Quorum-sensing inhibitory compounds from extremophilic microorganisms isolated from a hypersaline cyanobacterial mat

Advancing Antibiotic-Resistant Microbe Combat: Nanocarrier-Based Systems in Combination Therapy Targeting Quorum Sensing

The increase in antibiotic-resistant bacteria presents a significant risk to worldwide public health, emphasizing the necessity of novel approaches to address infections. Quorum sensing, an essential method of communication among bacteria, controls activities like the formation of biofilms, the production of virulence factors, and the synthesis of secondary metabolites according to the number of individuals in the population. Quorum quenching, which interferes with these processes, emerges as a vital approach to diminish bacterial virulence and prevent biofilm formation. Nanocarriers, characterized by their small size, high surface-area-to-volume ratio, and modifiable surface chemistry, offer a versatile platform for the disruption of bacterial communication by targeting various stages within the quorum sensing pathway. These features allow nanocarriers to infiltrate biofilms, disrupt cell membranes, and inhibit bacterial proliferation, presenting a promising alternative to traditional antibiotics. Integrating nanocarrier-based systems into combination therapies provides a multi-pronged approach to infection control, enhancing both the efficacy and specificity of treatment regimens. Nonetheless, challenges related to the stability, safety, and clinical effectiveness of nanomaterial-based antimicrobial treatments remain. Continued research and development are essential to overcoming these obstacles and fully harnessing the potential of nano-antimicrobial therapies. This review emphasizes the importance of quorum sensing in bacterial behavior and highlights the transformative potential of nanotechnology in advancing antimicrobial treatments, offering innovative solutions to combat antibiotic-resistant pathogens.

Exploring halophilic environments as a source of new antibiotics

Microbial natural products from microbes in extreme environments, including haloarchaea, and halophilic bacteria, possess a huge capacity to produce novel antibiotics. Additionally, enhanced isolation techniques and improved tools for genomic mining have expanded the efficiencies in the antibiotic discovery process. This review article provides a detailed overview of known antimicrobial compounds produced by halophiles from all three domains of life. We summarize that while halophilic bacteria, in particular actinomycetes, contribute the vast majority of these compounds the importance of understudied halophiles from other domains of life requires additional consideration. Finally, we conclude by discussing upcoming technologies- enhanced isolation and metagenomic screening, as tools that will be required to overcome the barriers to antimicrobial drug discovery. This review highlights the potential of these microbes from extreme environments, and their importance to the wider scientific community, with the hope of provoking discussion and collaborations within halophile biodiscovery. Importantly, we emphasize the importance of bioprospecting from communities of lesser-studied halophilic and halotolerant microorganisms as sources of novel therapeutically relevant chemical diversity to combat the high rediscovery rates. The complexity of halophiles will necessitate a multitude of scientific disciplines to unravel their potential and therefore this review reflects these research communities.

Carbazole and Quinazolinone Derivatives from a Fluoride-Tolerant Streptomyces Strain OUCMDZ-5511

Six new 9H-carbazole derivatives (1-6) and nine previously reported compounds (7-15) were isolated from a fermented solid medium of the Thailand mangrove-derived Streptomyces strain, OUCMDZ-5511, under fluoride stress. Compounds 2-5, 12, and 15 were exclusively present in the fluoride-supplemented fermentation medium, while compounds 7-9, 13, and 14 were newly discovered natural products. The molecular structures of the compounds were identified by a spectroscopic analysis. The new compound 2 displayed antiquorum sensing activity against Chromobacterium violaceum ATCC 12472 by reducing the violacein production and inhibiting the biofilm formation in a concentration-dependent manner. The study revealed that compound 2 could be a novel potential inhibitor of quorum sensing.

Quorum sensing signals: Aquaculture risk factor

Bacteria produce several virulence factors and cause massive mortality in fish and crustaceans. Abundant quorum sensing (QS) signals and high cell density are essentially required for the production of such virulence factors. Although several strategies have been developed to control aquatic pathogens through antibiotics and QS inhibition, the impact of pre‐existing QS signals in the aquatic environment has been overlooked. QS signals cause detrimental effects on mammalian cells and induce cell death by interfering with multiple cellular pathways. Moreover, QS signals not only function as a messenger, but also annihilate the functions of the host immune system which implies that QS signals should be designated as a major virulence factor. Despite QS signals' role has been well documented in mammalian cells, their impact on aquatic organisms is still at the budding stage. However, many aquatic organisms produce enzymes that degrade and detoxify such QS signals. In addition, physical and chemical factors also determine the stability of the QS signals in the aqueous environment. The balance between QS signals and existing QS signals degrading factors essentially determines the disease progression in aquatic organisms. In this review, we highlight the impact of QS signals on aquatic organisms and further discussed potential alternative strategies to control disease progression.

