Future research trends in the major chemical language of bacteria

Systematic Evaluation of Biotic and Abiotic Factors in Antifungal Microorganism Screening

Microorganisms have significant potential to control fungal contamination in various foods. However, the identification of strains that exhibit robust antifungal activity poses challenges due to highly context-dependent responses. Therefore, to fully exploit the potential of isolates as antifungal agents, it is crucial to systematically evaluate them in a variety of biotic and abiotic contexts. Here, we present an adaptable and scalable method using a robotic platform to study the properties of 1022 isolates obtained from maple sap. We tested the antifungal activity of isolates alone or in pairs on M17 + lactose (LM17), plate count agar (PCA), and sucrose-allantoin (SALN) culture media against Kluyveromyces lactis, Candida boidinii, and Saccharomyces cerevisiae. Microorganisms exhibited less often antifungal activity on SALN and PCA than LM17, suggesting that the latter is a better screening medium. We also analyzed the results of ecological interactions between pairs. Isolates that showed consistent competitive behaviors were more likely to show antifungal activity than expected by chance. However, co-culture rarely improved antifungal activity. In fact, an interaction-mediated suppression of activity was more prevalent in our dataset. These findings highlight the importance of incorporating both biotic and abiotic factors into systematic screening designs for the bioprospection of microorganisms with environmentally robust antifungal activity.

Quorum Sensing Signaling Alters Virulence Potential and Population Dynamics in Complex Microbiome-Host Interactomes

Despite the discovery of the first N-acyl homoserine lactone (AHL) based quorum sensing (QS) in the marine environment, relatively little is known about the abundance, nature and diversity of AHL QS systems in this diverse ecosystem. Establishing the prevalence and diversity of AHL QS systems and how they may influence population dynamics within the marine ecosystem, may give a greater insight into the evolution of AHLs as signaling molecules in this important and largely unexplored niche. Microbiome profiling of Stelletta normani and BD1268 sponge samples identified several potential QS active genera. Subsequent biosensor-based screening of a library of 650 marine sponge bacterial isolates identified 10 isolates that could activate at least one of three AHL biosensor strains. Each was further validated and profiled by Ultra-High Performance Liquid Chromatography Mass Spectrometry, with AHLs being detected in 8 out of 10 isolate extracts. Co-culture of QS active isolates with S. normani marine sponge samples led to the isolation of genera such as Pseudomonas and Paenibacillus, both of which were low abundance in the S. normani microbiome. Surprisingly however, addition of AHLs to isolates harvested following co-culture did not measurably affect either growth or biofilm of these strains. Addition of supernatants from QS active strains did however impact significantly on biofilm formation of the marine Bacillus sp. CH8a sporeforming strain suggesting a role for QS systems in moderating the microbe-microbe interaction in marine sponges. Genome sequencing and phylogenetic analysis of a QS positive Psychrobacter isolate identified several QS associated systems, although no classical QS synthase gene was identified. The stark contrast between the biodiverse sponge microbiome and the relatively limited diversity that was observed on standard culture media, even in the presence of QS active compounds, serves to underscore the extent of diversity that remains to be brought into culture.

Identification and chemical characterization of N-acyl-homoserine lactone quorum sensing signals across sponge species and time

Marine sponges form symbiotic relationships with complex microbial communities, yet little is known about the mechanisms by which these microbes regulate their behavior through gene expression. Many bacterial communities regulate gene expression using chemical signaling termed quorum sensing. While a few previous studies have shown presence of N-acyl-homoserine lactone (AHL)-based quorum sensing in marine sponges, the chemical identity of AHL signals has been published for only two sponge species. In this study, we screened for AHLs in extracts from 15 sponge species (109 specimens in total) from the Mediterranean and Red Sea, using a wide-range AHL biosensor. This is the first time that AHL presence was examined over time in sponges. We detected the presence of AHL in 46% of the sponge species and found that AHL signals differ for certain sponge species in time and across sponge individuals. Furthermore, for the Mediterranean sponge species Sarcotragus fasciculatus, we identified 14 different AHLs. The constant presence of specific AHL molecules in all specimens, together with varying signaling molecules between the different specimens, makes Sa. fasciculatus a good model to further investigate the function of quorum sensing in sponge-associated bacteria. This study extends the knowledge of AHL-based quorum sensing in marine sponges.

