Staffan Kjelleberg

Involvement of nitric oxide in biofilm dispersal of Pseudomonas aeruginosa

Publisher: American Society for Microbiology

Date: 11-2006

DOI: 10.1128/JB.00779-06

Abstract: Bacterial biofilms at times undergo regulated and coordinated dispersal events where sessile biofilm cells convert to free-swimming, planktonic bacteria. In the opportunistic pathogen Pseudomonas aeruginosa , we previously observed that dispersal occurs concurrently with three interrelated processes within mature biofilms: (i) production of oxidative or nitrosative stress-inducing molecules inside biofilm structures, (ii) bacteriophage induction, and (iii) cell lysis. Here we examine whether specific reactive oxygen or nitrogen intermediates play a role in cell dispersal from P. aeruginosa biofilms. We demonstrate the involvement of anaerobic respiration processes in P. aeruginosa biofilm dispersal and show that nitric oxide (NO), used widely as a signaling molecule in biological systems, causes dispersal of P. aeruginosa biofilm bacteria. Dispersal was induced with low, sublethal concentrations (25 to 500 nM) of the NO donor sodium nitroprusside (SNP). Moreover, a P. aeruginosa mutant lacking the only enzyme capable of generating metabolic NO through anaerobic respiration (nitrite reductase, Δ nirS ) did not disperse, whereas a NO reductase mutant (Δ norCB ) exhibited greatly enhanced dispersal. Strategies to induce biofilm dispersal are of interest due to their potential to prevent biofilms and biofilm-related infections. We observed that exposure to SNP (500 nM) greatly enhanced the efficacy of antimicrobial compounds (tobramycin, hydrogen peroxide, and sodium dodecyl sulfate) in the removal of established P. aeruginosa biofilms from a glass surface. Combined exposure to both NO and antimicrobial agents may therefore offer a novel strategy to control preestablished, persistent P. aeruginosa biofilms and biofilm-related infections.

Physiological and morphological changes during short term starvation of marine bacterial islates

Publisher: Springer Science and Business Media LLC

Date: 09-1985

DOI: 10.1007/BF00491898

Pseudomonas aeruginosa PAO1 Preferentially Grows as Aggregates in Liquid Batch Cultures and Disperses upon Starvation

Publisher: Public Library of Science (PLoS)

Date: 13-05-2009

DOI: 10.1371/JOURNAL.PONE.0005513

Solvent optimization for bacterial extracellular matrices: a solution for the insoluble

Publisher: Royal Society of Chemistry (RSC)

Date: 2015

DOI: 10.1039/C4RA10930A

Abstract: Ionic liquids enable solvent optimization for different biofilms through solubility parameter concept.

Biofilm shows spatially stratified metabolic responses to contaminant exposure

Publisher: Wiley

Date: 23-08-2012

DOI: 10.1111/J.1462-2920.2012.02850.X

Erratum for “Dynamic Remodeling of Microbial Biofilms by Functionally Distinct Exopolysaccharides”

Publisher: American Society for Microbiology

Date: 07-2015

DOI: 10.1128/MBIO.00688-15

Dynamics of biofilm formation under different nutrient levels and the effect on biofouling of a reverse osmosis membrane system

Publisher: Informa UK Limited

Date: 03-2013

DOI: 10.1080/08927014.2013.772141

Abstract: Pseudomonas aeruginosa PAO1 wild type and a mucoid derivative (FRD1) which over produces alginate were used to foul reverse osmosis (RO) membranes. When operated at a constant flux, biofilm formation on the RO membrane resulted in a slow rise in transmembrane pressure (TMP) of 22% for the initial four days of operation, followed by a sharp increase of 159% over the following two days. The initial slow increase in TMP was probably due to the formation of a biofilm on the membrane surface, which then accelerated the rate of biofouling through the effect of concentration polarization. At later stages of operation, most of the bacterial biomass consisted of dead cells. The amount of extracellular polymeric substances appeared to correlate positively with the number of dead cells. The results indicate that prolonging the initial stage of slow TMP increase and avoiding the latter stage of accelerated TMP increase would provide a sustainable operation of the RO system. These results suggest that nutrient limitation could reduce biofilm accumulation and delay the increase in TMP.

Relative changes in incorporation rates of leucine and methionine during starvation survival of two bacteria isolated from marine waters

Publisher: Oxford University Press (OUP)

Date: 11-1986

DOI: 10.1111/J.1574-6968.1986.TB01739.X

Ecology of type II secretion in marine gammaproteobacteria

Publisher: Wiley

Date: 24-01-2008

DOI: 10.1111/J.1462-2920.2007.01545.X

Abstract: Compelling findings on the direct association of the type II secretion (T2S) system with different ecological functions in marine bacteria have challenged the traditional view of the T2S pathway, the function of which has been mostly studied in pathogenic bacteria. The availability of a number of whole-genome sequence data sets enabled the analysis of the genetic composition of the T2S system across a number of Vibrios and Alteromonads. The widespread Gammaproteobacteria, in particular the Alteromonadales and the Vibrionales group, are recognized to play significant roles in the cycling of nutrients in coastal and pelagic marine ecosystems and are also found associated with marine eukaryotes. The combined analysis of the role and the genetic composition of the T2S system in Gammaproteobacteria provides important evidence for the significance of the T2S pathway in the ecology of environmental bacteria.

Metabolite-enabled mutualistic interaction between Shewanella oneidensis and Escherichia coli in a co-culture using an electrode as electron acceptor

Publisher: Springer Science and Business Media LLC

Date: 10-06-2015

DOI: 10.1038/SREP11222

Abstract: Mutualistic interactions in planktonic microbial communities have been extensively studied. However, our understanding on mutualistic communities consisting of co-existing planktonic cells and biofilms is limited. Here, we report a planktonic cells-biofilm mutualistic system established by the fermentative bacterium Escherichia coli and the dissimilatory metal-reducing bacterium Shewanella oneidensis in a bioelectrochemical device, where planktonic cells in the anode media interact with the biofilms on the electrode. Our results show that the transfer of formate is the key mechanism in this mutualistic system. More importantly, we demonstrate that the relative distribution of E. coli and S. oneidensis in the liquid media and biofilm is likely driven by their metabolic functions towards an optimum communal metabolism in the bioelectrochemical device. RNA sequencing-based transcriptomic analyses of the interacting organisms in the mutualistic system potentially reveal differential expression of genes involved in extracellular electron transfer pathways in both species in the planktonic cultures and biofilms.

Low temperature induced non-culturability and killing of Vibrio vulnificus

Publisher: Oxford University Press (OUP)

Date: 12-1992

DOI: 10.1111/J.1574-6968.1992.TB05704.X

VarR controls colonization and virulence in the marine macroalgal pathogen Nautella italica R11

Publisher: Frontiers Media SA

Date: 13-10-2015

DOI: 10.3389/FMICB.2015.01130

Multiple opportunistic pathogens can cause a bleaching disease in the red seaweed Delisea pulchra

Publisher: Wiley

Date: 15-07-2016

DOI: 10.1111/1462-2920.13403

Abstract: While macroalgae (or seaweeds) are increasingly recognized to suffer from disease, in most cases the causative agents are unknown. The model macroalga Delisea pulchra is susceptible to a bleaching disease and previous work has identified two epiphytic bacteria, belonging to the Roseobacter clade, that cause bleaching under laboratory conditions. However, recent environmental surveys have shown that these in vitro pathogens are not abundant in naturally bleached D. pulchra, suggesting the presence of other pathogens capable of causing this algal disease. To test this hypothesis, we cultured bacteria that were abundant on bleached tissue across multiple disease events and assessed their ability to cause bleaching disease. We identified the new pathogens Alteromonas sp. BL110, Aquimarina sp. AD1 and BL5 and Agarivorans sp BL7 that are phylogenetically erse, distinct from the previous two pathogens and can also be found in low abundance in healthy in iduals. Moreover, we found that bacterial communities of diseased in iduals that were infected with these pathogens were less erse and more ergent from each other than those of healthy algae. This study demonstrates that multiple and opportunistic pathogens can cause the same disease outcome for D. pulchra and we postulate that such pathogens are more common in marine systems than previously anticipated.

RhizoFlowCell system reveals early effects of micropollutants on aquatic plant rhizosphere

Publisher: Elsevier BV

Date: 12-2015

DOI: 10.1016/J.ENVPOL.2015.08.047

Abstract: In aquatic systems, one of the non-destructive ways to quantify toxicity of contaminants to plants is to monitor changes in root exudation patterns. In aquatic conditions, monitoring and quantifying such changes are currently challenging because of dilution of root exudates in water phase and lack of suitable instrumentation to measure them. Exposure to pollutants would not only change the plant exudation, but also affect the microbial communities that surround the root zone, thereby changing the metabolic profiles of the rhizosphere. This study aims at developing a device, the RhizoFlowCell, which can quantify metabolic response of plants, as well as changes in the microbial communities, to give an estimate of the stress to which the rhizosphere is exposed. The usefulness of RhizoFlowCell is demonstrated using naphthalene as a test pollutant. Results show that RhizoFlowCell system is useful in quantifying the dynamic metabolic response of aquatic rhizosphere to determine ecosystem health.

A stable synergistic microbial consortium for simultaneous azo dye removal and bioelectricity generation

Publisher: Elsevier BV

Date: 03-2014

DOI: 10.1016/J.BIORTECH.2013.12.078

Abstract: Microbial species coexist in natural or engineered settings, where they encounter extensive competition and cooperation. Interactions occurring through metabolite exchange or direct contact might be important in establishment of functional biodegradation consortium. Understanding these interactions can facilitate manipulation of selected communities and exploitation of their capacity for specific industrial applications. Here, a simple dual-species consortium (Pseudomonas putida and Shewanella oneidensis) was established for examining simultaneous Congo red bioremediation in planktonic culture and power generation in anode biofilms. Compared to mono-species cultures, co-cultures generated higher current densities and could concurrently degrade Congo red over 72h. Disabling the large secreted adhesion protein, LapA, of P. putida greatly enhanced S. oneidensis biofilm formation on the anode, which increased power generation in co-cultures. This demonstrates simultaneous control of specific planktonic and biofilm communities could be effective in manipulating microbial communities for targeted applications.

Competitive interactions in mixed-species biofilms containing the marine bacterium Pseudoalteromonas tunicata.

Publisher: American Society for Microbiology

Date: 04-2005

DOI: 10.1128/AEM.71.4.1729-1736.2005

Abstract: Pseudoalteromonas tunicata is a biofilm-forming marine bacterium that is often found in association with the surface of eukaryotic organisms. It produces a range of extracellular inhibitory compounds, including an antibacterial protein (AlpP) thought to be beneficial for P. tunicata during competition for space and nutrients on surfaces. As part of our studies on the interactions between P. tunicata and the epiphytic bacterial community on the marine plant Ulva lactuca , we investigated the hypothesis that P. tunicata is a superior competitor compared with other bacteria isolated from the plant. A number of U. lactuca bacterial isolates were (i) identified by 16S rRNA gene sequencing, (ii) characterized for the production of or sensitivity to extracellular antibacterial proteins, and (iii) labeled with a fluorescent color tag (either the red fluorescent protein DsRed or green fluorescent protein). We then grew single- and mixed-species bacterial biofilms containing P. tunicata in glass flow cell reactors. In pure culture, all the marine isolates formed biofilms containing microcolony structures within 72 h. However, in mixed-species biofilms, P. tunicata removed the competing strain unless its competitor was relatively insensitive to AlpP ( Pseudoalteromonas gracilis ) or produced strong inhibitory activity against P. tunicata ( Roseobacter gallaeciensis ). Moreover, biofilm studies conducted with an AlpP − mutant of P. tunicata indicated that the mutant was less competitive when it was introduced into preestablished biofilms, suggesting that AlpP has a role during competitive biofilm formation. When single-species biofilms were allowed to form microcolonies before the introduction of a competitor, these microcolonies coexisted with P. tunicata for extended periods of time before they were removed. Two marine bacteria ( R. gallaeciensis and P. tunicata ) were superior competitors in this study. Our data suggest that this dominance can be attributed to the ability of these organisms to rapidly form microcolonies and their ability to produce extracellular antibacterial compounds.

Starvation-induced modulations in binding protein-dependent glucose transport by the marine sp. S14

Publisher: Oxford University Press (OUP)

Date: 07-1990

DOI: 10.1016/S0378-1097(05)80040-0

The effect of cadmium on starved heterotrophic bacteria isolated from marine waters

Publisher: Oxford University Press (OUP)

Date: 06-1987

DOI: 10.1111/J.1574-6968.1987.TB02350.X

Bacterial scavenging: Utilization of fatty acids localized at a solid-liquid interface

Publisher: Springer Science and Business Media LLC

Date: 1982

DOI: 10.1007/BF00521286

Species-specific patterns in the vulnerability of ­carbon-starved bacteria to protist grazing

Publisher: Inter-Research Science Center

Date: 04-08-2011

DOI: 10.3354/AME01518

Functional genomic analysis of an uncultured delta-proteobacterium in the sponge Cymbastela concentrica

Publisher: Springer Science and Business Media LLC

Date: 02-09-2011

DOI: 10.1038/ISMEJ.2010.139

Reactive oxygen species drive evolution of pro-biofilm variants in pathogens by modulating cyclic-di-GMP levels

Publisher: The Royal Society

Date: 11-2016

DOI: 10.1098/RSOB.160162

Abstract: The host immune system offers a hostile environment with antimicrobials and reactive oxygen species (ROS) that are detrimental to bacterial pathogens, forcing them to adapt and evolve for survival. However, the contribution of oxidative stress to pathogen evolution remains elusive. Using an experimental evolution strategy, we show that exposure of the opportunistic pathogen Pseudomonas aeruginosa to sub-lethal hydrogen peroxide (H 2 O 2 ) levels over 120 generations led to the emergence of pro-biofilm rough small colony variants (RSCVs), which could be abrogated by l -glutathione antioxidants. Comparative genomic analysis of the RSCVs revealed that mutations in the wspF gene, which encodes for a repressor of WspR diguanylate cyclase (DGC), were responsible for increased intracellular cyclic-di-GMP content and production of Psl exopolysaccharide. Psl provides the first line of defence against ROS and macrophages, ensuring the survival fitness of RSCVs over wild-type P. aeruginosa . Our study demonstrated that ROS is an essential driving force for the selection of pro-biofilm forming pathogenic variants. Understanding the fundamental mechanism of these genotypic and phenotypic adaptations will improve treatment strategies for combating chronic infections.

Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts

Publisher: Proceedings of the National Academy of Sciences

Date: 13-06-2012

DOI: 10.1073/PNAS.1203287109

Abstract: Microorganisms often form symbiotic relationships with eukaryotes, and the complexity of these relationships can range from those with one single dominant symbiont to associations with hundreds of symbiont species. Microbial symbionts occupying equivalent niches in different eukaryotic hosts may share functional aspects, and convergent genome evolution has been reported for simple symbiont systems in insects. However, for complex symbiont communities, it is largely unknown how prevalent functional equivalence is and whether equivalent functions are conducted by evolutionarily convergent mechanisms. Sponges represent an evolutionarily ergent group of species with common physiological and ecological traits. They also host complex communities of microbial symbionts and thus are the ideal model to test whether functional equivalence and evolutionary convergence exist in complex symbiont communities across phylogenetically ergent hosts. Here we use a s ling design to determine the phylogenetic and functional profiles of microbial communities associated with six sponge species. We identify common functions in the six microbiomes, demonstrating the existence of functional equivalence. These core functions are consistent with our current understanding of the biological and ecological roles of sponge-associated microorganisms and also provide insight into symbiont functions. Importantly, core functions also are provided in each sponge species by analogous enzymes and biosynthetic pathways. Moreover, the abundance of elements involved in horizontal gene transfer suggests their key roles in the genomic evolution of symbionts. Our data thus demonstrate evolutionary convergence in complex symbiont communities and reveal the details and mechanisms that underpin the process.

Hybrid Conducting Biofilm with Built‐in Bacteria for High‐Performance Microbial Fuel Cells

Publisher: Wiley

Date: 12-02-2015

DOI: 10.1002/CELC.201402458

Surface-layer protein is a public-good matrix exopolymer for microbial community organisation in environmental anammox biofilms

Publisher: Springer Science and Business Media LLC

Date: 04-03-2023

DOI: 10.1038/S41396-023-01388-Y

Abstract: Extracellular polymeric substances (EPS) are core biofilm components, yet how they mediate interactions within and contribute to the structuring of biofilms is largely unknown, particularly for non-culturable microbial communities that predominate in environmental habitats. To address this knowledge gap, we explored the role of EPS in an anaerobic ammonium oxidation (anammox) biofilm. An extracellular glycoprotein, BROSI_A1236, from an anammox bacterium, formed envelopes around the anammox cells, supporting its identification as a surface (S-) layer protein. However, the S-layer protein also appeared at the edge of the biofilm, in close proximity to the polysaccharide-coated filamentous Chloroflexi bacteria but distal to the anammox bacterial cells. The Chloroflexi bacteria assembled into a cross-linked network at the edge of the granules and surrounding anammox cell clusters, with the S-layer protein occupying the space around the Chloroflexi . The anammox S-layer protein was also abundant at junctions between Chloroflexi cells. Thus, the S-layer protein is likely transported through the matrix as an EPS and also acts as an adhesive to facilitate the assembly of filamentous Chloroflexi into a three-dimensional biofilm lattice. The spatial distribution of the S-layer protein within the mixed species biofilm suggests that it is a “public-good” EPS, which facilitates the assembly of other bacteria into a framework for the benefit of the biofilm community, and enables key syntrophic relationships, including anammox.