Effects of hydroxyl group in cyclo(Pro-Tyr)-like cyclic dipeptides on their anti-QS activity and self-assembly

We investigated the influence of hydroxyl groups on the anti-quorum-sensing (anti-QS) and anti-biofilm activity of structurally similar cyclic dipeptides, namely cyclo(L-Pro-L-Tyr), cyclo(L-Hyp-L-Tyr), and cyclo(L-Pro-L-Phe), against Pseudomonas aeruginosa PAO1. Cyclo(L-Pro-L-Phe), lacking hydroxyl groups, displayed higher virulence factor inhibition and cytotoxicity, but showed less inhibitory ability in biofilm formation. Cyclo(L-Pro-L-Tyr) and cyclo(L-Hyp-L-Tyr) suppressed genes in both the las and rhl systems, whereas cyclo(L-Pro-L-Phe) mainly downregulated rhlI and pqsR expression. These cyclic dipeptides interacted with the QS-related protein LasR, with similar binding efficiency to the autoinducer 3OC12-HSL, except for cyclo(L-Pro-L-Phe) which had lower affinity. In addition, the introduction of hydroxyl groups significantly improved the self-assembly ability of these peptides. Both cyclo(L-Pro-L-Tyr) and cyclo(L-Hyp-L-Tyr) formed assembly particles at the highest tested concentration. The findings revealed the structure-function relationship of this kind of cyclic dipeptides and provided basis for our follow-up research in the design and modification of anti-QS compounds.

Antimicrobial Resistance and Recent Alternatives to Antibiotics for the Control of Bacterial Pathogens with an Emphasis on Foodborne Pathogens

Antimicrobial resistance (AMR) is one of the most important global public health problems. The imprudent use of antibiotics in humans and animals has resulted in the emergence of antibiotic-resistant bacteria. The dissemination of these strains and their resistant determinants could endanger antibiotic efficacy. Therefore, there is an urgent need to identify and develop novel strategies to combat antibiotic resistance. This review provides insights into the evolution and the mechanisms of AMR. Additionally, it discusses alternative approaches that might be used to control AMR, including probiotics, prebiotics, antimicrobial peptides, small molecules, organic acids, essential oils, bacteriophage, fecal transplants, and nanoparticles.

Bioactive Compounds from Endophytic Bacteria Bacillus subtilis Strain EP1 with Their Antibacterial Activities

Endophytic bacteria boost host plant defense and growth by producing vital compounds. In the current study, a bacterial strain was isolated from the Boswellia sacra plant and identified as Bacillus subtilis strain EP1 (accession number: MT256301) through 16S RNA gene sequencing. From the identified bacteria, four compounds-1 (4-(4-cinnamoyloxy)phenyl)butanoic acid), 2 (cyclo-(L-Pro-D-Tyr)), 3 (cyclo-(L-Val-L-Phe)), and 4 (cyclo-(L-Pro-L-Val))-were isolated and characterized by 1D and 2D NMR and mass spectroscopy. Moreover, antibacterial activity and beta-lactam-producing gene inhibition (δ-(l-α-aminoadipyl)-l-cysteinyl-d-valine synthetase (ACVS) and aminoadipate aminotransferase (AADAT)) assays were performed. Significant antibacterial activity was observed against the human pathogenic bacterial strains (E. coli) by compound 4 with a 13 ± 0.7 mm zone of inhibition (ZOI), followed by compound 1 having an 11 ± 0.7 mm ZOI. In contrast, the least antibacterial activity among the tested samples was offered by compound 2 with a 10 ± 0.9 mm ZOI compared to the standard (26 ± 1.2 mm). Similarly, the molecular analysis of beta-lactam inhibition determined that compounds 3 and 4 inhibited the two genes (2- to 4-fold) in the beta-lactam biosynthesis (ACVS and AADAT) pathway. From these results, it can be concluded that future research on these compounds could lead to the inhibition of antibiotic-resistant pathogenic bacterial strains.

Quorum quenching and anti-biofilm activities of halotolerant Bacillus strains isolated in different environments in Algeria

AIMS

The current study aimed to screen Bacillus strains with wide-spectrum quorum quenching (QQ) activity against N-acyl-l-homoserine lactones (AHLs), helpful in controlling virulence traits in Gram-negatives, including biofilm formation and also with anti-biofilm activity against Gram-positives.

METHODS AND RESULTS

A total of 94 halotolerant strains of Bacillus isolated from soil and salt-lake sediment samples in Algeria were examined for the presence of QQ activity against AHLs, the presence of the aiiA gene, encoding an AHL lactonase enzyme typical of Bacillus spp., antimicrobial and anti-biofilm activities against Pseudomonas aeruginosa and Streptococcus mutans. Of all strains of Bacillus spp. isolated, 48.9% showed antibacterial activity. In addition, 40% of these isolates showed a positive QQ activity against long-chain AHLs, of which seven strains presented the aiiA gene. Among the species with broad-spectrum QQ activity, the cell extract of Bacillus thuringiensis DZ16 showed antibiofilm activity against P. aeruginosa PAO1, reducing 60% using the Amsterdam active attachment (AAA) biofilm cultivation model. In addition, the cell extract of B. subtilis DZ17, also presenting a broad-spectrum QQ activity, significantly reduced Strep. mutans ATCC 25175 biofilm formations by 63% and 53% in the xCELLigence and the AAA model, respectively, without affecting growth. Strain DZ17 is of particular interest due to its explicit halophilic nature because it can thrive at salinities in the range of 6%-30%.

CONCLUSIONS

B. thuringiensis DZ16 and B. subtilis DZ17 strains have interesting antibacterial, QQ, and anti-biofilm activities. The high range of salinities accepted by these strains increases their biotechnological potential. This may open up their use as probiotics, the treatment and prevention of conventional and emerging infectious diseases.

