number heterogeneity inEnterococcus faecaliscells carrying plasmid pCF10. In this study, we examined whether biofilm growth affected the copy number and expression of antibiotic resistance determinants for several plasmids with diverse replication systems. Four differentE. faecalisplasmids, unrelated to pCF10, demonstrated increased copy number in biofilm cells. In biofilm cells, we also observed increased transcription of antibiotic resistance genes present on these plasmids. The increase in plasmid copy number correlated with increased plating efficiency on high concentrations of antibiotics. Single-cell analysis of strains carrying two different plasmids suggested that the increase in plasmid copy number associated with biofilm growth was restricted to a subpopulation of biofilm cells. Regrowth of harvested biofilm cells in liquid culture resulted in a rapid reduction of plasmid copy number to that observed in the planktonic state. These results suggest a possible mechanism by which biofilm growth could reduce susceptibility to antibiotics in clinical settings.

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Entomobacter blattae gen. nov., sp. nov., a new member of the Acetobacteraceae isolated from the gut of the cockroach Gromphadorhina portentosa

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004666 ◽

2019 ◽

Vol 71 (3) ◽

Cited By ~ 8

Author(s):

Juan Guzman ◽

Atena Sadat Sombolestani ◽

Anja Poehlein ◽

Rolf Daniel ◽

Ilse Cleenwerck ◽

...

Keyword(s):

Acetic Acid ◽

16S Rrna ◽

Type Species ◽

New Genus ◽

Protein Sequences ◽

Acetic Acid Bacteria ◽

Content Type ◽

Link Type ◽

The Family ◽

Gromphadorhina Portentosa

A novel bacterium designated G55GPT and pertaining to the family Acetobacteraceae was isolated from the gut of the Madagascar hissing cockroach Gromphadorhina portentosa. The Gram-negative cells were rod-shaped and non-motile. The complete 16S rRNA sequence of the strain G55GPT showed the highest pairwise similarity to Gluconacetobacter johannae CFN-Cf-55T (95.35 %), suggesting it represents a potential new genus of the family Acetobacteraceae . Phylogenetic analysis based on 16S rRNA gene and 106 orthologous housekeeping protein sequences revealed that G55GPT forms a monophyletic clade with the genus Commensalibacter , which thus far has also been isolated exclusively from insects. The G55GPT genome size was 2.70 Mbp, and the G+C content was 45.4 mol%, which is lower than most acetic acid bacteria (51–68 mol%) but comparable to Swingsia samuiensis AH83T (45.1 mol%) and higher than Commensalibacter intestini A911T (36.8 mol%). Overall genome relatedness indices based on gene and protein sequences strongly supported the assignment of G55GPT to a new genus within the family Acetobacteraceae . The percentage of conserved proteins, which is a useful metric for genus differentiation, was below 54 % when comparing G55GPT to type strains of acetic acid bacteria, thus strongly supporting our hypothesis that G55GPT is a member of a yet-undescribed genus. The fatty acid composition of G55GPT differed from that of closely related acetic acid bacteria, particularly given the presence of C19 : 1 ω9c/ω11c and the absence of C14 : 0 and C14 : 0 2-OH fatty acids. Strain G55GPT also differed in terms of metabolic features such as its ability to produce acid from d-mannitol, and its inability to produce acetic acid from ethanol or to oxidize glycerol to dihydroxyacetone. Based on the results of combined genomic, phenotypic and phylogenetic characterizations, isolate G55GPT (=LMG 31394T=DSM 111244T) is considered to represent a new species in a new genus, for which we propose the name Entomobacter blattae gen. nov., sp. nov.

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