Starvation of marine flounder, squid and laboratory mice and its effect on the intestinal microbiota

Publisher: Oxford University Press (OUP)

Date: 08-1986

DOI: 10.1111/J.1574-6968.1986.TB01728.X

Identification of Ciliate Grazers of Autotrophic Bacteria in Ammonia-Oxidizing Activated Sludge by RNA Stable Isotope Probing

Publisher: American Society for Microbiology

Date: 04-2010

DOI: 10.1128/AEM.02777-09

Abstract: It is well understood that protozoa play a major role in controlling bacterial biomass and regulating nutrient cycling in the environment. Little is known, however, about the movement of carbon from specific reduced substrates, through functional groups of bacteria, to particular clades of protozoa. In this study we first identified the active protozoan phylotypes present in activated sludge, via the construction of an rRNA-derived eukaryote clone library. Most of the sequences identified belonged to ciliates of the subclass Peritrichia and amoebae, confirming the dominance of surface-associated protozoa in the activated sludge environment. We then demonstrated that 13 C-labeled protozoan RNA can be retrieved from activated sludge amended with 13 C-labeled protozoa or 13 C-labeled Escherichia coli cells by using an RNA stable isotope probing (RNA-SIP) approach. Finally, we used RNA-SIP to track carbon from bicarbonate and acetate into protozoa under ammonia-oxidizing and denitrifying conditions, respectively. RNA-SIP analysis revealed that the peritrich ciliate Epistylis galea dominated the acquisition of carbon from bacteria with access to CO 2 under ammonia-oxidizing conditions, while there was no evidence of specific grazing on acetate consumers under denitrifying conditions.

Halogenated furanones from the red alga,Delisea pulchra, inhibit carbapenem antibiotic synthesis and exoenzyme virulence factor production in the phytopathogenErwinia carotovora

Publisher: Oxford University Press (OUP)

Date: 11-2001

DOI: 10.1111/J.1574-6968.2001.TB10936.X

Abstract: The plant pathogen Erwinia carotovora regulates expression of virulence factors and antibiotic production via an N-3-oxohexanoyl-L-homoserine lactone (3-oxo-C6-HSL) dependent quorum sensing mechanism. The marine alga Delisea pulchra produces halogenated furanones known to antagonise 3-oxo-C6-HSL activity. We have tested the effects of a halogenated furanone on the production of carbapenem, cellulase and protease in E. carotovora. Despite differences in the regulatory mechanisms controlling carbapenem and exoenzyme production each was inhibited by the algal metabolite. We present evidence to suggest that the furanone dependent inhibition of carbapenem production is a result of the disruption of the 3-oxo-C6-HSL dependent expression of the carABCDEFGH operon.

Synthesis of cephalosporin-3′-diazeniumdiolates: Biofilm dispersing NO-donor prodrugs activated by β-lactamase

Publisher: Royal Society of Chemistry (RSC)

Date: 2013

DOI: 10.1039/C3CC40869H

Abstract: Use of biofilm dispersing NO-donor compounds in combination with antibiotics has emerged as a promising new strategy for treating drug-resistant bacterial biofilm infections. This paper details the synthesis and preliminary evaluation of six cephalosporin-3'-diazeniumdiolates as biofilm-targeted NO-donor prodrugs. Each of the compounds is shown to selectively release NO following reaction with the bacteria-specific enzyme β-lactamase and to trigger dispersion of Pseudomonas aeruginosa biofilms in vitro.

Inhibition of luminescence and virulence in the black tiger prawn (Penaeus monodon) pathogen Vibrio harveyi by intercellular signal antagonists.

Publisher: American Society for Microbiology

Date: 05-2000

DOI: 10.1128/AEM.66.5.2079-2084.2000

Abstract: Expression of luminescence in the Penaeus monodon pathogen Vibrio harveyi is regulated by an intercellular quorum sensing mechanism involving the synthesis and detection of two signaling molecules, one of which is N -hydroxy butanoyl- l -homoserine lactone and the other of which is uncharacterized. Indirect evidence has suggested that virulence, associated with a toxic extracellular protein, and luminescence in V. harveyi are coregulated. In this study the effects of an acylated homoserine lactone antagonist produced by the marine alga Delisea pulchra on luminescence and toxin production in a virulent strain of V. harveyi were analyzed. Luminescence and toxin production were both inhibited by the signal antagonist at concentrations that had no impact on growth. Toxin production was found to be prematurely induced in V. harveyi cultures incubated in a 10% conditioned medium. Additionally, a significant reduction in the toxicity of concentrated supernatant extracts from V. harveyi cultures incubated in the presence of the signal antagonist, as measured by in vivo toxicity assays in mice and prawns, was observed. These results suggest that intercellular signaling antagonists have potential utility in the control of V. harveyi prawn infections.

Low Densities of Epiphytic Bacteria from the Marine Alga Ulva australis Inhibit Settlement of Fouling Organisms

Publisher: American Society for Microbiology

Date: 15-12-2007

DOI: 10.1128/AEM.01543-07

Abstract: Bacteria that produce inhibitory compounds on the surface of marine algae are thought to contribute to the defense of the host plant against colonization of fouling organisms. However, the number of bacterial cells necessary to defend against fouling on the plant surface is not known. Pseudoalteromonas tunicata and Phaeobacter sp. strain 2.10 (formerly Roseobacter gallaeciensis ) are marine bacteria often found in association with the alga Ulva australis and produce a range of extracellular inhibitory compounds against common fouling organisms. P. tunicata and Phaeobacter sp. strain 2.10 biofilms with cell densities ranging from 10 2 to 10 8 cells cm −2 were established on polystyrene petri dishes. Attachment and settlement assays were performed with marine fungi (uncharacterized isolates from U. australis ), marine bacteria ( Pseudoalteromonas gracilis , Alteromonas sp., and Cellulophaga fucicola ), invertebrate larvae ( Bugula neritina ), and algal spores ( Polysiphonia sp.) and gametes ( U. australis ). Remarkably low cell densities (10 2 to 10 3 cells cm −2 ) of P. tunicata were effective in preventing settlement of algal spores and marine fungi in petri dishes. P. tunicata also prevented settlement of invertebrate larvae at densities of 10 4 to 10 5 cells cm −2 . Similarly, low cell densities (10 3 to 10 4 cells cm −2 ) of Phaeobacter sp. strain 2.10 had antilarval and antibacterial activity. Previously, it has been shown that abundance of P. tunicata on marine eukaryotic hosts is low ( × 10 3 cells cm −2 ) (T. L. Skovhus et al., Appl. Environ. Microbiol. 70:2373-2382, 2004). Despite such low numbers of P. tunicata on U. australis in situ, our data suggest that P. tunicata and Phaeobacter sp. strain 2.10 are present in sufficient quantities on the plant to inhibit fouling organisms. This strongly supports the hypothesis that P. tunicata and Phaeobacter sp. strain 2.10 can play a role in defense against fouling on U. australis at cell densities that commonly occur in situ.

SmcR-Dependent Regulation of Adaptive Phenotypes in Vibrio vulnificus

Publisher: American Society for Microbiology

Date: 15-01-2001

DOI: 10.1128/JB.183.2.758-762.2001

Abstract: Vibrio vulnificus contains homologues of the V. harveyi luxR and luxS genes. A null mutation in smcR ( luxR ) resulted in a defect in starvation survival, inhibition of starvation-induced maintenance of culturability that occurs when V. vulnificus is starved prior to low-temperature incubation, and increased expression of stationary-phase phenotypes.

Sex, Scavengers, and Chaperones: Transcriptome Secrets of Divergent Symbiodinium Thermal Tolerances

Publisher: Oxford University Press (OUP)

Date: 11-10-2016

DOI: 10.1093/MOLBEV/MSW201

Unravelling the role of the ToxR-like transcriptional regulator WmpR in the marine antifouling bacterium Pseudoalteromonas tunicata

Publisher: Microbiology Society

Date: 05-2006

DOI: 10.1099/MIC.0.28740-0

Abstract: The dark-green-pigmented marine bacterium Pseudoalteromonas tunicata produces several target-specific compounds that act against a range of common fouling organisms, including bacteria, fungi, protozoa, invertebrate larvae and algal spores. The ToxR-like regulator WmpR has previously been shown to regulate expression of bioactive compounds, type IV pili and biofilm formation phenotypes which all appear at the onset of stationary phase. In this study a comparison of survival under starvation or stress between the wild-type P. tunicata strain and a wmpR mutant (D2W2) does not suggest a role for WmpR in regulating starvation- and stress-resistant phenotypes such as those that may be required in stationary phase. Both proteomic [2-dimensional PAGE (2D-PAGE)] and transcriptomic (RNA arbitrarily primed PCR) studies were used to discover members of the WmpR regulon. 2D-PAGE identified 11 proteins that were differentially expressed by WmpR. Peptide sequence data were obtained for six of these proteins and identified using the draft P. tunicata genome as being involved in protein synthesis, amino acid transamination and ubiquinone biosynthesis, as well as hypothetical proteins. The transcriptomic analysis identified three genes significantly up-regulated by WmpR, including a TonB-dependent outer-membrane protein, a non-ribosomal peptide synthetase and a hypothetical protein. Under iron-limitation the wild-type showed greater survival than D2W2, indicating the importance of WmpR under these conditions. Results from these studies show that WmpR controls the expression of genes encoding proteins involved in iron acquisition and uptake, amino acid metabolism and ubiquinone biosynthesis in addition to a number of proteins with as yet unknown functions.

Do marine natural products interfere with prokaryotic AHL regulatory systems?

Publisher: Inter-Research Science Center

Date: 1997

DOI: 10.3354/AME013085

Global analysis of physiological responses in marine bacteria

Publisher: Wiley

Date: 1997

DOI: 10.1002/ELPS.1150180819

Abstract: In this paper, we present results from studies on marine Vibrio species, in which complex adaptive responses have been investigated. The results of two-dimensional polyacrylamide gel electrophoresis serve to illustrate the usefulness of a global approach, and how it can be combined with other methodologies in order to achieve an improved understanding of the means by which bacteria adapt to alterations in environmental conditions. The overall strategies described in this paper are particularly useful for studies of bacteria for which efficient genetic tools, background genotypes and in depth physiological data are not yet available.

Pseudomonas aeruginosa PAO1 exopolysaccharides are important for mixed species biofilm community development and stress tolerance.

Publisher: Frontiers Media SA

Date: 20-08-2015

DOI: 10.3389/FMICB.2015.00851

Micro-fabricated polydimethyl siloxane (PDMS) surfaces regulate the development of marine microbial biofilm communities

Publisher: Informa UK Limited

Date: 21-02-2014

DOI: 10.1080/08927014.2013.872778

Abstract: This study explored an antifouling (AF) concept based on deployment of microfabricated polydimethyl siloxane (PDMS) surfaces with 1-10 μm periodicity corrugated topographies in temperate marine waters. The effect of the surfaces on the development of microbial biofilms over 28 days and during different seasons, including both summer and winter, was examined using confocal laser scanning microscopy (CLSM) as well as terminal restriction fragment (T-RF) analysis for phylogenetic fingerprinting. The microscale topography significantly impacted biofilm development by altering the attachment pattern and reducing microcolony formation on the 1, 2 and 4 μm PDMS surfaces. Also, field deployments over 28 days showed a significant reduction in biovolume on the 4 and 10 μm PDMS surfaces despite altered environmental conditions. The microfabricated PDMS surfaces further significantly impacted on the community composition of the biofilms, as revealed by changes in T-RF profiles, at different stages of development. Moreover, altered biofilm resistance was demonstrated by exposing pre-established biofilms on 10 μm micro-fabricated surfaces to enhanced flagellate predation by a heterotrophic protist, Rhynchomonas nasuta. Pronounced changes in the overall marine microbial biofilm development as well as community composition warrant exploring substratum modification for marine AF applications.

Larger π-extended anti-/syn-aroylenediimidazole polyaromatic compounds: synthesis, physical properties, self-assembly, and quasi-linear conjugation effect

Publisher: Royal Society of Chemistry (RSC)

Date: 2014

DOI: 10.1039/C4RA01049C

Abstract: Four polyaromatic compounds with 11- or 13-fused rings have been synthesized and their physical properties have been studied.

Transcriptome analyses and biofilm-forming characteristics of a clonal Pseudomonas aeruginosa from the cystic fibrosis lung

Publisher: Microbiology Society

Date: 12-2008

DOI: 10.1099/JMM.0.2008/005009-0

Abstract: Transmissible Pseudomonas aeruginosa clones potentially pose a serious threat to cystic fibrosis (CF) patients. The AES-1 clone has been found to infect up to 40 % of patients in five CF centres in eastern Australia. Studies were carried out on clonal and non-clonal (NC) isolates from chronically infected CF patients, and the reference strain PAO1, to gain insight into the properties of AES-1. The transcriptomes of AES-1 and NC isolates, and of PAO1, grown planktonically and as a 72 h biofilm were compared using PAO1 microarrays. Microarray data were validated using real-time PCR. Overall, most differentially expressed genes were downregulated. AES-1 differentially expressed bacteriophage genes, novel motility genes, and virulence and quorum-sensing-related genes, compared with both PAO1 and NC. AES-1 but not NC biofilms significantly downregulated aerobic respiration genes compared with planktonic growth, suggesting enhanced anaerobic/microaerophilic growth by AES-1. Biofilm measurement showed that AES-1 formed significantly larger and thicker biofilms than NC or PAO1 isolates. This may be related to expression of the gene PA0729, encoding a biofilm-enhancing bacteriophage, identified by PCR in all AES-1 but few NC isolates ( n =42). Links with the Liverpool epidemic strain included the presence of PA0729 and the absence of the bacteriophage gene cluster PA0632–PA0639. No common markers were found with the Manchester strain. No particular differentially expressed gene in AES-1 could definitively be ascribed a role in its infectivity, thus increasing the likelihood that AES-1 infectivity is multi-factorial and possibly involves novel genes. This study extends our understanding of the transcriptomic and genetic differences between clonal and NC strains of P. aeruginosa from CF lung.

Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis

Publisher: Springer Science and Business Media LLC

Date: 03-06-2010

DOI: 10.1038/ISMEJ.2010.74

Abstract: Sponges form close relationships with bacteria, and a remarkable phylogenetic ersity of yet-uncultured bacteria has been identified from sponges using molecular methods. In this study, we use a comparative metagenomic analysis of the bacterial community in the model sponge Cymbastela concentrica and in the surrounding seawater to identify previously unrecognized genomic signatures and functions for sponge bacteria. We observed a surprisingly large number of transposable insertion elements, a feature also observed in other symbiotic bacteria, as well as a set of predicted mechanisms that may defend the sponge community against the introduction of foreign DNA and hence contribute to its genetic resilience. Moreover, several shared metabolic interactions between bacteria and host include vitamin production, nutrient transport and utilization, and redox sensing and response. Finally, an abundance of protein-protein interactions mediated through ankyrin and tetratricopeptide repeat proteins could represent a mechanism for the sponge to discriminate between food and resident bacteria. These data provide new insight into the evolution of symbiotic ersity, microbial metabolism and host-microbe interactions in sponges.

Temperature induced bacterial virulence and bleaching disease in a chemically defended marine macroalga

Publisher: Wiley

Date: 15-10-2010

DOI: 10.1111/J.1462-2920.2010.02356.X

Abstract: Host-pathogen interactions have been widely studied in humans and terrestrial plants, but are much less well explored in marine systems. Here we show that a marine macroalga, Delisea pulchra, utilizes a chemical defence - furanones - to inhibit colonization and infection by a novel bacterial pathogen, Ruegeria sp. R11, and that infection by R11 is temperature dependent. Ruegeria sp. R11 formed biofilms, invaded and bleached furanone-free, but not furanone-producing D. pulchra thalli, at high (24°C) but not low (19°C) temperatures. Bleaching is commonly observed in natural populations of D. pulchra near Sydney, Australia, during the austral summer when ocean temperatures are at their peak and the chemical defences of the alga are reduced. Furanones, produced by D. pulchra as a chemical defence, inhibit quorum sensing (QS) in bacteria, and this may play a role in furanone inhibition of R11 infection of furanone-free thalli as R11 produces QS signals. This interplay between temperature, an algal chemical defence mechanism and bacterial virulence demonstrates the complex impact environmental change can have on an ecosystem.

The role of quorum sensing signalling in EPS production and the assembly of a sludge community into aerobic granules

Publisher: Springer Science and Business Media LLC

Date: 16-01-2014

DOI: 10.1038/ISMEJ.2013.240

Minimal increase in genetic diversity enhances predation resistance

Publisher: Wiley

Date: 29-12-2011

DOI: 10.1111/J.1365-294X.2011.05415.X

The alternative sigma factor RpoN regulates the quorum sensing gene rhlI in Pseudomonas aeruginosa.

Publisher: Oxford University Press (OUP)

Date: 03-2003

DOI: 10.1016/S0378-1097(03)00097-1

The correlation between biofilm biopolymer composition and membrane fouling in submerged membrane bioreactors

Publisher: Informa UK Limited

Date: 21-10-2014

DOI: 10.1080/08927014.2014.971238

Abstract: Biofouling, the combined effect of microorganism and biopolymer accumulation, significantly reduces the process efficiency of membrane bioreactors (MBRs). Here, four biofilm components, alpha-polysaccharides, beta-polysaccharides, proteins and microorganisms, were quantified in MBRs. The biomass of each component was positively correlated with the transmembrane pressure increase in MBRs. Proteins were the most abundant biopolymer in biofilms and showed the fastest rate of increase. The spatial distribution and co-localization analysis of the biofouling components indicated at least 60% of the extracellular polysaccharide (EPS) components were associated with the microbial cells when the transmembrane pressure (TMP) entered the jump phase, suggesting that the EPS components were either secreted by the biofilm cells or that the deposition of these components facilitated biofilm formation. It is suggested that biofilm formation and the accumulation of EPS are intrinsically coupled, resulting in biofouling and loss of system performance. Therefore, strategies that control biofilm formation on membranes may result in a significant improvement of MBR performance.

The role of RNA stability during bacterial stress responses and starvation

Publisher: Wiley

Date: 08-2000

DOI: 10.1046/J.1462-2920.2000.00119.X

Is there a role for quorum sensing signals in bacterial biofilms?