SIGNIFICANCE AND IMPACT OF STUDY

The use of safe, economical and effective probiotics is limited to control the infections related to multi-resistant bacteria. In our study, we provide two promising agents with QQ, anti-biofilm and antibacterial activities.

Chemical Investigation of Diketopiperazines and N-Phenethylacetamide Isolated from Aquimarina sp. MC085 and Their Effect on TGF-β-Induced Epithelial–Mesenchymal Transition

Chemical investigations of Aquimarina sp. MC085, which suppressed TGF-β-induced epithelial–mesenchymal transition (EMT) in A549 human lung cancer cells, led to the isolation of compounds 1–3. Structural characterization using spectroscopic data analyses in combination with Marfey’s analysis revealed that they were two diketopiperazines [cyclo(l-Pro-l-Leu) (1) and cyclo(l-Pro-l-Ile) (2)] and one N-phenethylacetamide (3). Cyclo(l-Pro-l-Leu) (1) and N-phenethylactamide (3) inhibited the TGF-β/Smad pathway and suppressed the metastasis of A549 cells by affecting TGF-β-induced EMT. However, cyclo(l-Pro-l-Ile) (2) downregulated mesenchymal factors via a non-Smad-mediated signaling pathway.

Exploration of the Quorum-Quenching Mechanism in Pseudomonas nitroreducens W-7 and Its Potential to Attenuate the Virulence of Dickeya zeae EC1

Quorum quenching (QQ) is a novel, promising strategy that opens up a new perspective for controlling quorum-sensing (QS)-mediated bacterial pathogens. QQ is performed by interfering with population-sensing systems, such as by the inhibition of signal synthesis, catalysis of degrading enzymes, and modification of signals. In many Gram-negative pathogenic bacteria, a class of chemically conserved signaling molecules named N-acyl homoserine lactones (AHLs) have been widely studied. AHLs are involved in the modulation of virulence factors in various bacterial pathogens including Dickeya zeae. Dickeya zeae is the causal agent of plant-rot disease of bananas, rice, maize, potatoes, etc., causing enormous economic losses of crops. In this study, a highly efficient AHL-degrading bacterial strain W-7 was isolated from activated-sludge samples and identified as Pseudomonas nitroreducens. Strain W-7 revealed a superior ability to degrade N-(3-oxododecanoyl)-l-homoserine lactone (OdDHL) and completely degraded 0.2 mmol/L of OdDHL within 48 h. Gas chromatography-mass spectrometry (GC-MS) identified N-cyclohexyl-propanamide as the main intermediate metabolite during AHL biodegradation. A metabolic pathway for AHL in strain W-7 was proposed based on the chemical structure of AHL and intermediate products. In addition to the degradation of OdDHL, this strain was also found to be capable of degrading a wide range of AHLs including N-(3-oxohexanoyl)-l-homoserine lactone (OHHL), N-(3-oxooctanoyl)-l-homoserine lactone (OOHL), and N-hexanoyl-l-homoserine lactone (HHL). Moreover, the application of strain W-7 as a biocontrol agent could substantially attenuate the soft rot caused by D. zeae EC1 to suppress tissue maceration in various host plants. Similarly, the application of crude enzymes of strain W-7 significantly reduced the disease incidence and severity in host plants. These original findings unveil the biochemical aspects of a highly efficient AHL-degrading bacterial isolate and provide useful agents that exhibit great potential for the control of infectious diseases caused by AHL-dependent bacterial pathogens.

Vibrio alginolyticus influences quorum sensing-controlled phenotypes of acute hepatopancreatic necrosis disease-causing Vibrio parahaemolyticus

BACKGROUND

Acute hepatopancreatic necrosis syndrome (AHPND) caused by Vibrio parahaemolyticus strain (VPAHPND) impacts the shrimp industry worldwide. With the increasing problem of antibiotic abuse, studies on quorum sensing (QS) system and anti-QS compounds bring potential breakthroughs for disease prevention and treatment.

METHODS

In this study, the cell-free culture supernatant (CFCS) and its extract of V. alginolyticus BC25 were investigated for anti-QS activity against a reporter bacteria, Chromobacterium violaceum DMST46846. The effects of CFCS and/ or extract on motility, biofilm formation and extracellular polymeric substances (EPSs) of VPAHPND PSU5591 were evaluated. Moreover, the effects of V. alginolyticus BC25 on virulence of VPAHPND PSU5591 were investigated by shrimp challenge test. The potentially active anti-QS compounds presented in the extract and effect on gene expression of VPAHPND PSU5591 were identified.

RESULTS

The CFCS of V. alginolyticus BC25 and its extract showed a significant anti-QS activity against the reporter bacteria as well as swimming and swarming motilities, biofilms, and EPSs production by VPAHPND PSU5591. Transcriptome analysis revealed that V. alginolyticus BC25 extract significantly reduced the flagella genes involved in biofilm formation and iron-controlled virulence regulatory gene of VPAHPND PSU5591. Whereas, the LuxR family transcriptional regulator gene, c-factor, a cell-cell signaling gene, and capsular polysaccharide were up-regulated. The potentially active anti-QS compounds identified in extract were Cyclo-(L-Leu-L-Pro), and Cyclo-(L-Phe-L-Pro). Furthermore, V. alginolyticus BC25 enhanced disease resistance against VPAHPND PSU5591 in tested shrimp larvae.