Insights into the Quorum Sensing Regulon of the Acidophilic Acidithiobacillus ferrooxidans Revealed by Transcriptomic in the Presence of an Acyl Homoserine Lactone Superagonist Analog

While a functional quorum sensing system has been identified in the acidophilic chemolithoautotrophic Acidithiobacillus ferrooxidans ATCC 23270(T) and shown to modulate cell adhesion to solid substrates, nothing is known about the genes it regulates. To address the question of how quorum sensing controls biofilm formation in A. ferrooxidans (T), the transcriptome of this organism in conditions in which quorum sensing response is stimulated by a synthetic superagonist AHL (N-acyl homoserine lactones) analog has been studied. First, the effect on biofilm formation of a synthetic AHL tetrazolic analog, tetrazole 9c, known for its agonistic QS activity, was assessed by fluorescence and electron microscopy. A fast adherence of A. ferrooxidans (T) cells on sulfur coupons was observed. Then, tetrazole 9c was used in DNA microarray experiments that allowed the identification of genes regulated by quorum sensing signaling, and more particularly, those involved in early biofilm formation. Interestingly, afeI gene, encoding the AHL synthase, but not the A. ferrooxidans quorum sensing transcriptional regulator AfeR encoding gene, was shown to be regulated by quorum sensing. Data indicated that quorum sensing network represents at least 4.5% (141 genes) of the ATCC 23270(T) genome of which 42.5% (60 genes) are related to biofilm formation. Finally, AfeR was shown to bind specifically to the regulatory region of the afeI gene at the level of the palindromic sequence predicted to be the AfeR binding site. Our results give new insights on the response of A. ferrooxidans to quorum sensing and on biofilm biogenesis.

A New N-Acyl Homoserine Lactone Synthase in an Uncultured Symbiont of the Red Sea Sponge Theonella swinhoei

Sponges harbor a remarkable diversity of microbial symbionts in which signal molecules can accumulate and enable cell-cell communication, such as quorum sensing (QS). Bacteria capable of QS were isolated from marine sponges; however, an extremely small fraction of the sponge microbiome is amenable to cultivation. We took advantage of community genome assembly and binning to investigate the uncultured majority of sponge symbionts. We identified a complete N-acyl-homoserine lactone (AHL)-QS system (designated TswIR) and seven partial luxI homologues in the microbiome of Theonella swinhoei. The TswIR system was novel and shown to be associated with an alphaproteobacterium of the order Rhodobacterales, here termed Rhodobacterales bacterium TS309. The tswI gene, when expressed in Escherichia coli, produced three AHLs, two of which were also identified in a T. swinhoei sponge extract. The taxonomic affiliation of the 16S rRNA of Rhodobacterales bacterium TS309 to a sponge-coral specific clade, its enrichment in sponge versus seawater and marine sediment samples, and the presence of sponge-specific features, such as ankyrin-like domains and tetratricopeptide repeats, indicate a likely symbiotic nature of this bacterium.

Impact of interspecific interactions on antimicrobial activity among soil bacteria

Certain bacterial species produce antimicrobial compounds only in the presence of a competing species. However, little is known on the frequency of interaction-mediated induction of antibiotic compound production in natural communities of soil bacteria. Here we developed a high-throughput method to screen for the production of antimicrobial activity by monocultures and pair-wise combinations of 146 phylogenetically different bacteria isolated from similar soil habitats. Growth responses of two human pathogenic model organisms, Escherichia coli WA321 and Staphylococcus aureus 533R4, were used to monitor antimicrobial activity. From all isolates, 33% showed antimicrobial activity only in monoculture and 42% showed activity only when tested in interactions. More bacterial isolates were active against S. aureus than against E. coli. The frequency of interaction-mediated induction of antimicrobial activity was 6% (154 interactions out of 2798) indicating that only a limited set of species combinations showed such activity. The screening revealed also interaction-mediated suppression of antimicrobial activity for 22% of all combinations tested. Whereas all patterns of antimicrobial activity (non-induced production, induced production and suppression) were seen for various bacterial classes, interaction-mediated induction of antimicrobial activity was more frequent for combinations of Flavobacteria and alpha- Proteobacteria. The results of our study give a first indication on the frequency of interference competitive interactions in natural soil bacterial communities which may forms a basis for selection of bacterial groups that are promising for the discovery of novel, cryptic antibiotics.