Publisher: Elsevier BV

Date: 06-2002

DOI: 10.1016/S1369-5274(02)00325-9

Abstract: Bacteria form multicellular biofilm communities on most surfaces. Genetic analysis of biofilm formation has led to the proposal that extracellular signals and quorum-sensing regulatory systems are essential for differentiated biofilms. Although such a model fits the concept of density-driven cell-cell communication and appear to describe biofilm development in several bacterial species and conditions, biofilm formation is multifactorial and complex. Hydrodynamics, nutrient load and intracellular carbon flux have major impacts, presumably by altering the expression of cellular traits essential for bacterial adaptation during the different stages of biofilm formation. Hence, differentiated biofilms may also be the net result of many independent interactions, rather than being determined by a particular global quorum sensing system.

Incorporation of tritiated thymidine by marine bacterial isolates when undergoing a starvation survival response

Publisher: Springer Science and Business Media LLC

Date: 03-1988

DOI: 10.1007/BF00425583

Should we stay or should we go: mechanisms and ecological consequences for biofilm dispersal

Publisher: Springer Science and Business Media LLC

Date: 28-11-2011

DOI: 10.1038/NRMICRO2695

Abstract: In most environments, bacteria reside primarily in biofilms, which are social consortia of cells that are embedded in an extracellular matrix and undergo developmental programmes resulting in a predictable biofilm 'life cycle'. Recent research on many different bacterial species has now shown that the final stage in this life cycle includes the production and release of differentiated dispersal cells. The formation of these cells and their eventual dispersal is initiated through erse and remarkably sophisticated mechanisms, suggesting that there are strong evolutionary pressures for dispersal from an otherwise largely sessile biofilm. The evolutionary aspect of biofilm dispersal is now being explored through the integration of molecular microbiology with eukaryotic ecological and evolutionary theory, which provides a broad conceptual framework for the ersity of specific mechanisms underlying biofilm dispersal. Here, we review recent progress in this emerging field and suggest that the merging of detailed molecular mechanisms with ecological theory will significantly advance our understanding of biofilm biology and ecology.

Quorum sensing-regulated chitin metabolism provides grazing resistance to Vibrio cholerae biofilms

Publisher: Springer Science and Business Media LLC

Date: 23-01-2015

DOI: 10.1038/ISMEJ.2014.265

The seaweed holobiont: understanding seaweed–bacteria interactions

Publisher: Oxford University Press (OUP)

Date: 05-2013

DOI: 10.1111/1574-6976.12011

Abstract: Seaweeds (macroalgae) form a erse and ubiquitous group of photosynthetic organisms that play an essential role in aquatic ecosystems. These ecosystem engineers contribute significantly to global primary production and are the major habitat formers on rocky shores in temperate waters, providing food and shelter for aquatic life. Like other eukaryotic organisms, macroalgae harbor a rich ersity of associated microorganisms with functions related to host health and defense. In particular, epiphytic bacterial communities have been reported as essential for normal morphological development of the algal host, and bacteria with antifouling properties are thought to protect chemically undefended macroalgae from detrimental, secondary colonization by other microscopic and macroscopic epibiota. This tight relationship suggests that macroalgae and epiphytic bacteria interact as a unified functional entity or holobiont, analogous to the previously suggested relationship in corals. Moreover, given that the impact of diseases in marine ecosystems is apparently increasing, understanding the role of bacteria as saprophytes and pathogens in seaweed communities may have important implications for marine management strategies. This review reports on the recent advances in the understanding of macroalgal-bacterial interactions with reference to the ersity and functional role of epiphytic bacteria in maintaining algal health, highlighting the holobiont concept.

Epigallocatechin Gallate Remodels Overexpressed Functional Amyloids in Pseudomonas aeruginosa and Increases Biofilm Susceptibility to Antibiotic Treatment

Publisher: Elsevier BV

Date: 12-2016

DOI: 10.1074/JBC.M116.739953

Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva australis

Publisher: Springer Science and Business Media LLC

Date: 04-11-2010

DOI: 10.1038/ISMEJ.2010.164

Use of 16S rRNA and rpoB Genes as Molecular Markers for Microbial Ecology Studies

Publisher: American Society for Microbiology

Date: 2007

DOI: 10.1128/AEM.01177-06

Abstract: Several characteristics of the 16S rRNA gene, such as its essential function, ubiquity, and evolutionary properties, have allowed it to become the most commonly used molecular marker in microbial ecology. However, one fact that has been overlooked is that multiple copies of this gene are often present in a given bacterium. These intragenomic copies can differ in sequence, leading to identification of multiple ribotypes for a single organism. To evaluate the impact of such intragenomic heterogeneity on the performance of the 16S rRNA gene as a molecular marker, we compared its phylogenetic and evolutionary characteristics to those of the single-copy gene rpoB . Full-length gene sequences and gene fragments commonly used for denaturing gradient gel electrophoresis were compared at various taxonomic levels. Heterogeneity found between intragenomic 16S rRNA gene copies was concentrated in specific regions of rRNA secondary structure. Such “heterogeneity hot spots” occurred within all gene fragments commonly used in molecular microbial ecology. This intragenomic heterogeneity influenced 16S rRNA gene tree topology, phylogenetic resolution, and operational taxonomic unit estimates at the species level or below. rpoB provided comparable phylogenetic resolution to that of the 16S rRNA gene at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution. This is particularly relevant in the context of a growing number of studies focusing on subspecies ersity, in which single-copy protein-encoding genes such as rpoB could complement the information provided by the 16S rRNA gene.

Animals in a bacterial world, a new imperative for the life sciences

Publisher: Proceedings of the National Academy of Sciences

Date: 07-02-2013

DOI: 10.1073/PNAS.1218525110

Abstract: In the last two decades, the widespread application of genetic and genomic approaches has revealed a bacterial world astonishing in its ubiquity and ersity. This review examines how a growing knowledge of the vast range of animal–bacterial interactions, whether in shared ecosystems or intimate symbioses, is fundamentally altering our understanding of animal biology. Specifically, we highlight recent technological and intellectual advances that have changed our thinking about five questions: how have bacteria facilitated the origin and evolution of animals how do animals and bacteria affect each other’s genomes how does normal animal development depend on bacterial partners how is homeostasis maintained between animals and their symbionts and how can ecological approaches deepen our understanding of the multiple levels of animal–bacterial interaction. As answers to these fundamental questions emerge, all biologists will be challenged to broaden their appreciation of these interactions and to include investigations of the relationships between and among bacteria and their animal partners as we seek a better understanding of the natural world.

Physiological and molecular adaptation to starvation and recovery from starvation by the marineVibriosp. S14

Publisher: Oxford University Press (OUP)

Date: 12-1990

DOI: 10.1111/J.1574-6968.1990.TB04059.X

Novel Antibacterial Proteins From The Microbial Communities Associated With The Sponge Cymbastela Concentrica And The Green Alga Ulva Australis

Publisher: American Society for Microbiology

Date: 15-02-2011

DOI: 10.1128/AEM.02038-10

Abstract: The functional metagenomic screening of the microbial communities associated with a temperate marine sponge and a green alga identified three novel hydrolytic enzymes with antibacterial activities. The results suggest that uncultured alpha- and gammaproteobacteria contain new classes of proteins that may be a source of antibacterial agents.

The ISME Journal: a major milestone for the International Society for Microbial Ecology and the microbial ecology community

Publisher: Springer Science and Business Media LLC

Date: 05-2007

DOI: 10.1038/ISMEJ.2007.14

Molecular insights into environmental microbes

Publisher: Oxford University Press (OUP)

Date: 05-2013

DOI: 10.1111/1574-6976.12017

Microbial biofilm formation: a need to act

Publisher: Wiley

Date: 06-05-2014

DOI: 10.1111/JOIM.12242

Chemical changes in cell envelope and poly-?-hydroxybutyrate during short term starvation of a marine bacterial isolate

Publisher: Springer Science and Business Media LLC

Date: 05-1986

DOI: 10.1007/BF00409882

Bacterial quorum sensing and interference by naturally occurring biomimics

Publisher: Springer Science and Business Media LLC

Date: 26-09-2006

DOI: 10.1007/S00216-006-0761-2

Abstract: Bacteria are able to coordinate gene expression as a community through the secretion and detection of signalling molecules so that the members of the community can simultaneously express specific behaviours. This mechanism of regulation of behaviour appears to be a key trait for adaptation to specific environments and has been shown to regulate a variety of important phenotypes, from virulence factor production to biofilm formation to symbiosis related behaviours such as bioluminescence. The ability to communicate and communally regulate gene expression is hypothesised to have evolved as a way for organisms to delay expression of phenotypes until numerical supremacy is reached. For ex le, in the case of infection, if an invading microorganism were to express virulence factors too early, the host may be able to mount a successful defence and repel the invaders. There is growing evidence that bacterial quorum sensing (QS) systems are involved in cross-kingdom signalling with eukaryotic organisms and that eukaryotes are capable of actively responding to bacteria in their environment by detecting and acting upon the presence of these signalling molecules. Likewise, eukaryotes produce compounds that can interfere with QS systems in bacteria by acting as agonists or antagonists. An exciting new field of study, biomimetics, takes inspiration from nature's models and attempts to design solutions to human problems, and biomimics of QS systems may be one such solution. This article presents the acylated homoserine lactone and autoinducer 2 QS systems in bacteria, the means of intercepting or interfering with bacterial QS systems evolved by eukaryotes, and the rational design of synthetic antagonists.

Identification of Five Structurally Unrelated Quorum-Sensing Inhibitors of Pseudomonas aeruginosa from a Natural-Derivative Database

Publisher: American Society for Microbiology

Date: 11-2013

DOI: 10.1128/AAC.00955-13

Abstract: Bacteria communicate by means of small signal molecules in a process termed quorum sensing (QS). QS enables bacteria to organize their activities at the population level, including the coordinated secretion of virulence factors. Certain small-molecule compounds, known as quorum-sensing inhibitors (QSIs), have been shown to effectively block QS and subsequently attenuate the virulence of Pseudomonas aeruginosa , as well as increasing its susceptibility to both antibiotics and the immune system. In this study, a structure-based virtual screening (SB-VS) approach was used for the discovery of novel QSI candidates. Three-dimensional structures of 3,040 natural compounds and their derivatives were obtained, after which molecular docking was performed using the QS receptor LasR as a target. Based on docking scores and molecular masses, 22 compounds were purchased to determine their efficacies as quorum-sensing inhibitors. Using a live reporter assay for quorum sensing, 5 compounds were found to be able to inhibit QS-regulated gene expression in P. aeruginosa in a dose-dependent manner. The most promising compound, G1, was evaluated by isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic analysis, and it was found to significantly affect the abundance of 46 proteins (19 were upregulated 27 were downregulated) in P. aeruginosa PAO1. It specifically reduced the expression of several quorum-sensing-regulated virulence factors, such as protease IV, chitinase, and pyoverdine synthetases. G1 was also able to reduce extracellular DNA release and inhibited the secretion of the virulence factor, elastase, whose expression is regulated by LasR. These results demonstrate the utility of SB-VS for the discovery of target-specific QSIs.

Biofilm development and cell death in the marine bacterium Pseudoalteromonas tunicata

Publisher: American Society for Microbiology

Date: 06-2004

DOI: 10.1128/AEM.70.6.3232-3238.2004

Abstract: The newly described green-pigmented bacterium Pseudoalteromonas tunicata (D2) produces target-specific inhibitory compounds against bacteria, algae, fungi, and invertebrate larvae and is frequently found in association with living surfaces in the marine environment. As part of our studies on the ecology of P. tunicata and its interaction with marine surfaces, we examined the ability of P. tunicata to form biofilms under continuous culture conditions within the laboratory. P. tunicata biofilms exhibited a characteristic architecture consisting of differentiated microcolonies surrounded by water channels. Remarkably, we observed a repeatable pattern of cell death during biofilm development of P. tunicata , similar to that recently reported for biofilms of Pseudomonas aeruginosa (J. S. Webb et al., J. Bacteriol. 185: 4585-4595, 2003). Killing and lysis occurred inside microcolonies, apparently resulting in the formation of voids within these structures. A subpopulation of viable cells was always observed within the regions of killing in the biofilm. Moreover, extensive killing in mature biofilms appeared to result in detachment of the biofilm from the substratum. A novel 190-kDa autotoxic protein produced by P. tunicata , designated AlpP, was found to be involved in this biofilm killing and detachment. A Δ alpP mutant derivative of P. tunicata was generated, and this mutant did not show cell death during biofilm development. We propose that AlpP-mediated cell death plays an important role in the multicellular biofilm development of P. tunicata and subsequent dispersal of surviving cells within the marine environment.

Improving charge collection in Escherichia coli–carbon electrode devices with conjugated oligoelectrolytes

Publisher: Royal Society of Chemistry (RSC)

Date: 2013

DOI: 10.1039/C3CP50437A

Abstract: It is important to tailor biotic-abiotic interfaces in order to maximize the utility of bioelectronic devices such as microbial fuel cells (MFCs), electrochemical sensors and bioelectrosynthetic systems. The efficiency of electron-equivalent extraction (or injection) across such biotic-abiotic interfaces is dependent on the choice of the microbe and the conductive electrode material. In this contribution, we show that spontaneous intercalation of a conjugated oligoelectrolyte, namely 4,4'-bis(4'-(N,N-bis(6''-(N,N,N-trimethylammonium)hexyl)amino)-styryl)stilbene tetraiodide (DSSN+), into the membranes of Escherichia coli leads to an increase in current generation in MFCs containing carbon-based electrodes. A combination of scanning electron microscopy (SEM) and confocal microscopy was employed to confirm the incorporation of DSSN+ into the cell membrane and biofilm formation atop carbon felt electrodes. Current collection was enhanced by more than 300% with addition of this conjugated oligoelectrolyte. The effect of DSSN+ concentration on electrical output was also investigated. Higher concentrations, up to 25 μM, lead to an overall increase in the number of charge equivalents transferred to the charge-collecting electrode, providing evidence in support of the central role of the synthetic system in improving device performance.

Hydrophobic and electrostatic characterization of surface structures of bacteria and its relationship to adhesion to an air-water interface

Publisher: Springer Science and Business Media LLC

Date: 06-1982

DOI: 10.1007/BF00411177

Nitric oxide signaling in Pseudomonas aeruginosa biofilms mediates phosphodiesterase activity, decreased cyclic di-GMP levels, and enhanced dispersal.

Publisher: American Society for Microbiology

Date: 12-2009

DOI: 10.1128/JB.00975-09

Abstract: Bacteria in biofilms often undergo active dispersal events and revert to a free-swimming, planktonic state to complete the biofilm life cycle. The signaling molecule nitric oxide (NO) was previously found to trigger biofilm dispersal in the opportunistic pathogen Pseudomonas aeruginosa at low, nontoxic concentrations (N. Barraud, D. J. Hassett, S. H. Hwang, S. A. Rice, S. Kjelleberg, and J. S. Webb, J. Bacteriol. 188:7344-7353, 2006). NO was further shown to increase cell motility and susceptibility to antimicrobials. Recently, numerous studies revealed that increased degradation of the secondary messenger cyclic di-GMP (c-di-GMP) by specific phosphodiesterases (PDEs) triggers a planktonic mode of growth in eubacteria. In this study, the potential link between NO and c-di-GMP signaling was investigated by performing (i) PDE inhibitor studies, (ii) enzymatic assays to measure PDE activity, and (iii) direct quantification of intracellular c-di-GMP levels. The results suggest a role for c-di-GMP signaling in triggering the biofilm dispersal event induced by NO, as dispersal requires PDE activity and addition of NO stimulates PDE and induces the concomitant decrease in intracellular c-di-GMP levels in P. aeruginosa . Furthermore, gene expression studies indicated global responses to low, nontoxic levels of NO in P. aeruginosa biofilms, including upregulation of genes involved in motility and energy metabolism and downregulation of adhesins and virulence factors. Finally, site-directed mutagenesis of candidate genes and physiological characterization of the corresponding mutant strains uncovered that the chemotaxis transducer BdlA is involved in the biofilm dispersal response induced by NO.

Integrative systems approach reveals dynamics of microbiome-metal-ion axis in mesocosms representing tropical urban freshwater canal ecosystem

Publisher: Cold Spring Harbor Laboratory

Date: 21-09-2020

DOI: 10.1101/2020.09.21.306803

Abstract: Freshwater ecosystems of tr opical u rban c anals s ystems (TrUCS), are highly dynamic and experience constant pressures from interspersed effects of land-use and rain. The dynamic nature of TrUCS ecosystems presents a unique opportunity to unravel the signature interactions between the macro-organisms (top-down), sed imentary mi crobial c ommunities (SedMICs), their functioning and the geochemical environment (bottom-up). A systems level understanding of the molecular and mechanistic basis of the highly dynamic behaviour that leads to specific ecosystem outcomes, is currently lacking. Therefore, a research framework to identify the direct link between top-down and bottom-up ecological effects on SedMICs in a highly dynamic urban canal sedimentary system is needed. Here, we present a framework of integrated multi-dimensional data across system-level biotic and abiotic ecological descriptors, such as environmental variables and active SedMICs. We followed the ecosystem shifts after a natural disturbance (rain) in two different anthropogenic disturbance (land-use) regimes. Shifts in profiles of metabolically active community were conserved across different land-use types, indicating resilience to perturbation is an intrinsic property of the TrUCs ecosystem. Three distinct phases, which were dominated sequentially by autotrophy, anoxic-heterotrophy and oxic-heterotrophy, were identified within these shifts. The first two phases were influenced by the bottom-up effects of specific metal-ion combinations of nitrates and sulfates with magnesium, aluminum and iron, and the third phase was triggered by top-down influences of bioturbation. This generalized systems-level approach, which provides an ecosystem-centric understanding of TrUCS and integrates them in sustainable management practices, can also be extended to other freshwater ecosystems.