CONCLUSION

These findings suggest that V. alginolyticus BC25 could provide natural anti-QS and anti-biofilms compounds and has great ability to be used as biocontrol agent against VPAHPND infection in shrimp aquaculture.

Loss of Motility as a Non-Lethal Mechanism for Intercolony Inhibition ("Sibling Rivalry") in Marinobacter

Bacteria from the genus Marinobacter are ubiquitous throughout the worlds' oceans as "opportunitrophs" capable of surviving a wide range of conditions, including colonization of surfaces of marine snow and algae. To prevent too many bacteria from occupying this ecological niche simultaneously, some sort of population dependent control must be operative. Here, we show that while Marinobacter do not produce or utilize an acylhomoserine lactone (AHL)-based quorum sensing system, "sibling" colonies of many species of Marinobacter exhibit a form of non-lethal chemical communication that prevents colonies from overrunning each other's niche space. Evidence suggests that this inhibition is the result of a loss in motility for cells at the colony interfaces. Although not the signal itself, we have identified a protein, glycerophosphoryl diester phosphodiesterase, that is enriched in the inhibition zone between the spreading colonies that may be part of the overall response.

Diversity of Bacteria and Bacterial Products as Antibiofilm and Antiquorum Sensing Drugs Against Pathogenic Bacteria

The increase in antibiotic resistance of pathogenic bacteria has led to the development of new therapeutic approaches to inhibit biofilm formation as well as interfere quorum sensing (QS) signaling systems. The QS system is a phenomenon in which pathogenic bacteria produce signaling molecules that are involved in cell to cell communication, production of virulence factors, biofilm maturation, and several other functions. In the natural environment, several non-pathogenic bacteria are present as mixed population along with pathogenic bacteria and they control the behavior of microbial community by producing secondary metabolites. Similarly, non-pathogenic bacteria also take advantages of the QS signaling molecule as a sole carbon source for their growth through catabolism with enzymes. Several enzymes are produced by bacteria which disrupt the biofilm architecture by degrading the composition of extracellular polymeric substances (EPS) such as exopolysaccharide, extracellular- DNA and protein. Thus, the interference of QS system by bacterial metabolic products and enzymatic catalysis, modification of the QS signaling molecules as well as enzymatic disruption of biofilm architecture have been considered as the alternative therapeutic approaches. This review article elaborates on the diversity of different bacterial species with respect to their metabolic products as well as enzymes and their molecular modes of action. The bacterial enzymes and metabolic products will open new and promising perspectives for the development of strategies against the pathogenic bacterial infections.

Archaea join the conversation: detection of AHL-like activity across a range of archaeal isolates

Quorum sensing is a mechanism of genetic control allowing single cell organisms to coordinate phenotypic response(s) across a local population and is often critical for ecosystem function. Although quorum sensing has been extensively studied in bacteria comparatively less is known about this mechanism in Archaea. Given the growing significance of Archaea in both natural and anthropogenic settings, it is important to delineate how widespread this phenomenon of signaling is in this domain. Employing a plasmid-based AHL biosensor in conjunction with thin-layer chromatography (TLC), the present study screened a broad range of euryarchaeota isolates for potential signaling activity. Data indicated the presence of 11 new Archaeal isolates with AHL-like activity against the LuxR-based AHL biosensor, including for the first time putative AHL activity in a thermophile. The presence of multiple signals and distinct changes between growth phases were also shown via TLC. Multiple signal molecules were detected using TLC in Haloferax mucosum, Halorubrum kocurii, Natronococcus occultus and Halobacterium salinarium. The finding of multiple novel signal producers suggests the potential for quorum sensing to play an important role not only in the regulation of complex phenotypes within Archaea but the potential for cross-talk with bacterial systems.

Increased algicidal activity of Aeromonas veronii in response to Microcystis aeruginosa: interspecies crosstalk and secondary metabolites synergism

Toxic Microcystis spp. blooms constitute a serious threat to water quality worldwide. Aeromonas veronii was isolated from Microcystis sp. colonies collected in Lake Kinneret. Spent Aeromonas media inhibits the growth of Microcystis aeruginosa MGK isolated from Lake Kinneret. The inhibition was much stronger when Aeromonas growth medium contained spent media from MGK suggesting that Aeromonas recognized its presence and produced secondary metabolites that inhibit Microcystis growth. Fractionations of the crude extract and analyses of the active fractions identified several secondary metabolites including lumichrome in Aeromonas media. Application of lumichrome at concentrations as low as 4 nM severely inhibited Microcystis growth. Inactivation of aviH in the lumichrome biosynthetic pathway altered the lumichrome level in Aeromonas and the extent of MGK growth inhibition. Conversely, the initial lag in Aeromonas growth was significantly longer when provided with Microcystis spent media but Aeromonas was able to resume normal growth. The longer was pre-exposure to Microcystis spent media the shorter was the lag phase in Aeromonas growth indicating the presence of, and acclimation to, secondary MGK metabolite(s) the nature of which was not revealed. Our study may help to control toxic Microcystis blooms taking advantage of chemical languages used in the interspecies communication.