Protein as chemical cue: non-nutritional growth enhancement by exogenous protein in Pseudomonas putida KT2440

Research pertaining to microbe-microbe and microbe-plant interactions has been largely limited to small molecules like quorum sensing chemicals. However, a few recent reports have indicated the role of complex molecules like proteins and polysaccharides in microbial communication. Here we demonstrate that exogenous proteins present in culture media can considerably accelerate the growth of Pseudomonas putida KT2440, even when such proteins are not internalized by the cells. The growth enhancement is observed when the exogenous protein is not used as a source of carbon or nitrogen. The data show non-specific nature of the protein inducing growth; growth enhancement was observed irrespective of the protein type. It is shown that growth enhancement is mediated via increased siderophore secretion in response to the exogenous protein, leading to better iron uptake. We highlight the ecological significance of the observation and hypothesize that exogenous proteins serve as chemical cues in the case of P.putida and are perceived as indicator of the presence of competitors in the environment. It is argued that enhanced siderophore secretion in response to exogenous protein helps P.putida establish numerical superiority over competitors by way of enhanced iron assimilation and quicker utilization of aromatic substrates.

Classifying the topology of AHL-driven quorum sensing circuits in proteobacterial genomes

Virulence and adaptability of many Gram-negative bacterial species are associated with an N-acylhomoserine lactone (AHL) gene regulation mechanism called quorum sensing (QS). The arrangement of quorum sensing genes is variable throughout bacterial genomes, although there are unifying themes that are common among the various topological arrangements. A bioinformatics survey of 1,403 complete bacterial genomes revealed characteristic gene topologies in 152 genomes that could be classified into 16 topological groups. We developed a concise notation for the patterns and show that the sequences of LuxR regulators and LuxI autoinducer synthase proteins cluster according to the topological patterns. The annotated topologies are deposited online with links to sequences and genome annotations at http://bacteria.itk.ppke.hu/QStopologies/.

Co-cultures of Pseudomonas aeruginosa and Roseobacter denitrificans reveal shifts in gene expression levels compared to solo cultures

Consistent biosynthesis of desired secondary metabolites (SMs) from pure microbial cultures is often unreliable. In a proof-of-principle study to induce SM gene expression and production, we describe mixed "co-culturing" conditions and monitoring of messages via quantitative real-time PCR (qPCR). Gene expression of model bacterial strains (Pseudomonas aeruginosa PAO1 and Roseobacter denitrificans Och114) was analyzed in pure solo and mixed cocultures to infer the effects of interspecies interactions on gene expression in vitro, Two P. aeruginosa genes (PhzH coding for portions of the phenazine antibiotic pathway leading to pyocyanin (PCN) and the RhdA gene for thiosulfate: cyanide sulfurtransferase (Rhodanese)) and two R. denitrificans genes (BetaLact for metallo-beta-lactamase and the DMSP gene for dimethylpropiothetin dethiomethylase) were assessed for differential expression. Results showed that R. denitrificans DMSP and BetaLact gene expression became elevated in a mixed culture. In contrast, P. aeruginosa co-cultures with R. denitrificans or a third species did not increase target gene expression above control levels. This paper provides insight for better control of target SM gene expression in vitro and bypass complex genetic engineering manipulations.