Variability and abundance of the epiphytic bacterial community associated with a green marine Ulvacean alga

Publisher: Springer Science and Business Media LLC

Date: 15-10-2009

DOI: 10.1038/ISMEJ.2009.107

Abstract: Marine Ulvacean algae are colonized by dense microbial communities predicted to have an important role in the development, defense and metabolic activities of the plant. Here we assess the ersity and seasonal dynamics of the bacterial community of the model alga Ulva australis to identify key groups within this epiphytic community. A total of 48 algal s les of U. australis that were collected as 12 in iduals at 3 monthly intervals, were processed by applying denaturing gradient gel electrophoresis (DGGE), and three s les from each season were subjected to catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). CARD-FISH revealed that the epiphytic microbial community was comprised mainly of bacterial cells (90%) and was dominated by the groups Alphaproteobacteria (70%) and Bacteroidetes (13%). A large portion (47%) of sequences from the Alphaproteobacteria fall within the Roseobacter clade throughout the different seasons, and an average relative proportion of 19% was observed using CARD-FISH. DGGE based spatial (between tidal pools) and temporal (between season) comparisons of bacterial community composition demonstrated that variation occurs. Between in iduals from both the same and different tidal pools, the variation was highest during winter (30%) and between seasons a 40% variation was observed. The community also includes a sub-population of bacteria that is consistently present. Sequences from excised DGGE bands indicate that members of the Alphaproteobacteria and the Bacteroidetes are part of this stable sub-population, and are likely to have an important role in the function of this marine epiphytic microbial community.

Oligotrophic and copiotrophic marine bacteria—observations related to attachment

Publisher: Oxford University Press (OUP)

Date: 04-1985

DOI: 10.1111/J.1574-6968.1985.TB01135.X

Real Time, Spatial, and Temporal Mapping of the Distribution of c-di-GMP during Biofilm Development.

Publisher: Elsevier BV

Date: 2017

DOI: 10.1074/JBC.M116.746743

The use of functional genomics for the identification of a gene cluster encoding for the biosynthesis of an antifungal tambjamine in the marine bacterium Pseudoalteromonas tunicata.

Publisher: Wiley

Date: 02-11-2007

DOI: 10.1111/J.1462-2920.2006.01177.X

Abstract: A large insert library was created in Escherichia coli from the DNA of the surface-associated marine bacterium Pseudoalteromonas tunicata. Screening of the library for antifungal activity resulted in the detection and identification of a large gene cluster encoding for the biosynthesis of an antifungal tambjamine. A biosynthetic pathway has been proposed based on analysis and annotation of the gene cluster.

Corrigendum

Publisher: Wiley

Date: 04-09-2015

DOI: 10.1111/JOIM.12370

Interactions within the microbiome alter microbial interactions with host chemical defences and affect disease in a marine holobiont

Publisher: Springer Science and Business Media LLC

Date: 04-02-2019

DOI: 10.1038/S41598-018-37062-Z

Abstract: Our understanding of diseases has been transformed by the realisation that people are holobionts, comprised of a host and its associated microbiome(s). Disease can also have devastating effects on populations of marine organisms, including dominant habitat formers such as seaweed holobionts. However, we know very little about how interactions between microorganisms within microbiomes - of humans or marine organisms – affect host health and there is no underpinning theoretical framework for exploring this. We applied ecological models of succession to bacterial communities to understand how interactions within a seaweed microbiome affect the host. We observed succession of surface microbiomes on the red seaweed Delisea pulchra in situ , following a disturbance, with communities ‘recovering’ to resemble undisturbed states after only 12 days. Further, if this recovery was perturbed, a bleaching disease previously described for this seaweed developed. Early successional strains of bacteria protected the host from colonisation by a pathogenic, later successional strain. Host chemical defences also prevented disease, such that within-microbiome interactions were most important when the host’s chemical defences were inhibited. This is the first experimental evidence that interactions within microbiomes have important implications for host health and disease in a dominant marine habitat-forming organism.

The Transient Phase Between Growth and Nongrowth of Heterotrophic Bacteria, with Emphasis on the Marine Environment

Publisher: Annual Reviews

Date: 10-1987

DOI: 10.1146/ANNUREV.MI.41.100187.000325

Abstract: Combinations of KIR3DL1 and HLA-Bw4 alleles protect against HIV infection and/or disease progression. These combinations enhance NK cell responsiveness through the ontological process of education. However, educated KIR3DL1(+) NK cells do not have enhanced degranulation upon direct recognition of autologous HIV-infected cells. Since antibody-dependent cellular cytotoxicity (ADCC) is associated with improved HIV infection outcomes and NK cells overcome inhibition through killer cell immunoglobulin-like receptors (KIR) to mediate ADCC, we hypothesized that KIR3DL1-educated NK cells mediate anti-HIV ADCC against autologous cells. A whole-blood flow cytometry assay was used to evaluate ADCC-induced activation of NK cells. This assay assessed activation (gamma interferon [IFN-γ] production and/or CD107a expression) of KIR3DL1(+) and KIR3DL1(-) NK cells, from HLA-Bw4(+) and HLA-Bw4(-) HIV-positive and HIV-negative in iduals, in response to autologous HIV-specific ADCC targets. KIR3DL1(+) NK cells were more functional than KIR3DL1(-) NK cells from HLA-Bw4(+), but not HLA-Bw4(-), healthy controls. In HIV-infected in iduals, no differences in NK cell functionality were observed between KIR3DL1(+) and KIR3DL1(-) NK cells in HLA-Bw4(+) in iduals, consistent with dysfunction of NK cells in the setting of HIV infection. Reflecting the partial normalization of NK cell responsiveness following initiation of antiretroviral therapy, a significant correlation was observed between the peripheral CD4(+) T-lymphocyte counts in antiretroviral therapy-treated subjects and the functionality of NK cells. However, peripheral CD4(+) T-lymphocyte counts were not correlated with an anti-HIV ADCC functional advantage in educated KIR3DL1(+) NK cells. The abrogation of the functional advantage of educated NK cells may enhance HIV disease progression. Strategies to enhance the potency of NK cell-mediated ADCC may improve HIV therapies and vaccines.

Chemical cues for surface colonization.

Publisher: Springer Science and Business Media LLC

Date: 2002

DOI: 10.1023/A:1020789625989

Abstract: Colonization of surfaces in marine benthic environments is often one of the most significant moments in the life history of benthic organisms, representing, for ex le, a change from a planktonic to a benthic existence, a shift from a mobile to a sessile life form, or the initiation of pathogenesis. Many of the surfaces that are colonized are, in fact, other marine organisms, and in a general sense there is widespread evidence that specific chemical cues derived from marine organisms affect colonization by both marine prokaryotes and eukaryotes. However, detailed information for any one system on the nature of such cues, their distribution in situ, and their effects on the demography of colonizers is rare. Here, we selectively review the literature on chemical cues for colonization in the sea, focussing on contrasts between positive (inducers) and negative (inhibitors, deterrents) cues and on prokaryote/eukaryote interactions. We also consider whether generalized life history or natural history characteristics of colonizers (i.e., the mobility of a propagule, the extent to which a species is a habitat generalist or specialist, etc.) affect their response to chemical cues, and we touch briefly on some recent highlights relevant to the critical interplay between hydrodynamics and chemistry. A number of important methodological concerns are now being addressed through the introduction of field assays and analyses for chemical cues, and through molecular techniques for the characterization of microbial biofilms. These developments are encouraging, as is the increasingly multidisciplinary and cross-taxonomic approach to research in this area.

The role of regulators in the expression of quorum-sensing signals in Pseudomonas aeruginosa.

Publisher: S. Karger AG

Date: 2003

DOI: 10.1159/000076739

Abstract: Quorum-sensing systems provide i Pseudomonas aeruginosa /i with a sensitive regulatory mechanism that allows for the induction of several phenotypic genes in a cell density fashion. In this work, a mathematical model of the acylated homoserine lactones regulatory network system in i P. aeruginosa /i has been developed. It is the first integrated model to consider both quorum-sensing systems. The model has allowed us to disentangle the complex behavior exhibited by the system as the concentration of extracellular OdDHL is increased. At either low or high levels of extracellular OdDHL, the bacterium remains in an uninduced or induced state, respectively. At moderate levels, the behavior is characterized by several states. Here, the bacteria can switch suddenly from an uninduced to an induced phenotype in response to small changes in the concentration of extracellular OdDHL. Additionally, we have been able to address the roles of RsaL and Vfr as regulators of the quorum-sensing system. An important result from this analysis suggests that RsaL will increase the concentration of extracellular OdDHL required to induce the system, and it is a key regulator of the inhibition of the quorum-sensing system under low cell densities. Most importantly, our results suggest that Vfr has strong regulatory effects on the system as an increased affinity between the LasR/OdDHL complex, and the i las /i R promoter leads to significant qualitative changes in induction patterns. We also show experimental data that demonstrate that Vfr is required for signal production in the early phase of growth, but that in the latter stages of growth, the i vfr /i mutant is able to synthesize wild-type levels of signal.

Characterization of the archaeal community fouling a membrane bioreactor

Publisher: Elsevier BV

Date: 03-2015

DOI: 10.1016/J.JES.2014.07.025

Abstract: Biofilm formation, one of the primary causes of biofouling, results in reduced membrane flux or increased transmembrane pressure and thus represents a major impediment to the wider implementation of membrane bioreactor (MBR) technologies for water purification. Most studies have focused on the role of bacteria in membrane fouling as they are the most dominant and best studied organisms present in the MBR. In contrast, there is limited information on the role of the archaeal community in biofilm formation in MBRs. This study investigated the composition of the archaeal community during the process of biofouling in an MBR. The archaeal community was observed to have lower richness and ersity in the biofilm than the sludge during the establishment of biofilms at low transmembrane pressure (TMP). Clustering of the communities based on the Bray-Curtis similarity matrix indicated that a subset of the sludge archaeal community formed the initial biofilms. The archaeal community in the biofilm was mainly composed of Thermoprotei, Thermoplasmata, Thermococci, Methanopyri, Methanomicrobia and Halobacteria. Among them, the Thermoprotei and Thermoplasmata were present at higher relative proportions in the biofilms than they were in the sludge. Additionally, the Thermoprotei, Thermoplasmata and Thermococci were the dominant organisms detected in the initial biofilms at low TMP, while as the TMP increased, the Methanopyri, Methanomicrobia, Aciduliprofundum and Halobacteria were present at higher abundances in the biofilms at high TMP.

Chemical defenses of seaweeds against microbial colonization

Publisher: Springer Science and Business Media LLC

Date: 1997

DOI: 10.1023/A:1008236901790

Metaproteogenomic analysis of a community of sponge symbionts

Publisher: Springer Science and Business Media LLC

Date: 02-02-2012

DOI: 10.1038/ISMEJ.2012.1

The role of quorum sensing mediated developmental traits in the resistance of Serratia marcescens biofilms against protozoan grazing.

Publisher: Wiley

Date: 16-02-2006

DOI: 10.1111/J.1462-2920.2006.00993.X

Abstract: Resistance against protozoan grazers is a crucial factor that is important for the survival of many bacteria in their natural environment. However, the basis of resistance to protozoans and how resistance factors are regulated is poorly understood. In part, resistance may be due to biofilm formation, which is known to protect bacteria from environmental stress conditions. The ubiquitous organism Serratia marcescens uses quorum sensing (QS) control to regulate virulence factor expression and biofilm formation. We hypothesized that the QS system of S. marcescens also regulates mechanisms that protect biofilms against protozoan grazing. To investigate this hypothesis, we compared the interactions of wild-type and QS mutant strains of S. marcescens biofilms with two protozoans having different feeding types under batch and flow conditions. Under batch conditions, S. marcescens forms microcolony biofilms, and filamentous biofilms are formed under flow conditions. The microcolony-type biofilms were protected from grazing by the suspension feeder, flagellate Bodo saltans, but were not protected from the surface feeder, Acanthamoeba polyphaga. In contrast, the filamentous biofilm provided protection against A. polyphaga. The main findings presented in this study suggest that (i) the QS system is not involved in grazing resistance of S. marcescens microcolony-type biofilms (ii) QS in S. marcescens regulates antiprotozoan factor(s) that do not interfere with the grazing efficiency of the protozoans and (iii) QS-controlled, biofilm-specific differentiation of filaments and cell chains in biofilms of S. marcescens provides an efficient mechanism against protozoan grazing.

Next-generation studies of microbial biofilm communities.

Publisher: Wiley

Date: 29-07-2016

DOI: 10.1111/1751-7915.12390

Nuclear transfer to prevent mitochondrial DNA diseases

Publisher: Elsevier BV

Date: 09-2006

DOI: 10.1016/S0140-6736(06)69326-4

Changes in viability, respiratory activity and morphology of the marine Vibrio sp. strain S14 during starvation of individual nutrients and subsequent recovery

Publisher: Oxford University Press (OUP)

Date: 08-1993

DOI: 10.1111/J.1574-6941.1993.TB00034.X

Analysis of microbial community composition in a lab‐scale membrane distillation bioreactor

Publisher: Oxford University Press (OUP)

Date: 15-02-2015

DOI: 10.1111/JAM.12759

Marine Pseudoalteromonas species are associated with higher organisms and produce biologically active extracellular agents

Publisher: Oxford University Press (OUP)

Date: 12-1999

DOI: 10.1111/J.1574-6941.1999.TB00656.X

Abstract: The newly established genus Pseudoalteromonas contains numerous marine species which synthesize biologically active molecules. The production of a range of compounds which are active against a variety of target organisms appears to be a unique characteristic for this genus and may greatly benefit Pseudoalteromonas cells in their competition for nutrients and colonization of surfaces. Species of Pseudoalteromonas are generally found in association with marine eukaryotes and display anti-bacterial, bacteriolytic, agarolytic and algicidal activities. Moreover, several Pseudoalteromonas isolates specifically prevent the settlement of common fouling organisms. While a wide range of inhibitory extracellular agents are produced, compounds promoting the survival of other marine organisms living in the vicinity of Pseudoalteromonas species have also been found.

Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life

Publisher: Springer Science and Business Media LLC

Date: 21-06-2012

DOI: 10.1038/ISMEJ.2012.62

Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion.

Publisher: Oxford University Press (OUP)

Date: 18-09-2009

DOI: 10.1093/NAR/GKP746

The presence and role of bacterial quorum sensing in activated sludge

Publisher: Wiley

Date: 14-05-2012

DOI: 10.1111/J.1751-7915.2012.00348.X

Selective extraction of bacterial DNA from the surfaces of macroalgaeδ

Publisher: American Society for Microbiology

Date: 2009

DOI: 10.1128/AEM.01630-08

Abstract: A novel method has been developed for the selective extraction of DNA from surface-associated bacterial communities from the two model marine benthic algae Ulva australis and Delisea pulchra . The extracted DNA had no detectable contamination with host DNA, was recovered in high yield and quality, and was representative of the bacterial community on the algal surfaces. The DNA is suitable for a variety of subsequent applications, including the construction of large-insert clone libraries and metagenomic sequencing.

Molecular Dynamics Unlocks Atomic Level Self-Assembly of the Exopolysaccharide Matrix of Water-Treatment Granular Biofilms

Publisher: American Chemical Society (ACS)

Date: 22-05-2012

DOI: 10.1021/BM3005808

Abstract: Biofilm formation, in which bacteria are embedded within an extracellular matrix, is the default form of microbial life in most natural and engineered habitats. In this work, atomistic molecular dynamics simulations were employed to examine the self-assembly of the polysaccharide Granulan to provide insight into the molecular interactions that lead to biofilm formation. Granulan is a major gel forming matrix component of granular microbial biofilms found in used-water treatment systems. Molecular dynamics simulations showed that Granulan forms an antiparallel double helix stabilized by complementary hydrogen bonds between the β-glucosamine of one strand and the N-acetyl-β-galactosamine-2-acetoamido-2-deoxy-α-galactopyranuronic pair of the other in both the presence and absence of Ca(2+). It is shown that Ca(2+) binds primarily to the carboxyl group of the terminal hexuronic acid of the sugar branch and that interactions between branches mediated by Ca(2+) suggest a possible mechanism for strengthening gels by facilitating interhelical bridging.

Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment

Publisher: Public Library of Science (PLoS)

Date: 24-09-2008

DOI: 10.1371/JOURNAL.PONE.0003252

How do non-differentiating bacteria adapt to starvation?

Publisher: Springer Science and Business Media LLC

Date: 1993

DOI: 10.1007/BF00871228

Clinical significance of seeding dispersal in biofilms

Publisher: Microbiology Society

Date: 11-2005

DOI: 10.1099/MIC.0.28295-0

Antidiatom and antibacterial activity of epiphytic bacteria isolated from Ulva lactuca in tropical waters

Publisher: Springer Science and Business Media LLC

Date: 18-11-2010

DOI: 10.1007/S11274-010-0606-1

A novel and sensitive method for the quantification of N‐3‐oxoacyl homoserine lactones using gas chromatography–mass spectrometry: application to a model bacterial biofilm

Publisher: Wiley

Date: 10-2000

DOI: 10.1046/J.1462-2920.2000.00136.X

Abstract: A method is reported for the quantification of 3-oxoacyl homoserine lactones (3-oxo AHLs), a major class of quorum-sensing signals found in Gram-negative bacteria. It is based on the conversion of 3-oxo AHLs to their pentafluorobenzyloxime derivatives followed by gas chromatography-mass spectrometry (electron capture-negative ion). The method used [13C16]-N-3-oxo-dodecanoyl homoserine lactone ([13C16]-OdDHL) as the internal standard, and its validity was tested by spiking the supernatant and cell fractions with three levels of 3-oxo AHLs, i.e. 1, 10 and 100 ng per s le. These showed the method to be both sensitive (S/N ratio >10:1 for 1 ng) and accurate. The assay was applied to the biofilm and effluent of a green fluorescent protein (GFP)-expressing strain of Pseudomonas aeruginosa (6294) culture grown in flow cells. Biofilm volume was determined for three replicate flow cells by confocal scanning laser microscopy. OdDHL was detected in the biofilm at 632 +/- 381 microM and the effluent at 14 +/- 3 nM. The biofilm concentration is the highest level so far reported for an AHL in a wild-type bacterial system. The next most abundant 3-oxo AHL in the biofilm and effluent was N-3-oxo-tetradecanoyl homoserine lactone (OtDHL) at 40 +/- 15 microM and 1.5 +/- 0.7 nM respectively. OtDHL is unreported for P. aeruginosa and has an activity equivalent to OdDHL in a lasR bioassay. Two other 3-oxo AHLs were detected at lower concentrations: N3-oxo-decanoyl homoserine lactone (ODHL) in the biofilm (3 +/- 2 microM) and effluent (1 +/- 0.1 nM) and N-3-oxo-octanoyl homoserine lactone (OOHL) in the effluent (0.1 +/- 0.1 nM).