Identification of Quorum Sensing Activators and Inhibitors in The Marine Sponge Sarcotragus spinosulus

Marine sponges, a well-documented prolific source of natural products, harbor highly diverse microbial communities. Their extracts were previously shown to contain quorum sensing (QS) signal molecules of the N-acyl homoserine lactone (AHL) type, known to orchestrate bacterial gene regulation. Some bacteria and eukaryotic organisms are known to produce molecules that can interfere with QS signaling, thus affecting microbial genetic regulation and function. In the present study, we established the production of both QS signal molecules as well as QS inhibitory (QSI) molecules in the sponge species Sarcotragus spinosulus. A total of eighteen saturated acyl chain AHLs were identified along with six unsaturated acyl chain AHLs. Bioassay-guided purification led to the isolation of two brominated metabolites with QSI activity. The structures of these compounds were elucidated by comparative spectral analysis of ¹HNMR and HR-MS data and were identified as 3-bromo-4-methoxyphenethylamine (1) and 5,6-dibromo-N,N-dimethyltryptamine (2). The QSI activity of compounds 1 and 2 was evaluated using reporter gene assays for long- and short-chain AHL signals (Escherichia coli pSB1075 and E. coli pSB401, respectively). QSI activity was further confirmed by measuring dose-dependent inhibition of proteolytic activity and pyocyanin production in Pseudomonas aeruginosa PAO1. The obtained results show the coexistence of QS and QSI in S. spinosulus, a complex signal network that may mediate the orchestrated function of the microbiome within the sponge holobiont.

Extremophilic Natrinema versiforme Against Pseudomonas aeruginosa Quorum Sensing and Biofilm

Pseudomonas aeruginosa is an opportunistic pathogen that causes high morbidity and mortality rates due to its biofilm form. Biofilm formation is regulated via quorum sensing (QS) mechanism and provides up to 1000 times more resistance against conventional antibiotics. QS related genes are expressed according to bacterial population density via signal molecules. QS inhibitors (QSIs) from natural sources are widely studied evaluating various extracts from extreme environments. It is suggested that extremely halophilic Archaea may also produce QSI compounds. For this purpose, we tested QS inhibitory potentials of ethyl acetate extracts from cell free supernatants and cells of Natrinema versiforme against QS and biofilm formation of P. aeruginosa. To observe QS inhibition, all extracts were tested on P. aeruginosa lasB-gfp, rhlA-gfp, and pqsA-gfp biosensor strains and biofilm inhibition was studied using P. aeruginosa PAO1. According to our results, QS inhibition ratios of cell free supernatant extract (CFSE) were higher than cell extract (CE) on las system, whereas CE was more effective on rhl system. In addition, anti-biofilm effect of CFSE was higher than CE. Structural analysis revealed that the most abundant compound in the extracts was trans 4-(2-carboxy-vinyl) benzoic acid.

Antagonism of Quorum Sensing Phenotypes by Analogs of the Marine Bacterial Secondary Metabolite 3-Methyl-N-(2'-Phenylethyl)-Butyramide

Quorum sensing (QS) antagonists have been proposed as novel therapeutic agents to combat bacterial infections. We previously reported that the secondary metabolite 3-methyl-N-(2'-phenylethyl)-butyramide, produced by a marine bacterium identified as Halobacillus salinus, inhibits QS controlled phenotypes in multiple Gram-negative reporter strains. Here we report that N-phenethyl hexanamide, a structurally-related compound produced by the marine bacterium Vibrio neptunius, similarly demonstrates QS inhibitory properties. To more fully explore structure-activity relationships within this new class of QS inhibitors, a panel of twenty analogs was synthesized and biologically evaluated. Several compounds were identified with increased attenuation of QS-regulated phenotypes, most notably N-(4-fluorophenyl)-3-phenylpropanamide against the marine pathogen Vibrio harveyi (IC₅₀ = 1.1 µM). These findings support the opportunity to further develop substituted phenethylamides as QS inhibitors.

Four pairs of proline-containing cyclic dipeptides from Nocardiopsis sp. HT88, an endophytic bacterium of Mallotus nudiflorus L

Strain HT88 was isolated from the fresh stems of Mallotus nudiflorus L, and it was identified as Nocardiopsis sp. by analyzing its morphology and the 16S rRNA sequence. The extracts of fermented HT88 showed potent antimicrobial activities. Bioassay guided separation of extracts led to eight proline (or hydroxyproline, Hyp)-containing cyclic dipeptides. Their structures were determined by 1D and 2D NMR spectroscopy and ESI mass spectrometry and further comparison with existing ¹H and ¹³C NMR, melting points and specific rotation data. The eight 2,5-diketopiperazines (DKPs) were identified as cyclo(L-Pro-L-Leu) (1), cyclo(Pro-Leu) (2), cyclo(L-trans-Hyp-L-Leu) (3), cyclo(D-trans-Hyp-D-Leu) (4), and cyclo(D-Pro-L-Phe) (5), cyclo(L-Pro-L-Phe) (6), and cyclo(D-cis-Hyp-L-Phe) (7), cyclo(L-trans-Hyp-L-Phe) (8), respectively. Up to date, this is the first isolation of four pairs of proline based DKPs from Nocardiopsis sp.