Quorum activation at a distance: spatiotemporal patterns of gene regulation from diffusion of an autoinducer signal

Quorum sensing (QS) bacteria regulate gene expression collectively by exchanging diffusible signal molecules known as autoinducers. Although QS is often studied in well-stirred laboratory cultures, QS bacteria colonize many physically and chemically heterogeneous environments where signal molecules are transported primarily by diffusion. This raises questions of the effective distance range of QS and the degree to which colony behavior can be synchronized over such distances. We have combined experiments and modeling to investigate the spatiotemporal patterns of gene expression that develop in response to a diffusing autoinducer signal. We embedded a QS strain in a narrow agar lane and introduced exogenous autoinducer at one terminus of the lane. We then measured the expression of a QS reporter as a function of space and time as the autoinducer diffused along the lane. The diffusing signal readily activates the reporter over distances of ~1 cm on time scales of ~10 h. However, the patterns of activation are qualitatively unlike the familiar spreading patterns of simple diffusion, as the kinetics of response are surprisingly insensitive to the distance the signal has traveled. We were able to reproduce these patterns with a mathematical model that combines simple diffusion of the signal with logistic growth of the bacteria and cooperative activation of the reporter. In a wild-type QS strain, we also observed the propagation of a unique spatiotemporal excitation. Our results show that a chemical signal transported only by diffusion can be remarkably effective in synchronizing gene expression over macroscopic distances.

AHL signals induce rubrifacine production in a bruI mutant of Brenneria rubrifaciens

Several members of the bacterial genus Brenneria are pathogenic on different tree species. Cell-free extracts from the bacterial phytopathogens Brenneria rubrifaciens, B. salicis, and B. nigrifluens induced production of the red pigment rubrifacine in the B. rubrifaciens bruI insertional mutant Br-212. Analysis of the bruI locus identified an adjacent open reading frame, designated bruR, with homology to luxR. High-performance liquid chromatography and mass spectrometry analysis of ethyl acetate extracts from wild-type B. rubrifaciens and Escherichia coli expressing the bruI gene identified two acyl homoserine lactone (AHL) peaks, N-(3-oxohexanoyl)-homoserine lactone (3OC6HSL) and N-hexanoyl-homoserine lactone (C6HSL). Addition of synthetic 3OC6HSL and C6HSL at 10 μM to the bruI mutant, strain Br-212, induced rubrifacine production and the ability to elicit a hypersensitive reaction (HR) in tobacco leaves. Synthetic C6HSL was less effective at inducing pigment production than 3OC6HSL at 10 μM. The bruI mutant Br-212 did not produce detectable AHLs, indicating that C6HSL and 3OC6HSL are the major AHLs produced by this species. The AHLs N-heptanoyl-DL-homoserine lactone (C7HSL), N-octanoyl-DL-homoserine lactone (C8HSL), and N-(3-oxooctanoyl)-DL-homoserine lactone (3OC8HSL) also induced pigment production in Br-212 and restored its ability to elicit an HR in tobacco, suggesting that cross-talk with other bacterial species may be possible.

Cholinergic chemosensory cells in the auditory tube

The luminal composition of the auditory tube influences its function. The mechanisms involved in the monitoring are currently not known. For the lower respiratory epithelium, such a sentinel role is carried out by cholinergic brush cells. Here, using two different mouse strains expressing eGFP under the control of the promoter of choline acetyltransferase (ChAT), we show the presence of solitary cholinergic villin-positive brush cells also in the mouse auditory tube epithelium. They express the vesicular acetylcholine (ACh) transporter and proteins of the taste transduction pathway such as α-gustducin, phospholipase C beta 2 (PLC(β2)) and transient receptor potential cation channel subfamily M member 5 (TRPM5). Immunoreactivity for TRPM5 and PLCβ2 was found regularly, whereas α-gustducin was absent in approximately 15% of the brush cells. Messenger RNA for the umami taste receptors (TasR), Tas1R1 and 3, and for the bitter receptors, Tas2R105 and Tas2R108, involved in perception of cycloheximide and denatonium were detected in the auditory tube. Using a transgenic mouse that expresses eGFP under the promotor of the nicotinic ACh receptor α3-subunit, we identified cholinoceptive nerve fibers that establish direct contacts to brush cells in the auditory tube. A subpopulation of these fibers displayed also CGRP immunoreactivity. Collectively, we show for the first time the presence of brush cells in the auditory tube. These cells are equipped with all proteins essential for sensing the composition of the luminal microenvironment and for communication of the changes to the CNS via attached sensory nerve fibers.