Inhibition of Fungal Colonization by Pseudoalteromonas tunicata Provides a Competitive Advantage during Surface Colonization

Publisher: American Society for Microbiology

Date: 09-2006

DOI: 10.1128/AEM.00559-06

Abstract: The marine epiphytic bacterium Pseudoalteromonas tunicata produces a range of extracellular secondary metabolites that inhibit an array of common fouling organisms, including fungi. In this study, we test the hypothesis that the ability to inhibit fungi provides P. tunicata with an advantage during colonization of a surface. Studies on a transposon-generated antifungal-deficient mutant of P. tunicata , FM3, indicated that a long-chain fatty acid-coenzyme A ligase is involved in the production of a broad-range antifungal compound by P. tunicata . Flow cell experiments demonstrated that production of an antifungal compound provided P. tunicata with a competitive advantage against a marine yeast isolate during surface colonization. This compound enabled P. tunicata to disrupt an already established fungal biofilm by decreasing the number of yeast cells attached to the surface by 66% ± 9%. For in vivo experiments, the wild-type and FM3 strains of P. tunicata were used to inoculate the surface of the green alga Ulva australis . Double-gradient denaturing gradient gel electrophoresis analysis revealed that after 48 h, the wild-type P. tunicata had outcompeted the surface-associated fungal community, whereas the antifungal-deficient mutant had no effect on the fungal community. Our data suggest that P. tunicata is an effective competitor against fungal surface communities in the marine environment.

Biogeography of bacteria associated with the marine sponge Cymbastela concentrica

Publisher: Wiley

Date: 10-01-2005

DOI: 10.1111/J.1462-2920.2004.00711.X

Abstract: Recent debate regarding microbial biogeography has focused largely on free-living microbes, yet those microbes associated with host organisms are also of interest from a biogeographical perspective. Marine eukaryotes and associated bacteria should provide ideal systems in which to consider microbial biogeography, as (i) bacteria in seawater should be able to disperse among in iduals of the same host species, yet (ii) potential for adaptation to particular hosts (and thus speciation) also exists. We used 16S rDNA-DGGE (denaturing gradient gel electrophoresis) to examine geographic variability in bacterial community composition in the marine sponge Cymbastela concentrica. Denaturing gradient gel electrophoresis banding patterns (and phylogenetic analysis of excised DGGE bands) indicated different communities in Cymbastela concentrica from tropical versus temperate Australia. In contrast, communities were very similar over a 500-km portion of the sponge's temperate range. Variation in bacterial community composition was also considered with respect to ocean current patterns. We speculate that the ergent communities in different parts of the sponge's range provide evidence of endemism attributed to host association, although variation in environmental factors such as light and temperature could also explain the observed results. Interestingly, bacterial communities in seawater varied much less between tropical and temperate locations than did those in C. concentrica, supporting the concept of widespread dispersal among these free-living microbes.

Enhanced benzaldehyde tolerance in Zymomonas mobilis biofilms and the potential of biofilm applications in fine-chemical production (vol 72, pg 1639, 2006)

Publisher: American Society for Microbiology

Date: 08-2006

DOI: 10.1128/AEM.01321-06

The application of nitric oxide to control biofouling of membrane bioreactors

Publisher: Wiley

Date: 06-03-2015

DOI: 10.1111/1751-7915.12261

Quorum‐sensing cross talk: isolation and chemical characterization of cyclic dipeptides from Pseudomonas aeruginosa and other Gram‐negative bacteria

Publisher: Wiley

Date: 09-1999

DOI: 10.1046/J.1365-2958.1999.01577.X

Abstract: In cell-free Pseudomonas aeruginosa culture supernatants, we identified two compounds capable of activating an N-acylhomoserine lactone (AHL) biosensor. Mass spectrometry and NMR spectroscopy revealed that these compounds were not AHLs but the diketopiperazines (DKPs), cyclo(DeltaAla-L-Val) and cyclo(L-Pro-L-Tyr) respectively. These compounds were also found in cell-free supernatants from Proteus mirabilis, Citrobacter freundii and Enterobacter agglomerans [cyclo(DeltaAla-L-Val) only]. Although both DKPs were absent from Pseudomonas fluorescens and Pseudomonas alcaligenes, we isolated, from both pseudomonads, a third DKP, which was chemically characterized as cyclo(L-Phe-L-Pro). Dose-response curves using a LuxR-based AHL biosensor indicated that cyclo(DeltaAla-L-Val), cyclo(L-Pro-L-Tyr) and cyclo(L-Phe-L-Pro) activate the biosensor in a concentration-dependent manner, albeit at much higher concentrations than the natural activator N-(3-oxohexanoyl)-L-homoserine lactone (3-oxo-C6-HSL). Competition studies showed that cyclo(DeltaAla-L-Val), cyclo(L-Pro-L-Tyr) and cyclo(L-Phe-L-Pro) antagonize the 3-oxo-C6-HSL-mediated induction of bioluminescence, suggesting that these DKPs may compete for the same LuxR-binding site. Similarly, DKPs were found to be capable of activating or antagonizing other LuxR-based quorum-sensing systems, such as the N-butanoylhomoserine lactone-dependent swarming motility of Serratia liquefaciens. Although the physiological role of these DKPs has yet to be established, their activity suggests the existence of cross talk among bacterial signalling systems.

QUANTITATIVE ANALYSIS OF BACTERIAL HYDROPHOBICITY STUDIED BY THE BINDING OF DODECANOIC ACID

Publisher: Oxford University Press (OUP)

Date: 1980

DOI: 10.1111/J.1574-6941.1980.TB01572.X

Dynamic Remodeling of Microbial Biofilms by Functionally Distinct Exopolysaccharides

Publisher: American Society for Microbiology

Date: 29-08-2014

DOI: 10.1128/MBIO.01536-14

Abstract: Biofilms are densely populated communities of microbial cells protected and held together by a matrix of extracellular polymeric substances. The structure and rheological properties of the matrix at the microscale influence the retention and transport of molecules and cells in the biofilm, thereby dictating population and community behavior. Despite its importance, quantitative descriptions of the matrix microstructure and microrheology are limited. Here, particle-tracking microrheology in combination with genetic approaches was used to spatially and temporally study the rheological contributions of the major exopolysaccharides Pel and Psl in Pseudomonas aeruginosa biofilms. Psl increased the elasticity and effective cross-linking within the matrix, which strengthened its scaffold and appeared to facilitate the formation of microcolonies. Conversely, Pel reduced effective cross-linking within the matrix. Without Psl, the matrix becomes more viscous, which facilitates biofilm spreading. The wild-type biofilm decreased in effective cross-linking over time, which would be advantageous for the spreading and colonization of new surfaces. This suggests that there are regulatory mechanisms to control production of the exopolysaccharides that serve to remodel the matrix of developing biofilms. The exopolysaccharides were also found to have profound effects on the spatial organization and integration of P. aeruginosa in a mixed-species biofilm model of P. aeruginosa - Staphylococcus aureus . Pel was required for close association of the two species in mixed-species microcolonies. In contrast, Psl was important for P. aeruginosa to form single-species biofilms on top of S. aureus biofilms. Our results demonstrate that Pel and Psl have distinct physical properties and functional roles during biofilm formation. IMPORTANCE Most bacteria grow as biofilms in the environment or in association with eukaryotic hosts. Removal of biofilms that form on surfaces is a challenge in clinical and industrial settings. One of the defining features of a biofilm is its extracellular matrix. The matrix has a heterogeneous structure and is formed from a secretion of various biopolymers, including proteins, extracellular DNA, and polysaccharides. It is generally known to interact with biofilm cells, thus affecting cell physiology and cell-cell communication. Despite the fact that the matrix may comprise up to 90% of the biofilm dry weight, how the matrix properties affect biofilm structure, maturation, and interspecies interactions remain largely unexplored. This study reveals that bacteria can use specific extracellular polymers to modulate the physical properties of their microenvironment. This in turn impacts biofilm structure, differentiation, and interspecies interactions.

Voltammetric profiling of redox-active metabolites expressed by Pseudomonas aeruginosa for diagnostic purposes

Publisher: Royal Society of Chemistry (RSC)

Date: 2015

DOI: 10.1039/C4CC08590F

Abstract: Voltammetric analysis of Pseudomonas aeruginosa growth cultures unveils the interplay between PQS and phenazines under a potential bias.

Glucose Starvation-Induced Dispersal of Pseudomonas aeruginosa Biofilms Is cAMP and Energy Dependent

Publisher: Public Library of Science (PLoS)

Date: 14-08-2012

DOI: 10.1371/JOURNAL.PONE.0042874

Enhancing Bidirectional Electron Transfer of Shewanella oneidensis by a Synthetic Flavin Pathway

Publisher: American Chemical Society (ACS)

Date: 05-02-2015

DOI: 10.1021/SB500331X

Abstract: Flavins regulate the rate and direction of extracellular electron transfer (EET) in Shewanella oneidensis. However, low concentration of endogenously secreted flavins by the wild-type S. oneidensis MR-1 limits its EET efficiency in bioelectrochemical systems (BES). Herein, a synthetic flavin biosynthesis pathway from Bacillus subtilis was heterologously expressed in S. oneidensis MR-1, resulting in ∼25.7 times' increase in secreted flavin concentration. This synthetic flavin module enabled enhanced bidirectional EET rate of MR-1, in which its maximum power output in microbial fuel cells increased ∼13.2 times (from 16.4 to 233.0 mW/m(2)), and the inward current increased ∼15.5 times (from 15.5 to 255.3 μA/cm(2)).

Comparison of flavins and a conjugated oligoelectrolyte in stimulating extracellular electron transport from Shewanella oneidensis MR-1

Publisher: Elsevier BV

Date: 04-2014

DOI: 10.1016/J.ELECOM.2014.01.025

The role of quorum sensing and the effect of environmental conditions on biofilm formation by strains ofVibrio vulnificus

Publisher: Informa UK Limited

Date: 2006

DOI: 10.1080/08927010600743431

Pseudomonas aeruginosawithLasIQuorum-Sensing Deficiency during Corneal Infection

Publisher: Association for Research in Vision and Ophthalmology (ARVO)

Date: 06-2004

DOI: 10.1167/IOVS.03-0980

Abstract: To understand the importance of Pseudomonas aeruginosa quorum-sensing systems in the development of corneal infection, the genotypic characteristics and pathogenesis of seven ocular isolates with low-protease and acyl homoserine lactone (AHL) activity and quorum-sensing mutants of PAO1 deficient in lasI, lasR, or rhlR were investigated in the study. The possession of the quorum-sensing genes lasI, lasR, rhlI, rhlR, and the quorum-sensing controlled genes lasB, aprA, and rhlAB in the clinical isolates were determined by polymerase chain reaction and Southern blot hybridization. Elastinolytic activity, controlled by the las system, was assayed using elastin Congo red and rhamnolipid production controlled by the rhl system was assessed using agar plates containing methylene blue/cetyltrimethyl ammonium bromide. Induction of keratitis was examined in a scarified inbred BALB/c mouse model. The clinical isolates Paer1 and -3 were lasI and lasR negative, and the isolates Paer2 and -4 were rhlR and rhlAB negative. The isolates Paer17, Paer26, 6294 and 6206 possessed all the genes examined. There was no rhamnolipid production in clinical isolates Paer2 and -4. The isolates Paer1 and -3 were virtually avirulent in the scarified mouse corneas. Using isogenic PAO1 mutants, strain lasI showed a markedly reduced virulence in the corneal infection model. The remainder of the clinical isolates and the lasR or rhlR mutant strains caused severe keratitis. These results indicate that quorum-sensing deficiency may occur naturally in clinical isolates, and the possession of lasI and hence a functional Las quorum-sensing system may be important in development of corneal infection.

Marine Bacteria from Danish Coastal Waters Show Antifouling Activity against the Marine Fouling Bacterium Pseudoalteromonas sp. Strain S91 and Zoospores of the Green Alga Ulva australis Independent of

Publisher: American Society for Microbiology

Date: 15-12-2011

DOI: 10.1128/AEM.06038-11

Abstract: The aims of this study were to determine if marine bacteria from Danish coastal waters produce antifouling compounds and if antifouling bacteria could be ascribed to specific niches or seasons. We further assess if antibacterial effect is a good proxy for antifouling activity. We isolated 110 bacteria with anti- Vibrio activity from different s le types and locations during a 1-year s ling from Danish coastal waters. The strains were identified as Pseudoalteromonas , Phaeobacter , and Vibrionaceae based on phenotypic tests and partial 16S rRNA gene sequence similarity. The numbers of bioactive bacteria were significantly higher in warmer than in colder months. While some species were isolated at all s ling locations, others were niche specific. We repeatedly isolated Phaeobacter gallaeciensis at surfaces from one site and Pseudoalteromonas tunicata at two others. Twenty-two strains, representing the major taxonomic groups, different seasons, and isolation strategies, were tested for antiadhesive effect against the marine biofilm-forming bacterium Pseudoalteromonas sp. strain S91 and zoospores of the green alga Ulva australis . The antiadhesive effects were assessed by quantifying the number of strain S91 or Ulva spores attaching to a preformed biofilm of each of the 22 strains. The strongest antifouling activity was found in Pseudoalteromonas strains. Biofilms of Pseudoalteromonas piscicida , Pseudoalteromonas tunicata , and Pseudoalteromonas ulvae prevented Pseudoalteromonas S91 from attaching to steel surfaces. P. piscicida killed S91 bacteria in the suspension cultures, whereas P. tunicata and P. ulvae did not however, they did prevent adhesion by nonbactericidal mechanism(s). Seven Pseudoalteromonas species, including P. piscicida and P. tunicata , reduced the number of settling Ulva zoospores to less than 10% of the number settling on control surfaces. The antifouling alpP gene was detected only in P. tunicata strains (with purple and yellow pigmentation), so other compounds/mechanisms must be present in the other Pseudoalteromonas strains with antifouling activity.

Membrane permeabilization underlies the enhancement of extracellular bioactivity in Shewanella oneidensis by a membrane-spanning conjugated oligoelectrolyte

Publisher: Springer Science and Business Media LLC

Date: 05-08-2014

DOI: 10.1007/S00253-014-5973-3

Abstract: A stilbene-based membrane spanning conjugated oligoelectrolyte 4,4'-bis(4'-N,N-bis(6"-(N,N,N-trimethyl ammonium) hexyl) amino)-styryl) stilbene tetraiodide (DSSN+) has been reported to be able to interact with bacterial cells and enhance their bioelectricity generation in bioelectrochemical devices, although the mechanism remains elusive. The goal of this study was to elucidate the impacts of DSSN+ on extracellular bioactivity and the underlying mechanism. Specifically, extracellular ferrihydrite reduction by Shewanella oneidensis was used to evaluate the influence of cell-DSSN+ interaction. Our results show that DSSN+ enhanced ferrihydrite reduction by S. oneidensis in a growth-dependent manner. The incorporation of DSSN+ into S. oneidensis cell membrane increased the extracellular concentration of redox shuttles, i.e., flavins, and extracellular enzyme activities without significantly decreasing cell viability. The findings suggested that membrane permeabilization is the dominant mechanism for the enhancement of extracellular bioactivity in S. oneidensis by DSSN+. We further demonstrated that the interaction between DSSN+ and S. oneidensis cells enhanced biofilm formation and stability without compromising the overall biofilm activity. Taken together, our results suggest that membrane spanning conjugated oligoelectrolytes, of which DSSN+ is one of many possible molecular structures, may be applied to enhance extracellular bioactivity in bacteria toward more efficient biofilm-based biocatalysis.

Free nitrous acid (FNA) inhibition on denitrifying poly-phosphate accumulating organisms (DPAOs)

Publisher: Springer Science and Business Media LLC

Date: 29-07-2010

DOI: 10.1007/S00253-010-2780-3

Abstract: Free nitrous acid (FNA) has been identified to be a ubiquitous inhibitor of a wide range of microorganisms, including bacteria involved in wastewater treatment. The FNA-induced inhibition on the anoxic (nitrite as electron acceptor) metabolism of denitrifying poly-phosphate accumulating organisms (DPAOs) was investigated using sludge from a sequencing batch reactor performing carbon, nitrogen, and phosphorus removal from synthetic wastewater. We found that FNA had a much stronger inhibitory effect on phosphorus (P) uptake and glycogen production than on poly-beta-hydroxyalkanoate degradation and nitrite reduction. The intracellular adenosine triphosphate levels decreased sharply during the FNA incubation, and the decreasing rates were positively correlated with increasing FNA concentrations. The electron transport activity of DPAOs when exposed to FNA displayed a similar trend. Further, at FNA concentrations above 0.044 mg HNO(2)-N/L, the anaerobic metabolism of DPAOs was initiated despite of the presence of nitrite, as evidenced by the release of phosphorus and the consumption of glycogen. DPAO metabolism did not recover completely from FNA inhibition in the subsequent FNA-free environment. The recovery rate depended on the concentration of FNA applied in the previous anoxic period. These results suggest that the inhibitory effects are erse and may be attributable to different mechanisms operating simultaneously.