Widespread Existence of Quorum Sensing Inhibitors in Marine Bacteria: Potential Drugs to Combat Pathogens with Novel Strategies

Quorum sensing (QS) is a phenomenon of intercellular communication discovered mainly in bacteria. A QS system consisting of QS signal molecules and regulatory protein components could control physiological behaviors and virulence gene expression of bacterial pathogens. Therefore, QS inhibition could be a novel strategy to combat pathogens and related diseases. QS inhibitors (QSIs), mainly categorized into small chemical molecules and quorum quenching enzymes, could be extracted from diverse sources in marine environment and terrestrial environment. With the focus on the exploitation of marine resources in recent years, more and more QSIs from the marine environment have been investigated. In this article, we present a comprehensive review of QSIs from marine bacteria. Firstly, screening work of marine bacteria with potential QSIs was concluded and these marine bacteria were classified. Afterwards, two categories of marine bacteria-derived QSIs were summarized from the aspects of sources, structures, QS inhibition mechanisms, environmental tolerance, effects/applications, etc. Next, structural modification of natural small molecule QSIs for future drug development was discussed. Finally, potential applications of QSIs from marine bacteria in human healthcare, aquaculture, crop cultivation, etc. were elucidated, indicating promising and extensive application perspectives of QS disruption as a novel antimicrobial strategy.

Isolation of novel quorum-sensing active bacteria from microbial mats in Shark Bay Australia

Quorum sensing is a potent system of genetic control allowing phenotypes to be coordinated across localized communities. In this study, quorum sensing systems in Shark Bay microbial mats were delineated using a targeted approach analyzing whole mat extractions as well as the creation of an isolate library. A library of 165 isolates from different mat types were screened using the AHL biosensor E. coli MT102. Based on sequence identity 30 unique isolates belonging to Proteobacteria, Actinobacteria and Firmicutes were found to activate the AHL biosensor, suggesting AHLs or analogous compounds were potentially present. Several of the isolates have not been shown previously to produce signal molecules, particularly the members of the Actinobacteria and Firmicutes phyla including Virgibacillus, Halobacillius, Microbacterium and Brevibacterium. These active isolates were further screened using thin-layer chromatography (TLC) providing putative identities of AHL molecules present within the mat communities. Nine isolates were capable of producing several spots of varying sizes after TLC separation, suggesting the presence of multiple signalling molecules. This study is the first to delineate AHL-based signalling in the microbial mats of Shark Bay, and suggests quorum sensing may play a role in the ecosphysiological coordination of complex phenotypes across microbial mat communities.

Saline Environments as a Source of Potential Quorum Sensing Disruptors to Control Bacterial Infections: A Review

Saline environments, such as marine and hypersaline habitats, are widely distributed around the world. They include sea waters, saline lakes, solar salterns, or hypersaline soils. The bacteria that live in these habitats produce and develop unique bioactive molecules and physiological pathways to cope with the stress conditions generated by these environments. They have been described to produce compounds with properties that differ from those found in non-saline habitats. In the last decades, the ability to disrupt quorum-sensing (QS) intercellular communication systems has been identified in many marine organisms, including bacteria. The two main mechanisms of QS interference, i.e., quorum sensing inhibition (QSI) and quorum quenching (QQ), appear to be a more frequent phenomenon in marine aquatic environments than in soils. However, data concerning bacteria from hypersaline habitats is scarce. Salt-tolerant QSI compounds and QQ enzymes may be of interest to interfere with QS-regulated bacterial functions, including virulence, in sectors such as aquaculture or agriculture where salinity is a serious environmental issue. This review provides a global overview of the main works related to QS interruption in saline environments as well as the derived biotechnological applications.

Quorum Sensing Inhibitors from Marine Microorganisms and Their Synthetic Derivatives

Quorum sensing inhibitors (QSIs) present a promising alternative or potent adjuvants of conventional antibiotics for the treatment of antibiotic-resistant bacterial strains, since they could disrupt bacterial pathogenicity without imposing selective pressure involved in antibacterial treatments. This review covers a series of molecules showing quorum sensing (QS) inhibitory activity that are isolated from marine microorganisms, including bacteria, actinomycetes and fungi, and chemically synthesized based on QSIs derived from marine microorganisms. This is the first comprehensive overview of QSIs derived from marine microorganisms and their synthetic analogues with QS inhibitory activity.

Phototrophic marine benthic microbiomes: the ecophysiology of these biological entities

Phototrophic biofilms are multispecies, self-sustaining and largely closed microbial ecosystems. They form macroscopic structures such as microbial mats and stromatolites. These sunlight-driven consortia consist of a number of functional groups of microorganisms that recycle the elements internally. Particularly, the sulfur cycle is discussed in more detail as this is fundamental to marine benthic microbial communities and because recently exciting new insights have been obtained. The cycling of elements demands a tight tuning of the various metabolic processes and require cooperation between the different groups of microorganisms. This is likely achieved through cell-to-cell communication and a biological clock. Biofilms may be considered as a macroscopic biological entity with its own physiology. We review the various components of some marine phototrophic biofilms and discuss their roles in the system. The importance of extracellular polymeric substances (EPS) as the matrix for biofilm metabolism and as substrate for biofilm microorganisms is discussed. We particularly assess the importance of extracellular DNA, horizontal gene transfer and viruses for the generation of genetic diversity and innovation, and for rendering resilience to external forcing to these biological entities.