Quorum sensing in Acinetobacter: an emerging pathogen

Acinetobacter is emerging as one of the major nosocomial infectious pathogens, facilitated by tolerance to desiccation and multidrug resistance. Quorum sensing (autoinducer-receptor mechanism) plays role in biofilm formation in Acinetobacter, though its role in regulation of other virulence factors is yet to be established. Phylogenetic studies indicate that Acinetobacter baumannii is closely related to Burkholderia ambifaria but its quorum sensing genes (abaI and abaR) were acquired horizontally from Halothiobacillus neapolitanus. The prospects of quorum quenching to control the infections caused by Acinetobacter have also been discussed.

Different aspects of bacterial communication signals

The communication or quorum-sensing signal molecules (QSSM) are specialized molecules used by numerous gram-negative bacterial pathogens of animals and plants to regulate or modulate bacterial virulence factor production. In plant-associated bacteria, genes encoding the production of these signal molecules, QSSMs, were discovered to be linked with the phenotype of bacterium, because mutation of these genes typically disrupts some behaviors of bacteria. There are other regulator genes which respond to the presence of signal molecule and regulate the production of signal molecule as well as some virulence factors. The synthesis and regulator genes (collectively called quorum-sensing genes hereafter) are repressed in low bacterial population but induced when bacteria reach to high cell density. Multiple regulatory components have been identified in the bacteria that are under control of quorum sensing. This review describes different communication signal molecules, and the various chemical, physical and genomic factors known to synthesize signals. Likewise, the role of some signal-degrading enzymes or compounds and the interaction of QSSMs with eukaryotic metabolism will be discussed here.

Role of planktonic and sessile extracellular metabolic byproducts on Pseudomonas aeruginosa and Escherichia coli intra and interspecies relationships

Bacterial species are found primarily as residents of complex surface-associated communities, known as biofilms. Although these structures prevail in nature, bacteria still exist in planktonic lifestyle and differ from those in morphology, physiology, and metabolism. This study aimed to investigate the influence of physiological states of Pseudomonas aeruginosa and Escherichia coli in cell-to-cell interactions. Filtered supernatants obtained under planktonic and biofilm cultures of each single species were supplemented with tryptic soy broth (TSB) and used as the growth media (conditioned media) to planktonic and sessile growth of both single- and two-species cultures. Planktonic bacterial growth was examined through OD(640) measurement. One-day-old biofilms were evaluated in terms of biofilm biomass (CV), respiratory activity (XTT), and CFU number. Conditioned media obtained either in biofilm or in planktonic mode of life triggered a synergistic effect on planktonic growth, mainly for E. coli single cultures growing in P. aeruginosa supernatants. Biofilms grown in the presence of P. aeruginosa biofilms-derived metabolites presented less mass and activity. These events highlight that, when developed in biofilm, P. aeruginosa release signals or metabolites able to prejudice single and binary biofilm growth of others species and of their own species. However, products released by their planktonic counterparts did not impair biofilm growth or activity. E. coli, living as planktonic or sessile cultures, released signals and metabolites or removed un-beneficial compounds which promoted the growth and activity of all the species. Our findings revealed that inter and intraspecies behaviors depend on the involved bacteria and their adopted mode of life.

Co-swarming and local collapse: quorum sensing conveys resilience to bacterial communities by localizing cheater mutants in Pseudomonas aeruginosa

Background

Members of swarming bacterial consortia compete for nutrients but also use a co-operation mechanism called quorum sensing (QS) that relies on chemical signals as well as other secreted products (“public goods”) necessary for swarming. Deleting various genes of this machinery leads to cheater mutants impaired in various aspects of swarming cooperation.

Methodology/Principal Findings

Pairwise consortia made of Pseudomonas aeruginosa, its QS mutants as well as B. cepacia cells show that a interspecies consortium can “combine the skills” of its participants so that the strains can cross together barriers that they could not cross alone. In contrast, deleterious mutants are excluded from consortia either by competition or by local population collapse. According to modeling, both scenarios are the consequence of the QS signalling mechanism itself.

Conclusion/Significance

The results indirectly explain why it is an advantage for bacteria to maintain QS systems that can cross-talk among different species, and conversely, why certain QS mutants which can be abundant in isolated niches, cannot spread and hence remain localized.