A new system for estimating the bacterial cheomotactic response applied to a model oligotrophic marine system

Publisher: Elsevier BV

Date: 11-1987

DOI: 10.1016/0167-7012(87)90007-8

Development of novel drugs from marine surface associated microorganisms

Publisher: MDPI AG

Date: 03-2010

DOI: 10.3390/MD8030438

Comparative Genomic Analysis of Malaria Mosquito Vector-Associated Novel Pathogen Elizabethkingia anophelis

Publisher: Oxford University Press (OUP)

Date: 05-2014

DOI: 10.1093/GBE/EVU094

Functional metagenomic analysis of quorum sensing signaling in a nitrifying community

Publisher: Springer Science and Business Media LLC

Date: 28-10-2021

DOI: 10.1038/S41522-021-00250-3

Abstract: Quorum sensing (QS) can function to shape the microbial community interactions, composition, and function. In wastewater treatment systems, acylated homoserine lactone (AHL)-based QS has been correlated with the conversion of floccular biomass into microbial granules, as well as EPS production and the nitrogen removal process. However, the role of QS in such complex communities is still not fully understood, including the QS-proficient taxa and the functional QS genes involved. To address these questions, we performed a metagenomic screen for AHL genes in an activated sludge microbial community from the Ulu Pandan wastewater treatment plant (WWTP) in Singapore followed by functional validation of luxI activity using AHL biosensors and LC–MSMS profiling. We identified 13 luxI and 30 luxR homologs from the activated sludge metagenome. Of those genes, two represented a cognate pair of luxIR genes belonging to a Nitrospira spp. and those genes were demonstrated to be functionally active. The LuxI homolog synthesized AHLs that were consistent with the dominant AHLs in the activated sludge system. Furthermore, the LuxR homolog was shown to bind to and induce expression of the luxI promoter, suggesting this represents an autoinduction feedback system, characteristic of QS circuits. Additionally, a second, active promoter was upstream of a gene encoding a protein with a GGDEF/EAL domain, commonly associated with modulating the intracellular concentration of the secondary messenger, c-di-GMP. Thus, the metagenomic approach used here was demonstrated to effectively identify functional QS genes and suggests that Nitrospira spp. maybe QS is active in the activated sludge community.

Bacterial biofilms: prokaryotic adventures in multicellularity

Publisher: Elsevier BV

Date: 12-2003

DOI: 10.1016/J.MIB.2003.10.014

Abstract: The development of bacterial biofilms includes both the initial social behavior of undifferentiated cells, as well as cell death and differentiation in the mature biofilm, and displays several striking similarities with higher organisms. Recent advances in the field provide new insight into differentiation and cell death events in bacterial biofilm development and propose that biofilms have an unexpected level of multicellularity.

Marine Biofilm Bacteria Evade Eukaryotic Predation by Targeted Chemical Defense

Publisher: Public Library of Science (PLoS)

Date: 23-07-2008

DOI: 10.1371/JOURNAL.PONE.0002744

Role of quorum sensing by Pseudomonas aeruginosa in microbial keratitis and cystic fibrosis

Publisher: Microbiology Society

Date: 08-2008

DOI: 10.1099/MIC.0.2008/019281-0

Abstract: Pseudomonas aeruginosa is a ubiquitous bacterium that causes opportunistic infections in a range of host tissues and organs. Infections by P. aeruginosa are difficult to treat and hence there is interest in the development of effective therapeutics. One of the key mechanisms that P. aeruginosa uses to control the expression of many virulence factors is the N-acylated homoserine lactone (AHL) regulatory system. Hence, there is considerable interest in targeting this regulatory pathway to develop novel therapeutics for infection control. P. aeruginosa is the principal cause of microbial keratitis and of infections in cystic fibrosis (CF) sufferers, and AHL-dependent cell-to-cell signalling has been shown to be important for both infection types. However, keratitis tends to be an acute infection whereas infection of CF patients develops into a chronic, life-long infection. Thus, it is unclear whether AHL-regulated virulence plays the same role during these infections. This review presents a comparison of the role of AHL signalling in P. aeruginosa-mediated microbial keratitis and chronic lung infections of CF patients.

Multivariate Optimization of Polymerase Chain Reaction for Microbial Community Analysis

Publisher: Springer Science and Business Media LLC

Date: 09-2002

DOI: 10.1007/S10126-002-0011-3

Abstract: A multivariate regression, partial least square (PLS) approach was used to optimize a polymerase chain reaction (PCR) method for mixed communities. This approach, in contrast to univariate ones, provided information on the relative influence of the different factors to be optimized, as well as the interactions between factors. Models that predicted the outcome of further optimization were constructed from the initial experiments and verified experimentally. The models constructed were able to predict the outcome of a second set of experiments with high accuracy. PCR- lification of DNA from environmental s les is often the first step in microbial community fingerprinting. Inhibitors and low cell numbers in the s les can cause problems with yield, for which compensation is normally made by increasing the number of cycles in the PCR- lification reaction. Increasing the number of cycles, however, can cause other problems such as heteroduplex formation and increased bias. To avoid these problems the effects of different times of denaturing, annealing, and extension on yield were investigated for 2 different s les, one that consisted of a mixture of 9 laboratory strains, and one that represented the microbial community from the surface of the red alga Delisea pulchra. The multivariate approach showed, in addition to the successful optimization of yield, that the different factors affected the PCR depending on s le type. Annealing time had the largest effect on yield for the mixture of laboratory strains, whereas extension time was most important for the D. pulchra community. We suggest that multivariate optimization is a useful tool for PCR optimization and can be used irrespectively of the particular factors that are being investigated.

Sex, Scavengers, and Chaperones: Transcriptome Secrets of DivergentSymbiodiniumThermal Tolerances

Publisher: Oxford University Press (OUP)

Date: 14-06-2016

DOI: 10.1093/MOLBEV/MSW119

Uncovering alternate charge transfer mechanisms in Escherichia coli chemically functionalized with conjugated oligoelectrolytes

Publisher: Royal Society of Chemistry (RSC)

Date: 2014

DOI: 10.1039/C4CC02784A

Abstract: Conjugated oligoelectrolytes integrated in Escherichia coli have been proposed to induce release of electroactive cytosolic components, which contributes to extracellular electron transfer.

Ecogenomics Reveals Metals and Land-Use Pressures on Microbial Communities in the Waterways of a Megacity

Publisher: American Chemical Society (ACS)

Date: 21-01-2015

DOI: 10.1021/ES504531S

Abstract: Networks of engineered waterways are critical in meeting the growing water demands in megacities. To capture and treat rainwater in an energy-efficient manner, approaches can be developed for such networks that use ecological services from microbial communities. Traditionally, engineered waterways were regarded as homogeneous systems with little responsiveness of ecological communities and ensuing processes. This study provides ecogenomics-derived key information to explain the complexity of urban aquatic ecosystems in well-managed watersheds with densely interspersed land-use patterns. Overall, sedimentary microbial communities had higher richness and evenness compared to the suspended communities in water phase. On the basis of PERMANOVA analysis, variation in structure and functions of microbial communities over space within same land-use type was not significant. In contrast, this difference was significant between different land-use types, which had similar chemical profiles. Of the 36 environmental parameters from spatial analysis, only three metals, namely potassium, copper and aluminum significantly explained between 7% and 11% of the variation in taxa and functions, based on distance-based linear models (DistLM). The ecogenomics approach adopted here allows the identification of key drivers of microbial communities and their functions at watershed-scale. These findings can be used to enhance microbial services, which are critical to develop ecologically friendly waterways in rapidly urbanizing environments.

Antifouling activities expressed by marine surface associated Pseudoalteromonas species

Publisher: Oxford University Press (OUP)

Date: 07-2002

DOI: 10.1111/J.1574-6941.2002.TB00965.X

Abstract: Abstract Members of the marine bacterial genus Pseudoalteromonas have been found in association with living surfaces and are suggested to produce bioactive compounds against settlement of algal spores, invertebrate larvae, bacteria and fungi. To determine the extent by which these antifouling activities and the production of bioactive compounds are distributed amongst the members of the genus Pseudoalteromonas, 10 different Pseudoalteromonas species mostly derived from different host organisms were tested in a broad range of biofouling bioassays. These assays included the settlement of larvae of two ubiquitous invertebrates Hydroides elegans and Balanus hitrite as well as the settlement of spores of the common fouling algae Ulva lactuca and Polysiphonia sp. The growth of bacteria and fungi, which are the initial fouling organisms on marine surfaces, was also assayed in the presence of each of the 10 Pseudoalteromonas species. It was found that most members of this genus produced a variety of bioactive compounds. The broadest range of inhibitory activities was expressed by Pseudoalteromonas tunicata which inhibited all target fouling organisms. Only two species, Pseudoalteromonas haloplanktis and Pseudoalteromonas nigrifaciens, displayed negligible activity in the bioassays. These were also the only two non-pigmented species tested in this study which indicates a correlation between production of bioactive compounds and expression of pigment. Three members, P. tunicata, Pseudoalteromonas citrea and Pseudoalteromonas rubra, were demonstrated to express autoinhibitory activity. It is suggested that most Pseudoalteromonas species are efficient producers of antifouling agents and that the production of inhibitory compounds by surface associated Pseudoalteromonas species may aid the host against colonisation of its surface.

Recruitment of the sea urchin Heliocidaris erythrogramma and the distribution and abundance of inducing bacteria in the field

Publisher: Inter-Research Science Center

Date: 29-09-2008

DOI: 10.3354/AME01239

SiaA and SiaD are essential for inducing autoaggregation as a specific response to detergent stress in Pseudomonas aeruginosa

Publisher: Wiley

Date: 12-2009

DOI: 10.1111/J.1462-2920.2009.02012.X

Abstract: Cell aggregation is a stress response and serves as a survival strategy for Pseudomonas aeruginosa strain PAO1 during growth with the toxic detergent Na-dodecylsulfate (SDS). This process involves the psl operon and is linked to c-di-GMP signalling. The induction of cell aggregation in response to SDS was studied. Transposon and site-directed mutagenesis revealed that the cupA-operon and the co-transcribed genes siaA (PA0172) and siaD (PA0169) were essential for SDS-induced aggregation. While siaA encodes a putative membrane protein with a HAMP and a PP2C-like phosphatase domain, siaD encodes a putative diguanylate cyclase involved in the biosynthesis of c-di-GMP. Complementation studies uncovered that the loss of SDS-induced aggregation in the formerly isolated spontaneous mutant strain N was caused by a non-functional siaA allele. DNA-microarray analysis of SDS-grown cells revealed consistent activation of eight genes, including cupA1, with known or presumptive important functions in cell aggregation in the parent strain compared with non-aggregating siaA and siaD mutants. A siaAD-dependent increase of cupA1 mRNA levels in SDS-grown cells was also shown by Northern blots. These results clearly demonstrate that SiaAD are essential for inducing cell aggregation as a specific response to SDS and suggest that they are responsible for perceiving and transducing SDS-related stress.

Cell Death in Pseudomonas aeruginosa Biofilm Development

Publisher: American Society for Microbiology

Date: 08-2003

DOI: 10.1128/JB.185.15.4585-4592.2003

Abstract: Bacteria growing in biofilms often develop multicellular, three-dimensional structures known as microcolonies. Complex differentiation within biofilms of Pseudomonas aeruginosa occurs, leading to the creation of voids inside microcolonies and to the dispersal of cells from within these voids. However, key developmental processes regulating these events are poorly understood. A normal component of multicellular development is cell death. Here we report that a repeatable pattern of cell death and lysis occurs in biofilms of P. aeruginosa during the normal course of development. Cell death occurred with temporal and spatial organization within biofilms, inside microcolonies, when the biofilms were allowed to develop in continuous-culture flow cells. A subpopulation of viable cells was always observed in these regions. During the onset of biofilm killing and during biofilm development thereafter, a bacteriophage capable of superinfecting and lysing the P. aeruginosa parent strain was detected in the fluid effluent from the biofilm. The bacteriophage implicated in biofilm killing was closely related to the filamentous phage Pf1 and existed as a prophage within the genome of P. aeruginosa . We propose that prophage-mediated cell death is an important mechanism of differentiation inside microcolonies that facilitates dispersal of a subpopulation of surviving cells.

Influence of petroleum contamination and biostimulation treatment on the diversity of Pseudomonas spp. in soil microcosms as evaluated by 16S rRNA based-PCR and DGGE

Publisher: Oxford University Press (OUP)

Date: 02-2004

DOI: 10.1111/J.1472-765X.2003.01455.X

Abstract: The aim of this study was to apply a group specific PCR system followed by denaturing gradient gel electrophoresis (DGGE) analysis to evaluate the effect of oil contamination and the biostimulation process on the ersity of Pseudomonas populations in soil ecosystems. Direct DNA extraction from biostimulated- and oil-contaminated soil s les was performed. Primers specific for the genus Pseudomonas spp. were used to lify 16S rRNA genes and then a semi-nested PCR reaction was applied to obtain smaller fragments for comparing the PCR products by DGGE. Whether in bulk, oil-contaminated or biostimulated soils, the DGGE profiles revealed little change in Pseudomonas community throughout the 270 days of experiment. The presence of a few additional bands observed only in treated s les indicated that a bacterial shift occurred with the addition of nutrients and with oil contamination. The combination of semi-nested PCR and DGGE was found to be a rapid and sensitive technique to study the ersity within the genus Pseudomonas and may be suitable for further studies concerning the role of this bacterial group in large-scale oil-contaminated areas.

Bacterial community assembly based on functional genes rather than species

Publisher: Proceedings of the National Academy of Sciences

Date: 08-08-2011

DOI: 10.1073/PNAS.1101591108

Abstract: The principles underlying the assembly and structure of complex microbial communities are an issue of long-standing concern to the field of microbial ecology. We previously analyzed the community membership of bacterial communities associated with the green macroalga Ulva australis , and proposed a competitive lottery model for colonization of the algal surface in an attempt to explain the surprising lack of similarity in species composition across different algal s les. Here we extend the previous study by investigating the link between community structure and function in these communities, using metagenomic sequence analysis. Despite the high phylogenetic variability in microbial species composition on different U. australis (only 15% similarity between s les), similarity in functional composition was high (70%), and a core of functional genes present across all algal-associated communities was identified that were consistent with the ecology of surface- and host-associated bacteria. These functions were distributed widely across a variety of taxa or phylogenetic groups. This observation of similarity in habitat (niche) use with respect to functional genes, but not species, together with the relative ease with which bacteria share genetic material, suggests that the key level at which to address the assembly and structure of bacterial communities may not be “species” (by means of rRNA taxonomy), but rather the more functional level of genes.

Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1T)

Publisher: Springer Science and Business Media LLC

Date: 22-12-2011

DOI: 10.4056/SIGS.2215005

‘Big things in small packages: the genetics of filamentous phage and effects on fitness of their host’

Publisher: Oxford University Press (OUP)

Date: 10-02-2015

DOI: 10.1093/FEMSRE/FUU007

Abstract: This review synthesizes recent and past observations on filamentous phages and describes how these phages contribute to host phentoypes. For ex le, the CTXφ phage of Vibrio cholerae encodes the cholera toxin genes, responsible for causing the epidemic disease, cholera. The CTXφ phage can transduce non-toxigenic strains, converting them into toxigenic strains, contributing to the emergence of new pathogenic strains. Other effects of filamentous phage include horizontal gene transfer, biofilm development, motility, metal resistance and the formation of host morphotypic variants, important for the biofilm stress resistance. These phages infect a wide range of Gram-negative bacteria, including deep-sea, pressure-adapted bacteria. Many filamentous phages integrate into the host genome as prophage. In some cases, filamentous phages encode their own integrase genes to facilitate this process, while others rely on host-encoded genes. These differences are mediated by different sets of 'core' and 'accessory' genes, with the latter group accounting for some of the mechanisms that alter the host behaviours in unique ways. It is increasingly clear that despite their relatively small genomes, these phages exert signficant influence on their hosts and ultimately alter the fitness and other behaviours of their hosts.

Evidence for a Role of rpoE in Stressed and Unstressed Cells of Marine Vibrio angustum Strain S14

Publisher: American Society for Microbiology

Date: 15-12-2000

DOI: 10.1128/JB.182.24.6964-6974.2000

Abstract: We report the cloning, sequencing, and characterization of the rpoE homolog in Vibrio angustum S14. The rpoE gene encodes a protein with a predicted molecular mass of 19.4 kDa and has been demonstrated to be present as a single-copy gene by Southern blot analysis. The deduced amino acid sequence of RpoE is most similar to that of the RpoE homolog of Sphingomonas aromaticivorans , ς 24 , displaying sequence similarity and identity of 63 and 43%, respectively. Northern blot analysis demonstrated the induction of rpoE 6, 12, and 40 min after a temperature shift to 40°C. An rpoE mutant was constructed by gene disruption. There was no difference in viability during logarithmic growth, stationary phase, or carbon starvation between the wild type and the rpoE mutant strain. In contrast, survival of the mutant was impaired following heat shock during exponential growth, as well as after oxidative stress at 24 h of carbon starvation. The mutant exhibited microcolony formation during optimal growth temperatures (22 to 30°C), and cell area measurements revealed an increase in cell volume of the mutant during growth at 30°C, compared to the wild-type strain. Moreover, outer membrane and periplasmic space protein analysis demonstrated many alterations in the protein profiles for the mutant during growth and carbon starvation, as well as following oxidative stress, in comparison with the wild-type strain. It is thereby concluded that RpoE has an extracytoplasmic function and mediates a range of specific responses in stressed as well as unstressed cells of V. angustum S14.

Relative Contributions of Vibrio Polysaccharide and Quorum Sensing to the Resistance of Vibrio cholerae to Predation by Heterotrophic Protists

Publisher: Public Library of Science (PLoS)

Date: 18-02-2013

DOI: 10.1371/JOURNAL.PONE.0056338

Microbial landscapes: new paths to biofilm research

Publisher: Springer Science and Business Media LLC

Date: 2007

DOI: 10.1038/NRMICRO1556

Abstract: It is the best of times for biofilm research. Systems biology approaches are providing new insights into the genetic regulation of microbial functions, and sophisticated modelling techniques are enabling the prediction of microbial community structures. Yet it is also clear that there is a need for ecological theory to contribute to our understanding of biofilms. Here, we suggest a concept for biofilm research that is spatially explicit and solidly rooted in ecological theory, which might serve as a universal approach to the study of the numerous facets of biofilms.

Use of solid-phase extraction to enable enhanced detection of acyl homoserine lactones (AHLs) in environmental samples

Publisher: Springer Science and Business Media LLC

Date: 05-08-2005

DOI: 10.1007/S00216-005-3387-X

Abstract: A challenge for understanding the role of bacterial cell-cell signalling in the environment is the detection of those signals, which are often present in low (nmol L(-1)) concentrations. We describe here a simple purification method, solid-phase extraction (SPE), for increasing the sensitivity of detection for one such group of signals, acyl homoserine lactones (AHLs), in environmental s les. Spiking of dried marine sponge tissue (Stylinos sp.) with AHLs resulted in detection down to 0.01 ppm for 3-oxo-hexanoyl homoserine lactone (3-oxo C6-HSL) and 1 ppm for hexanoyl homoserine lactone (C6-HSL). Compared with liquid extraction methods use of SPE resulted in twofold and tenfold improvements in sensitivity, respectively.