Review on Molecular Mechanisms of Antifouling Compounds: An Update since 2012

Better understanding of the mechanisms of antifouling compounds is recognized to be of high value in establishing sensitive biomarkers, allowing the targeted optimization of antifouling compounds and guaranteeing environmental safety. Despite vigorous efforts to find new antifouling compounds, information about the mechanisms of antifouling is still scarce. This review summarizes the progress into understanding the molecular mechanisms underlying antifouling activity since 2012. Non-toxic mechanisms aimed at specific targets, including inhibitors of transmembrane transport, quorum sensing inhibitors, neurotransmission blockers, adhesive production/release inhibitors and enzyme/protein inhibitors, are put forward for natural antifouling products or shelf-stable chemicals. Several molecular targets show good potential for use as biomarkers in future mechanistic screening, such as acetylcholine esterase for neurotransmission, phenoloxidase/tyrosinase for the formation of adhesive plaques, N-acyl homoserine lactone for quorum sensing and intracellular Ca²⁺ levels as second messenger. The studies on overall responses to challenges by antifoulants can be categorized as general targets, including protein expression/metabolic activity regulators, oxidative stress inducers, neurotransmission blockers, surface modifiers, biofilm inhibitors, adhesive production/release inhibitors and toxic killing. Given the current situation and the knowledge gaps regarding the development of alternative antifoulants, a basic workflow is proposed that covers the indispensable steps, including preliminary mechanism- or bioassay-guided screening, evaluation of environmental risks, field antifouling performance, clarification of antifouling mechanisms and the establishment of sensitive biomarkers, which are combined to construct a positive feedback loop.

Quorum quenching properties of Actinobacteria isolated from Malaysian tropical soils

In this study, a total of 147 soil actinobacterial strains were screened for their ability to inhibit response of Chromobacterium violaceum CV026 to short chain N-acyl homoserine lactone (AHL) which is a quorum sensing molecule. Of these, three actinobacterial strains showed positive for violacein inhibition. We further tested these strains for the inhibition of Pseudomonas aeruginosa PAO1 quorum sensing-regulated phenotypes, namely, swarming and pyocyanin production. The three strains were found to inhibit at least one of the quorum sensing-regulated phenotypes of PAO1. Phylogenetic analysis of the 16S rRNA gene sequences indicated that these strains belong to the genera Micromonospora, Rhodococcus and Streptomyces. This is the first report presenting quorum quenching activity by a species of the genus Micromonospora. Our data suggest that Actinobacteria may be a rich source of active compounds that can act against bacterial quorum sensing system.

Quorum Sensing Inhibitors from the Sea Discovered Using Bacterial N-acyl-homoserine Lactone-Based Biosensors

Marine natural products with antibiotic activity have been a rich source of drug discovery; however, the emergence of antibiotic-resistant bacterial strains has turned attention towards the discovery of alternative innovative strategies to combat pathogens. In many pathogenic bacteria, the expression of virulence factors is under the regulation of quorum sensing (QS). QS inhibitors (QSIs) present a promising alternative or potential synergistic treatment since they disrupt the signaling pathway used for intra- and interspecies coordination of expression of virulence factors. This review covers the set of molecules showing QSI activity that were isolated from marine organisms, including plants (algae), animals (sponges, cnidarians, and bryozoans), and microorganisms (bacteria, fungi, and cyanobacteria). The compounds found and the methods used for their isolation are the emphasis of this review.

In Vitro Reconstruction of Nonribosomal Peptide Biosynthesis Directly from DNA Using Cell-Free Protein Synthesis

Genome sequencing has revealed that a far greater number of natural product biosynthetic pathways exist than there are known natural products. To access these molecules directly and deterministically, a new generation of heterologous expression methods is needed. Cell-free protein synthesis has not previously been used to study nonribosomal peptide biosynthesis, and provides a tunable platform with advantages over conventional methods for protein expression. Here, we demonstrate the use of cell-free protein synthesis to biosynthesize a cyclic dipeptide with correct absolute stereochemistry. From a single-pot reaction, we measured the expression of two nonribosomal peptide synthetases larger than 100 kDa, and detected high-level production of a diketopiperazine. Using quantitative LC-MS and synthetically prepared standard, we observed production of this metabolite at levels higher than previously reported from cell-based recombinant expression, approximately 12 mg/L. Overall, this work represents a first step to apply cell-free protein synthesis to discover and characterize new natural products.

Extremophiles and biotechnology: current uses and prospects

Biotechnology has almost unlimited potential to change our lives in very exciting ways. Many of the chemical reactions that produce these products can be fully optimized by performing them at extremes of temperature, pressure, salinity, and pH for efficient and cost-effective outcomes. Fortunately, there are many organisms (extremophiles) that thrive in extreme environments found in nature and offer an excellent source of replacement enzymes in lieu of mesophilic ones currently used in these processes. In this review, I discuss the current uses and some potential new applications of extremophiles and their products, including enzymes, in biotechnology.