Biofilm formation and sloughing in Serratia marcescens is controlled by quorum sensing and nutrient conditions

Publisher: American Society for Microbiology

Date: 15-05-2005

DOI: 10.1128/JB.187.10.3477-3485.2005

Abstract: We describe here a role for quorum sensing in the detachment, or sloughing, of Serratia marcescens filamentous biofilms, and we show that nutrient conditions affect the biofilm morphotype. Under reduced carbon or nitrogen conditions, S. marcescens formed a classical biofilm consisting of microcolonies. The filamentous biofilm could be converted to a microcolony-type biofilm by switching the medium after establishment of the biofilm. Similarly, when initially grown as a microcolony biofilm, S. marcescens could be converted back to a filamentous biofilm by increasing the nutrient composition. Under high-nutrient conditions, an N -acyl homoserine lactone quorum-sensing mutant formed biofilms that were indistinguishable from the wild-type biofilms. Similarly, other quorum-sensing-dependent behaviors, such as swarming motility, could be rendered quorum sensing independent by manipulating the growth medium. Quorum sensing was also found to be involved in the sloughing of the filamentous biofilm. The biofilm formed by the bacterium consistently sloughed from the substratum after approximately 75 to 80 h of development. The quorum-sensing mutant, when supplemented with exogenous signal, formed a wild-type filamentous biofilm and sloughed at the same time as the wild type, and this was independent of surfactant production. When we removed the signal from the quorum-sensing mutant prior to the time of sloughing, the biofilm did not undergo significant detachment. Together, the data suggest that biofilm formation by S. marcescens is a dynamic process that is controlled by both nutrient cues and the quorum-sensing system.

Attenuation of Pseudomonas aeruginosa virulence by quorum sensing inhibitors

Publisher: Wiley

Date: 08-2003

DOI: 10.1093/EMBOJ/CDG366

Microbial Investigations of Surface Microlayers, Water Column, Ice and Sediment in the Arctic Ocean

Publisher: Inter-Research Science Center

Date: 1982

DOI: 10.3354/MEPS009101

In Situ Mapping of the Mechanical Properties of Biofilms by Particle-tracking Microrheology.

Publisher: MyJove Corporation

Date: 04-12-2015

DOI: 10.3791/53093

Modeling the effect of acylated homoserine lactone antagonists in Pseudomonas aeruginosa

Publisher: Elsevier BV

Date: 05-2005

DOI: 10.1016/J.BIOSYSTEMS.2004.11.008

Abstract: Pseudomonas aeruginosa is a gram-negative bacterium that causes serious illnesses, particularly in immunocompromised in iduals, often with a fatal outcome. The finding that the acylated homoserine lactone quorum sensing (QS) system controls the production of virulence factors in P. aeruginosa makes this system a possible target for antimicrobial therapy. It has been suggested that an N-(3-oxododecanoyl)-homoserine lactone (3O-C12-HSL) antagonist, a QS blocker (QSB), would interfere efficiently with the quorum sensing system in P. aeruginosa and thus reduce the virulence of this pathogen. In this work, a mathematical model of the QS system in P. aeruginosa has been developed. The model was used to virtually add 3O-C12-HSL antagonists that differed in their affinity for the receptor protein and for their ability to mediate degradation of the receptor. The model suggests that very small differences in these parameters for different 3O-C12-HSL antagonists can greatly affect the success of QSB based inhibition of the QS system in P. aeruginosa. Most importantly, it is proposed that the ability of the 3O-C12-HSL antagonist to mediate degradation of LasR is the core parameter for successful QSB based inhibition of the QS system in P. aeruginosa. Finally, this study demonstrates that QSBs can shift the system to a low steady state, corresponding to an uninduced state and thus, suggests that the use of 3O-C12-HSL antagonists may constitute a promising therapeutic approach against P. aeruginosa involved infections.

Molecular investigation of the distribution, abundance and diversity of the genus Pseudoalteromonas in marine samples

Publisher: Oxford University Press (OUP)

Date: 08-2007

DOI: 10.1111/J.1574-6941.2007.00339.X

Abstract: The genus Pseudoalteromonas has attracted interest because it has frequently been found in association with eukaryotic hosts, and because many Pseudoalteromonas species produce biologically active compounds. One distinct group of Pseudoalteromonas species is the antifouling subgroup containing Pseudoalteromonas tunicata and Ps. ulvae, which both produce extracellular compounds that inhibit growth and colonization by different marine organisms. PCR primers targeting the 16S rRNA gene of the genus Pseudoalteromonas and the antifouling subgroup were developed and applied in this study. Real-time quantitative PCR (qPCR) was applied to determine the relative bacterial abundance of the genus and the antifouling subgroup, and denaturing gradient gel electrophoresis (DGGE) was applied to study the ersity of the genus in 11 different types of marine s les from Danish coastal waters. The detection of Ps. tunicata that contain the antifouling subgroup was achieved through specific PCR lification of the antibacterial protein gene (alpP). The Pseudoalteromonas species accounted for 1.6% of the total bacterial abundance across all s les. The Pseudoalteromonas ersity on the three unfouled marine organisms Ciona intestinalis, Ulva lactuca and Ulvaria fusca was found to be low, and Ps. tunicata was only detected on these three hosts, which all contain accessible cellulose polymers in their cell walls.

The biofilm matrix scaffold of Pseudomonas aeruginosa contains G-quadruplex extracellular DNA structures

Publisher: Springer Science and Business Media LLC

Date: 19-03-2021

DOI: 10.1038/S41522-021-00197-5

Abstract: Extracellular DNA, or eDNA, is recognised as a critical biofilm component however, it is not understood how it forms networked matrix structures. Here, we isolate eDNA from static-culture Pseudomonas aeruginosa biofilms using ionic liquids to preserve its biophysical signatures of fluid viscoelasticity and the temperature dependency of DNA transitions. We describe a loss of eDNA network structure as resulting from a change in nucleic acid conformation, and propose that its ability to form viscoelastic structures is key to its role in building biofilm matrices. Solid-state analysis of isolated eDNA, as a proxy for eDNA structure in biofilms, reveals non-canonical Hoogsteen base pairs, triads or tetrads involving thymine or uracil, and guanine, suggesting that the eDNA forms G-quadruplex structures. These are less abundant in chromosomal DNA and disappear when eDNA undergoes conformation transition. We verify the occurrence of G-quadruplex structures in the extracellular matrix of intact static and flow-cell biofilms of P. aeruginosa , as displayed by the matrix to G-quadruplex-specific antibody binding, and validate the loss of G-quadruplex structures in vivo to occur coincident with the disappearance of eDNA fibres. Given their stability, understanding how extracellular G-quadruplex structures form will elucidate how P. aeruginosa eDNA builds viscoelastic networks, which are a foundational biofilm property.

AHL-driven quorum-sensing circuits: Their frequency and function among the Proteobacteria

Publisher: Springer Science and Business Media LLC

Date: 14-02-2008

DOI: 10.1038/ISMEJ.2008.13

Bis-(3′-5′)-Cyclic Dimeric GMP Regulates Antimicrobial Peptide Resistance in Pseudomonas aeruginosa

Publisher: American Society for Microbiology

Date: 05-2013

DOI: 10.1128/AAC.02499-12

Abstract: Bis-(3′-5′)-cyclic dimeric GMP (c-di-GMP) is an intracellular second messenger that controls the lifestyles of many bacteria. A high intracellular level of c-di-GMP induces a biofilm lifestyle, whereas a low intracellular level of c-di-GMP stimulates dispersal of biofilms and promotes a planktonic lifestyle. Here, we used the expression of different reporters to show that planktonic cells, biofilm cells, and cells dispersed from biofilms (DCells) had distinct intracellular c-di-GMP levels. Proteomics analysis showed that the low intracellular c-di-GMP level of DCells induced the expression of proteins required for the virulence and development of antimicrobial peptide resistance in Pseudomonas aeruginosa . In accordance with this, P. aeruginosa cells with low c-di-GMP levels were found to be more resistant to colistin than P. aeruginosa cells with high c-di-GMP levels. This finding contradicts the current dogma stating that dispersed cells are inevitably more susceptible to antibiotics than their sessile counterparts.

Fimbriae mediated nonspecific adhesion of Salmonella typhimurium to mineral particles

Publisher: Springer Science and Business Media LLC

Date: 10-1985

DOI: 10.1007/BF00414759

Abstract: In eukaryotic cells, ribosomes are pre-assembled in the nucleus and exported to the cytoplasm where they undergo final maturation. This involves the release of trans-acting shuttling factors, transport factors, incorporation of the remaining ribosomal proteins, and final rRNA processing steps. Recent work, particularly on the large (60S) ribosomal subunit, has confirmed that the 60S subunit is exported from the nucleus in a functionally inactive state. Its arrival in the cytoplasm triggers events that render it translationally competent. Here we focus on these cytoplasmic maturation events and speculate why eukaryotic cells have evolved such an elaborate maturation pathway.

Enhanced benzaldehyde tolerance in Zymomonas mobilis biofilms and the potential of biofilm applications in fine-chemical production.

Publisher: American Society for Microbiology

Date: 02-2006

DOI: 10.1128/AEM.72.2.1639-1644.2006

Abstract: Biotransformation plays an increasingly important role in the industrial production of fine chemicals due to its high product specificity and low energy requirement. One challenge in biotransformation is the toxicity of substrates and/or products to biocatalytic microorganisms and enzymes. Biofilms are known for their enhanced tolerance of hostile environments compared to planktonic free-living cells. Zymomonas mobilis was used in this study as a model organism to examine the potential of surface-associated biofilms for biotransformation of chemicals into value-added products. Z. mobilis formed a biofilm with a complex three-dimensional architecture comprised of microcolonies with an average thickness of 20 μm, interspersed with water channels. Microscopic analysis and metabolic activity studies revealed that Z. mobilis biofilm cells were more tolerant to the toxic substrate benzaldehyde than planktonic cells were. When exposed to 50 mM benzaldehyde for 1 h, biofilm cells exhibited an average of 45% residual metabolic activity, while planktonic cells were completely inactivated. Three hours of exposure to 30 mM benzaldehyde resulted in sixfold-higher residual metabolic activity in biofilm cells than in planktonic cells. Cells inactivated by benzaldehyde were evenly distributed throughout the biofilm, indicating that the resistance mechanism was different from mass transfer limitation. We also found that enhanced tolerance to benzaldehyde was not due to the conversion of benzaldehyde into less toxic compounds. In the presence of glucose, Z. mobilis biofilms in continuous cultures transformed 10 mM benzaldehyde into benzyl alcohol at a steady rate of 8.11 g (g dry weight) −1 day −1 with a 90% molar yield over a 45-h production period.

The future of management programmes for heart failure

Publisher: Elsevier BV

Date: 09-2008

DOI: 10.1016/S0140-6736(08)61317-3

Microbial colonization and competition on the marine alga ulva australis

Publisher: American Society for Microbiology

Date: 08-2006

DOI: 10.1128/AEM.00449-06

Abstract: Pseudalteromonas tunicata and Roseobacter gallaeciensis are biofilm-forming marine bacteria that are often found in association with the surface of the green alga Ulva australis . They are thought to benefit the plant host by producing inhibitory compounds that are active against common fouling organisms. We investigated factors that influence the ability of P. tunicata and R. gallaeciensis to attach to and colonize the plant surface and also the competitive interactions that occur between these organisms and other isolates from U. australis during biofilm formation on the plant surface. A surprisingly high number of P. tunicata cells, at least 10 8 cells ml −1 , were required for colonization and establishment of a population of cells that persists on axenic surfaces of U. australis . Factors that enhanced colonization of P. tunicata included inoculation in the dark and pregrowth of inocula in medium containing cellobiose as the sole carbon source (cellulose is a major surface polymer of U. australis ). It was also found that P. tunicata requires the presence of a mixed microbial community to colonize effectively. In contrast, R. gallaeciensis effectively colonized the plant surface under all conditions tested. Studies of competitive interactions on the plant surface revealed that P. tunicata was numerically dominant compared with all other bacterial isolates tested (except R. gallaeciensis ), and this dominance was linked to production of the antibacterial protein AlpP. Generally, P. tunicata was able to coexist with competing strains, and each strain existed as microcolonies in spatially segregated regions of the plant. R. gallaeciensis was numerically dominant compared with all strains tested and was able to invade and disperse preestablished biofilms. This study highlighted the fact that microbial colonization of U. australis surfaces is a dynamic process and demonstrated the differences in colonization strategies exhibited by the epiphytic bacteria P. tunicata and R. gallaeciensis .

Genomes and Virulence Factors of Novel Bacterial Pathogens Causing Bleaching Disease in the Marine Red Alga Delisea pulchra

Publisher: Public Library of Science (PLoS)

Date: 05-12-2011

DOI: 10.1371/JOURNAL.PONE.0027387

Reinvestigation of the sulfuric acid-catalysed cyclisation of brominated 2-alkyllevulinic acids to 3-alkyl-5-methylene-2(5H)-furanones

Publisher: Elsevier BV

Date: 11-1997

DOI: 10.1016/S0040-4020(97)10034-5

Assessing the effectiveness of functional genetic screens for the identification of bioactive metabolites

Publisher: MDPI AG

Date: 27-12-2013

DOI: 10.3390/MD11010040

Microcolonies, quorum sensing and cytotoxicity determine the survival of Pseudomonas aeruginosa biofilms exposed to protozoan grazing.

Publisher: Wiley

Date: 29-01-2004

DOI: 10.1111/J.1462-2920.2004.00556.X

Abstract: This study was based on the hypothesis that biofilms of the opportunistic pathogen Pseudomonas aeruginosa are successfully adapted to situations of protozoan grazing. We tested P. aeruginosa wild type and strains that were genetically altered, in structural and regulatory features of biofilm development, in response to the common surface-feeding flagellate Rhynchomonas nasuta. Early biofilms of the wild type showed the formation of grazing resistant microcolonies in the presence of the flagellate, whereas biofilms without the predator were undifferentiated. Grazing on biofilms of quorum sensing mutants (lasR and rhlR/lasR) also resulted in the formation of microcolonies, however, in lower numbers and size compared to the wild type. Considerably fewer microcolonies than the wild type were formed by mutant cells lacking type IV pili, whereas no microcolonies were formed by flagella-deficient cells. The alginate-overproducing strain PDO300 developed larger microcolonies in response to grazing. These observations suggest a role of quorum sensing in early biofilms and involvement of flagella, type IV pili, and alginate in microcolony formation in the presence of grazing. More mature biofilms of the wild type exhibited acute toxicity to the flagellate R. nasuta. Rapid growth of the flagellate on rhlR/lasR mutant biofilms indicated a key role of quorum sensing in the upregulation of lethal factors and in grazing protection of late biofilms. Both the formation of microcolonies and the production of toxins are effective mechanisms that may allow P. aeruginosa biofilms to resist protozoan grazing and to persist in the environment.

Three faces of biofilms: a microbial lifestyle, a nascent multicellular organism, and an incubator for diversity

Publisher: Springer Science and Business Media LLC

Date: 10-11-2021

DOI: 10.1038/S41522-021-00251-2

Abstract: Biofilms are organised heterogeneous assemblages of microbial cells that are encased within a self-produced matrix. Current estimates suggest that up to 80% of bacterial and archaeal cells reside in biofilms. Since biofilms are the main mode of microbial life, understanding their biology and functions is critical, especially as controlling biofilm growth is essential in industrial, infrastructure and medical contexts. Here we discuss biofilms both as collections of in idual cells, and as multicellular biological in iduals, and introduce the concept of biofilms as unique incubators of ersity for the microbial world.

Biofilms: an emergent form of bacterial life

Publisher: Springer Science and Business Media LLC

Date: 11-08-2016

DOI: 10.1038/NRMICRO.2016.94

Abstract: Bacterial biofilms are formed by communities that are embedded in a self-produced matrix of extracellular polymeric substances (EPS). Importantly, bacteria in biofilms exhibit a set of 'emergent properties' that differ substantially from free-living bacterial cells. In this Review, we consider the fundamental role of the biofilm matrix in establishing the emergent properties of biofilms, describing how the characteristic features of biofilms - such as social cooperation, resource capture and enhanced survival of exposure to antimicrobials - all rely on the structural and functional properties of the matrix. Finally, we highlight the value of an ecological perspective in the study of the emergent properties of biofilms, which enables an appreciation of the ecological success of biofilms as habitat formers and, more generally, as a bacterial lifestyle.

rpoB -Based Microbial Community Analysis Avoids Limitations Inherent in 16S rRNA Gene Intraspecies Heterogeneity

Publisher: American Society for Microbiology

Date: 08-2000

DOI: 10.1128/AEM.66.8.3376-3380.2000

Abstract: Contemporary microbial community analysis frequently involves PCR- lified sequences of the 16S rRNA gene (rDNA). However, this technology carries the inherent problem of heterogeneity between copies of the 16S rDNA in many species. As an alternative to 16S rDNA sequences in community analysis, we employed the gene for the RNA polymerase beta subunit ( rpoB ), which appears to exist in one copy only in bacteria. In the present study, the frequency of 16S rDNA heterogeneity in bacteria isolated from the marine environment was assessed using bacterial isolates from the red alga Delisea pulchra and from the surface of a marine rock. Ten strains commonly used in our laboratory were also assessed for the degree of heterogeneity between the copies of 16S rDNA and were used to illustrate the effect of this heterogeneity on microbial community pattern analysis. The rock isolates and the laboratory strains were also used to confirm nonheterogeneity of rpoB , as well as to investigate the versatility of the primers. In addition, a comparison between 16S rDNA and rpoB PCR-DGGE (denaturing gradient gel electrophoresis)-based community analyses was performed using a DNA mixture of nine isolates from D. pulchra . Eight out of 14 isolates from D. pulchra , all rock isolates, and 6 of 10 laboratory strains displayed multiple bands for 16S rDNA when analyzed by DGGE. There was no indication of heterogeneity for either the rock isolates or the laboratory strains when rpoB was used for PCR-DGGE analysis. Microbial community pattern analysis using 16S rDNA PCR-DGGE showed an overestimation of the number of laboratory strains in the s le, while some strains were not represented. Therefore, the 16S rDNA PCR-DGGE-based community analysis was proven to be severely limited by 16S rDNA heterogeneity. The mixture of isolates from D. pulchra proved to be more accurately described using rpoB , compared to the 16S rDNA-based PCR-DGGE.

Enhanced Biofilm Formation and Increased Resistance to Antimicrobial Agents and Bacterial Invasion Are Caused by Synergistic Interactions in Multispecies Biofilms

Publisher: American Society for Microbiology

Date: 06-2006

DOI: 10.1128/AEM.03022-05

Abstract: Most biofilms in their natural environments are likely to consist of consortia of species that influence each other in synergistic and antagonistic manners. However, few reports specifically address interactions within multispecies biofilms. In this study, 17 epiphytic bacterial strains, isolated from the surface of the marine alga Ulva australis , were screened for synergistic interactions within biofilms when present together in different combinations. Four isolates, Microbacterium phyllosphaerae , Shewanella japonica , Dokdonia donghaensis , and Acinetobacter lwoffii , were found to interact synergistically in biofilms formed in 96-well microtiter plates: biofilm biomass was observed to increase by % in biofilms formed by the four strains compared to biofilms composed of single strains. When exposed to the antibacterial agent hydrogen peroxide or tetracycline, the relative activity (exposed versus nonexposed biofilms) of the four-species biofilm was markedly higher than that in any of the single-species biofilms. Moreover, in biofilms established on glass surfaces in flow cells and subjected to invasion by the antibacterial protein-producing Pseudoalteromonas tunicata , the four-species biofilms resisted invasion to a greater extent than did the biofilms formed by the single species. Replacement of each strain by its cell-free culture supernatant suggested that synergy was dependent both on species-specific physical interactions between cells and on extracellular secreted factors or less specific interactions. In summary, our data strongly indicate that synergistic effects promote biofilm biomass and resistance of the biofilm to antimicrobial agents and bacterial invasion in multispecies biofilms.

Vibrio cholerae Strains Possess Multiple Strategies for Abiotic and Biotic Surface Colonization

Publisher: American Society for Microbiology

Date: 15-07-2007

DOI: 10.1128/JB.01867-06

Abstract: Despite its notoriety as a human pathogen, Vibrio cholerae is an aquatic microbe suited to live in freshwater, estuarine, and marine environments where biofilm formation may provide a selective advantage. Here we report characterization of biofilms formed on abiotic and biotic surfaces by two non-O1/O139 V. cholerae strains, TP and SIO, and by the O1 V. cholerae strain N16961 in addition to the isolation of 44 transposon mutants of SIO and TP impaired in biofilm formation. During the course of characterizing the mutants, 30 loci which have not previously been associated with V. cholerae biofilms were identified. These loci code for proteins which perform a wide variety of functions, including amino acid metabolism, ion transport, and gene regulation. Also, when the plankton colonization abilities of strains N16961, SIO, and TP were examined, each strain showed increased colonization of dead plankton compared with colonization of live plankton (the dinoflagellate Lingulodinium polyedrum and the copepod Tigriopus californicus ). Surprisingly, most of the biofilm mutants were not impaired in plankton colonization. Only mutants impaired in motility or chemotaxis showed reduced colonization. These results indicate the presence of both conserved and variable genes which influence the surface colonization properties of different V. cholerae subspecies.

Biofilm development and enhanced stress resistance of a model, mixed-species community biofilm.

Publisher: Springer Science and Business Media LLC

Date: 24-10-2014

DOI: 10.1038/ISMEJ.2013.194

Surfactant enhanced lipase containing films characterized by confocal laser scanning microscopy

Publisher: Elsevier BV

Date: 02-2011

DOI: 10.1016/J.COLSURFB.2010.08.042

Abstract: Confocal laser scanning microscopy (CLSM) in combination with a fluorescently labeling enzyme dye, LavaPurple™, was demonstrated as a technique for the visualization of Thermomyces (Humicola) lanuginosa lipase (LIP(HLL)) and Candida antarctica lipase A (LIP(CA)) within a transparent latex coating. Addition of Teric Surfactants (C(16) non-ionic Teric 475, 1.8% (w/w) or C(10) non-ionic Teric 460, 2.0% (w/w)) significantly increased the accumulation of both LIP(HLL) and LIP(CA) to the surface of a latex coating. An α-naphthyl acetate substrate assay was used to quantify the accumulated lipase. The results derived from the acetate assay correlated with the enzyme accumulation (at the surface) observed in the CLSM images of the latex coating. This correlation demonstrated that the increased enzyme accumulation within the top 2μm of the latex film was responsible for the increase in surface enzymatic activity. The combination of CLSM imagery and quantifiable image analysis provided a valuable tool for the optimization of surfactant concentrations for maximizing the activity of an enzyme (and potentially other additives) within a latex coating.

A CARD–FISH protocol for the identification and enumeration of epiphytic bacteria on marine algae

Publisher: Elsevier BV

Date: 06-2006

DOI: 10.1016/J.MIMET.2005.09.006

Abstract: A CARD-FISH protocol was developed and applied to analyse surface-associated bacteria on the marine algae Ulva lactuca, Delisea pulchra, Corallina officinalis, Amphiroa anceps, Porphyra sp. and Sargassum linearifolium. The combination of Alexa(546)-labelled tyramide as the reporter molecule with SYBR Green II counterstain allowed for superior detection of the hybridised probe fluorescence against plant tissue from which pigment autofluorescence has been reduced.

Employing a Flexible and Low‐Cost Polypyrrole Nanotube Membrane as an Anode to Enhance Current Generation in Microbial Fuel Cells

Publisher: Wiley

Date: 04-2015

DOI: 10.1002/SMLL.201403328

Abstract: The flexible and low-cost polypyrrole nanotube membrane is demonstrated as a promising anode in microbial fuel cells, which significantly enhances the extracellular electron transfer between Shewanella oneidensis MR-1 and the electrode, owing to the large active surface area and high electrical conductivity.

Pseudomonas aeruginosa uses type III secretion system to kill biofilm-associated amoebae

Publisher: Springer Science and Business Media LLC

Date: 15-05-2008

DOI: 10.1038/ISMEJ.2008.47

Isolation and Structure Elucidation of a Novel Yellow Pigment from the Marine Bacterium Pseudoalteromonas tunicata

Publisher: MDPI AG

Date: 31-10-2005

DOI: 10.3390/10101286

Luminescence control in the marine bacterium Vibrio fischeri : an analysis of the dynamics of lux regulation 1 1Edited by D. E. Draper

Publisher: Elsevier BV

Date: 03-2000

DOI: 10.1006/JMBI.1999.3484

Aroyleneimidazophenazine: A Sensitive Probe for Detecting CN⁻Anion and its Solvatochromism Effect

Publisher: Wiley

Date: 24-10-2014

DOI: 10.1002/JHET.2214

Community Structure and Functional Gene Profile of Bacteria on Healthy and Diseased Thalli of the Red Seaweed Delisea pulchra

Publisher: Public Library of Science (PLoS)

Date: 03-12-2012

DOI: 10.1371/JOURNAL.PONE.0050854

All together now: experimental multispecies biofilm model systems.

Publisher: Wiley

Date: 2017

DOI: 10.1111/1462-2920.13594

Abstract: Studies of microorganisms have traditionally focused on single species populations, which have greatly facilitated our understanding of the genetics and physiology that underpin microbial growth, adaptation and biofilm development. However, given that most microorganisms exist as multispecies consortia, the field is increasingly exploring microbial communities using a range of technologies traditionally limited to populations, including meta-omics based approaches and high resolution imaging. The experimental communities currently being explored range from relatively low ersity, for ex le, two to four species, to significantly more complex systems, comprised of several hundred species. Results from both defined and undefined communities have revealed a number of emergent properties, including improved stress tolerance, increased biomass production, community level signalling and metabolic cooperation. Based on results published to date, we submit that community-based studies are timely and increasingly reveal new properties associated with multispecies consortia that could not be predicted by studies of the in idual component species. Here, we review a range of defined and undefined experimental systems used to study microbial community interactions.

Dispersed cells represent a distinct stage in the transition from bacterial biofilm to planktonic lifestyles

Publisher: Springer Science and Business Media LLC

Date: 21-07-2014

DOI: 10.1038/NCOMMS5462

Abstract: Bacteria assume distinct lifestyles during the planktonic and biofilm modes of growth. Increased levels of the intracellular messenger c-di-GMP determine the transition from planktonic to biofilm growth, while a reduction causes biofilm dispersal. It is generally assumed that cells dispersed from biofilms immediately go into the planktonic growth phase. Here we use single-nucleotide resolution transcriptomic analysis to show that the physiology of dispersed cells from Pseudomonas aeruginosa biofilms is highly different from those of planktonic and biofilm cells. In dispersed cells, the expression of the small regulatory RNAs RsmY and RsmZ is downregulated, whereas secretion genes are induced. Dispersed cells are highly virulent against macrophages and Caenorhabditis elegans compared with planktonic cells. In addition, they are highly sensitive towards iron stress, and the combination of a biofilm-dispersing agent, an iron chelator and tobramycin efficiently reduces the survival of the dispersed cells.

Increased Microbial Butanol Tolerance by Exogenous Membrane Insertion Molecules

Publisher: Wiley

Date: 25-09-2015

DOI: 10.1002/CSSC.201500194

Abstract: Butanol is an ideal biofuel, although poor titers lead to high recovery costs by distillation. Fluidization of microbial membranes by butanol is one of the major factors limiting titers in butanol-producing bioprocesses. Starting with the hypothesis that certain membrane insertion molecules would stabilize the lipid bilayer in the presence of butanol, we applied a combination of in vivo and in vitro techniques within an in silico framework to describe a new approach to achieve solvent tolerance in bacteria. Single-molecule tracking of a model supported bilayer showed that COE1-5C, a five-ringed oligo-polyphenylenevinylene conjugated oligoelectrolyte (COE), reduced the diffusion rate of phospholipids in a microbially derived lipid bilayer to a greater extent than three-ringed and four-ringed COEs. Furthermore, COE1-5C treatment increased the specific growth rate of E. coli K12 relative to a control at inhibitory butanol concentrations. Consequently, to confer butanol tolerance to microbes by exogenous means is complementary to genetic modification of strains in industrial bioprocesses, extends the physiological range of microbes to match favorable bioprocess conditions, and is amenable with complex and undefined microbial consortia for biobutanol production. Molecular dynamics simulations indicated that the π-conjugated aromatic backbone of COE1-5C likely acts as a hydrophobic tether for glycerophospholipid acyl chains by enhancing bilayer integrity in the presence of high butanol concentrations, which thereby counters membrane fluidization. COE1-5C-mitigated E. coli K12 membrane depolarization by butanol is consistent with the hypothesis that improved growth rates in the presence of butanol are a consequence of improved bilayer stability.

Inhibition of fouling by marine bacteria immobilised in κ-carrageenan beads

Publisher: Informa UK Limited

Date: 2007

DOI: 10.1080/08927010701366280

Abstract: Antifouling solutions that leave little or no impact in the world's oceans are constantly being sought. This study employed the immobilisation of the antifouling bacterium Pseudoalteromonas tunicata in kappa-carrageenan to demonstrate how a surface may be protected from fouling by bacteria, i.e. a 'living paint'. Attempts so far to produce a 'living paint' have been limited in both longevity of effectiveness and demonstration of applicability, most noticeably regarding the lack of any field data. Here survival of bacteria immobilised in kappa-carrageenan for 12 months in the laboratory is demonstrated and evidence presented for inhibition of fouling for up to 7 weeks in the field (Sydney Harbour, NSW, Australia).

Functional biogeography and host specificity of bacterial communities associated with the Marine Green Alga Ulva spp.

Publisher: Wiley

Date: 13-03-2018

DOI: 10.1111/MEC.14529

Abstract: Bacterial communities play an essential role for the function of marine macroalgae. Recent work has shown that bacterial communities associated with in idual macroalgae possess on a local scale a functional core that is likely derived from erse members of functional guilds. It is not known whether such functional cores also exist across large spatial scales or between closely related host species. To address this, we studied here the bacterial communities on three species of the green macroalgal genus Ulva from different geographic locations. While the taxonomic composition was too variable to describe a community core, we identified genes that were enriched across all Ulva s les as compared to the communities of the surrounding seawater. Of these core functions, 70% were consistently found and independent of the Ulva species and biogeography, while the remaining functions (~30%) are possibly involved in local or host-specific adaptations. For each host in idual, the core functions are provided by bacteria with distinct phylogenetic origin and these bacteria could constitute a global guild of Ulva-associated bacteria. Together, our results demonstrate the presence of a stable core set of functional genes in the bacterial communities associated with closely related host species and across large biogeographies.

Quorum Sensing-Controlled Biofilm Development in Serratia liquefaciens MG1

Publisher: American Society for Microbiology

Date: 02-2004

DOI: 10.1128/JB.186.3.692-698.2004

Abstract: Serratia liquefaciens MG1 contains an N- acylhomoserine lactone-mediated quorum-sensing system that is known to regulate swarming motility colonization. In this study, we describe for S. liquefaciens MG1 the development of a novel biofilm consisting of cell aggregates and differentiated cell types, such as cell chains and long filamentous cells. Furthermore, quorum sensing is shown to be crucial for normal biofilm development and for elaborate differentiation. A mutant of S. liquefaciens MG1 that was incapable of synthesizing extracellular signal formed a thin and nonmature biofilm lacking cell aggregates and differentiated cell chains. Signal-based complementation of this mutant resulted in a biofilm with the wild-type architecture. Two quorum-sensing-regulated genes ( bsmA and bsmB ) involved in biofilm development were identified, and we propose that these genes are engaged in fine-tuning the formation of cell aggregates at a specific point in biofilm development.

[12] Genetic and chemical tools for investigating signaling processes in biofilms

Publisher: Elsevier

Date: 2001

DOI: 10.1016/S0076-6879(01)36584-9

Climate change and disease: bleaching of a chemically defended seaweed

Publisher: Wiley

Date: 15-06-2011

DOI: 10.1111/J.1365-2486.2011.02456.X

Virus ecology

Publisher: Springer Science and Business Media LLC

Date: 06-1991

DOI: 10.1038/351612B0

Biofilm dispersal cells of a cystic fibrosis Pseudomonas aeruginosa isolate exhibit variability in functional traits likely to contribute to persistent infection

Publisher: Oxford University Press (OUP)

Date: 11-2012

DOI: 10.1111/J.1574-695X.2012.01006.X

A characterization of DNA release in Pseudomonas aeruginosa cultures and biofilms

Publisher: Wiley

Date: 12-12-2005

DOI: 10.1111/J.1365-2958.2005.05008.X

Abstract: Pseudomonas aeruginosa produces extracellular DNA which functions as a cell-to-cell interconnecting matrix component in biofilms. Comparison of extracellular DNA and chromosomal DNA by the use of polymerase chain reaction and Southern analysis suggested that the extracellular DNA is similar to whole-genome DNA. Evidence that the extracellular DNA in P. aeruginosa biofilms and cultures is generated via lysis of a subpopulation of the bacteria was obtained through experiments where extracellular beta-galactosidase released from lacZ-containing P. aeruginosa strains was assessed. Experiments with the wild type and lasIrhlI, pqsA, pqsL and fliMpilA mutants indicated that the extracellular DNA is generated via a mechanism which is dependent on acyl homoserine lactone and Pseudomonas quinolone signalling, as well as on flagella and type IV pili. Microscopic investigation of flow chamber-grown wild-type P. aeruginosa biofilms stained with different DNA stains suggested that the extracellular DNA is located primarily in the stalks of mushroom-shaped multicellular structures, with a high concentration especially in the outer part of the stalks forming a border between the stalk-forming bacteria and the cap-forming bacteria. Biofilms formed by lasIrhlI, pqsA and fliMpilA mutants contained less extracellular DNA than biofilms formed by the wild type, and the mutant biofilms were more susceptible to treatment with sodium dodecyl sulphate than the wild-type biofilm.

Comparisons of diversity of bacterial communities associated with three sessile marine eukaryotes

Publisher: Inter-Research Science Center

Date: 09-08-2007

DOI: 10.3354/AME048217

Ecological advantages of autolysis during the development and dispersal of Pseudoalteromonas tunicata biofilms

Publisher: American Society for Microbiology

Date: 08-2006

DOI: 10.1128/AEM.00546-06

Abstract: In the ubiquitous marine bacterium Pseudoalteromonas tunicata , subpopulations of cells are killed by the production of an autocidal protein, AlpP, during biofilm development. Our data demonstrate an involvement of this process in two parameters, dispersal and phenotypic ersification, which are of importance for the ecology of this organism and for its survival within the environment. Cell death in P. tunicata wild-type biofilms led to a major reproducible dispersal event after 192 h of biofilm development. The dispersal was not observed with a ΔAlpP mutant strain. Using flow cytometry and the fluorescent dye DiBAC 4 (3), we also show that P. tunicata wild-type cells that disperse from biofilms have enhanced metabolic activity compared to those cells that disperse from ΔAlpP mutant biofilms, possibly due to nutrients released from dead cells. Furthermore, we report that there was considerable phenotypic variation among cells dispersing from wild-type biofilms but not from the ΔAlpP mutant. Wild-type cells that dispersed from biofilms showed significantly increased variations in growth, motility, and biofilm formation, which may be important for successful colonization of new surfaces. These findings suggest for the first time that the autocidal events mediated by an antibacterial protein can confer ecological advantages to the species by generating a metabolically active and phenotypically erse subpopulation of dispersal cells.

Differential Gene Expression To Investigate the Effect of ( 5Z )-4-Bromo- 5-(Bromomethylene)-3-Butyl-2( 5H )-Furanone on Ba