Quorum quenching agents: resources for antivirulence therapy

The continuing emergence of antibiotic-resistant pathogens is a concern to human health and highlights the urgent need for the development of alternative therapeutic strategies. Quorum sensing (QS) regulates virulence in many bacterial pathogens, and thus, is a promising target for antivirulence therapy which may inhibit virulence instead of cell growth and division. This means that there is little selective pressure for the evolution of resistance. Many natural quorum quenching (QQ) agents have been identified. Moreover, it has been shown that many microorganisms are capable of producing small molecular QS inhibitors and/or macromolecular QQ enzymes, which could be regarded as a strategy for bacteria to gain benefits in competitive environments. More than 30 species of marine QQ bacteria have been identified thus far, but only a few of them have been intensively studied. Recent studies indicate that an enormous number of QQ microorganisms are undiscovered in the highly diverse marine environments, and these marine microorganism-derived QQ agents may be valuable resources for antivirulence therapy.

Anaerobic thermophiles

The term "extremophile" was introduced to describe any organism capable of living and growing under extreme conditions. With the further development of studies on microbial ecology and taxonomy, a variety of "extreme" environments have been found and an increasing number of extremophiles are being described. Extremophiles have also been investigated as far as regarding the search for life on other planets and even evaluating the hypothesis that life on Earth originally came from space. The first extreme environments to be largely investigated were those characterized by elevated temperatures. The naturally "hot environments" on Earth range from solar heated surface soils and water with temperatures up to 65 °C, subterranean sites such as oil reserves and terrestrial geothermal with temperatures ranging from slightly above ambient to above 100 °C, to submarine hydrothermal systems with temperatures exceeding 300 °C. There are also human-made environments with elevated temperatures such as compost piles, slag heaps, industrial processes and water heaters. Thermophilic anaerobic microorganisms have been known for a long time, but scientists have often resisted the belief that some organisms do not only survive at high temperatures, but actually thrive under those hot conditions. They are perhaps one of the most interesting varieties of extremophilic organisms. These microorganisms can thrive at temperatures over 50 °C and, based on their optimal temperature, anaerobic thermophiles can be subdivided into three main groups: thermophiles with an optimal temperature between 50 °C and 64 °C and a maximum at 70 °C, extreme thermophiles with an optimal temperature between 65 °C and 80 °C, and finally hyperthermophiles with an optimal temperature above 80 °C and a maximum above 90 °C. The finding of novel extremely thermophilic and hyperthermophilic anaerobic bacteria in recent years, and the fact that a large fraction of them belong to the Archaea has definitely made this area of investigation more exciting. Particularly fascinating are their structural and physiological features allowing them to withstand extremely selective environmental conditions. These properties are often due to specific biomolecules (DNA, lipids, enzymes, osmolites, etc.) that have been studied for years as novel sources for biotechnological applications. In some cases (DNA-polymerase, thermostable enzymes), the search and applications successful exceeded preliminary expectations, but certainly further exploitations are still needed.

Hyperhalophilic archaeal biofilms: growth kinetics, structure, and antagonistic interaction in continuous culture

Biofilms by the hyperhalophilic archaea Halorubrum sp. and Halobacterium sp. were analyzed, and for the first time the progression of structural features and the developmental parameters of these sessile populations are described. Optical slicing and digital analysis of sequential micrographs showed that their three dimensional structure was microorganism dependent. Biofilms of Halobacterium sp. developed in clusters that covered about 30% of the supporting surface at the interface level and expanded over about 86 ± 4 μm in thickness, while Halorubrum sp. biofilms covered less than 20% of the surface and reached a thickness of 41 ± 1 μm. The kinetics of growth was lower in biofilms, with generation times of 27 ± 1 and 36 ± 2 h for Halobacterium sp. and Halorubrum sp., respectively, as compared to 8.4 ± 0.3 and 14 ± 1 h in planktonic cultures. Differences between microorganisms were also observed at the cell morphology level. The interaction between the two microorganisms was also evaluated, showing that Halobacterium sp. can outcompete already established Halorubrum sp. biofilms by a mechanism that might include the combined action of tunnelling swimmers and antimicrobial compounds.

Identification and characterization of extracellular cyclic dipeptides as quorum-sensing signal molecules from Shewanella baltica, the specific spoilage organism of Pseudosciaena crocea during 4 °C storage

Quorum-sensing (QS) signaling molecules are able to mediate specific gene expression inside spoilage bacteria in response to population density and thus are implicated in food spoilage. In the present work, a total of 102 strains of spoilage bacteria were isolated from Pseudosciaena crocea at 4 °C storage, and of these, 60 strains were identified as Shewanella spp., and 48 strains (47.1%) were identified as S. baltica. In addition, the spoilage capabilities of three different S. baltica strains (00A, 00B, and 00C) were compared by total volatile base nitrogen (TVB-N) and sensory analysis (off-odors). Furthermore, four cyclic dipeptides (diketopiperazines, DKPs) that function as QS signal molecules were isolated and characterized from the extracellular metabolites of S. baltica 00C which had the strongest spoilage activity based on gas chromatography mass spectrometry (GC-MS). By supplementation of four synthesized DKPs, the spoilage capability of S. baltica could be significantly enhanced. So far, this was the first attempt to characterize DKPs as the signaling molecules in QS of S. baltica. Our study may provide some evidence of the role of DKPs involved in microbial spoilage.