Arthrobacter strain VAI-A utilizes acyl-homoserine lactone inactivation products and stimulates quorum signal biodegradation by Variovorax paradoxus

Pseudomonas forestsoilum sp. nov. and P. tohonis biocontrol bacterial wilt by quenching 3-hydroxypalmitic acid methyl ester

Bacterial wilt caused by Ralstonia solanacearum ranks the second top important bacterial plant disease worldwide. It is also the most important bacterial disease threatening the healthy development of Casuarina equisetifolia protection forest. 3-hydroxypalmitic acid methyl ester (3-OH PAME) functions as an important quorum sensing (QS) signal regulating the expression of virulence genes in R. solanacearum, and has been regarded as an ideal target for disease prevention and control. To screen native microorganisms capable of degrading 3-OH PAME, samples of C. equisetifolia branches and forest soil were collected and cultured in the medium containing 3-OH PAME as the sole carbon source. Bacteria with over 85% degradation rates of 3-OH PAME after 7-day incubation were further separated and purified. As a result, strain Q1-7 isolated from forest soil and strain Q4-3 isolated from C. equisetifolia branches were obtained and identified as Pseudomonas novel species Pseudomonas forestsoilum sp. nov. and P. tohonis, respectively, according to whole genome sequencing results. The degradation efficiencies of 3-OH PAME of strains Q1-7 and Q4-3 were 95.80% and 100.00% at 48 h, respectively. Both strains showed high esterase activities and inhibited R. solanacearum exopolysaccharide (EPS) and cellulase production. Application of strains Q1-7 and Q4-3 effectively protects C. equisetifolia, peanut and tomato plants from infection by R. solanacearum. Findings in this study provide potential resources for the prevention and control of bacterial wilt caused by R. solanacearum, as well as valuable materials for the identification of downstream quenching genes and the research and development of quenching enzymes for disease control.

Bacterial chemolithoautotrophy via manganese oxidation

Manganese is among Earth’s most abundant elements. Its oxidation had long been theorized¹, yet undemonstrated^2–4, to fuel chemolithoautotrophic microbial growth. Here, an enrichment culture exhibiting Mn(II)-oxidation-dependent, exponential growth was refined to a two species co-culture. Oxidation required viable bacteria at permissive temperatures, resulting in the generation of small Mn oxide nodules to which the cells associated. The majority member of the culture, ‘Candidatus Manganitrophus noduliformans’, affiliates within phylum Nitrospirae (Nitrospirota) but is distantly related to known Nitrospira and Leptospirillum species. The minority member has been isolated, but does not oxidise Mn(II) alone. Stable isotope probing revealed Mn(II)-oxidation-dependent, ¹³CO₂-fixation into cellular biomass. Transcriptomics reveals candidate pathways for coupling extracellular manganese oxidation to aerobic energy conservation and to autotrophic CO₂-fixation. These findings expand the known diversity of inorganic metabolisms supporting life, while completing a biogeochemical energy cycle for manganese^5,6, one that may interface with other major global elemental cycles.

Convection and the Extracellular Matrix Dictate Inter- and Intra-Biofilm Quorum Sensing Communication in Environmental Systems

The mechanisms and impact of bacterial quorum sensing (QS) for the coordination of population-level behaviors are well studied under laboratory conditions. However, it is unclear how, in otherwise open environmental systems, QS signals accumulate to sufficient concentration to induce QS phenotypes, especially when quorum quenching (QQ) organisms are also present. We explore the impact of QQ activity on QS signaling in spatially organized biofilms in scenarios that mimic open systems of natural and engineered environments. Using a functionally differentiated biofilm system, we show that the extracellular matrix, local flow, and QQ interact to modulate communication. In still aqueous environments, convection facilitates signal dispersal while the matrix absorbs and relays signals to the cells. This process facilitates inter-biofilm communication even at low extracellular signal concentrations. Within the biofilm, the matrix further regulates the transport of the competing QS and QQ molecules, leading to heterogenous QS behavior. Importantly, only extracellular QQ enzymes can effectively control QS signaling, suggesting that the intracellular QQ enzymes may not have evolved to degrade environmental QS signals for competition.

Novel N-Acyl Homoserine Lactone-Degrading Bacteria Isolated From Penicillin-Contaminated Environments and Their Quorum-Quenching Activities

N-Acyl homoserine lactones (AHLs) are signaling molecules used in the quorum sensing (QS) of Gram-negative bacteria. Some bacteria interfere with the QS system using AHL-inactivating enzymes, commonly known as quorum-quenching (QQ) enzymes. We have recently isolated a new QQ bacterium showing high resistance to multiple β-lactam antibiotics, and its QQ enzyme (MacQ) confers β-lactam antibiotic resistance and exhibits QQ activities. This observation suggests the possibility of isolating novel QQ bacteria from β-lactam antibiotic-resistant bacteria. In this direction, we attempted to isolate penicillin G (PENG)-resistant bacteria from penicillin-contaminated river sediments and activated sludge treating penicillin-containing wastewater and characterize their QQ activities. Of 19 PENG-resistant isolates, six isolates showed high QQ activity toward a broad range of AHLs, including AHLs with 3-oxo substituents. Five of the six AHL-degraders showed AHL-acylase activity and hydrolyzed the amide bond of AHLs, whereas the remaining one strain did not show AHL-acylase activity, suggesting that this isolate may likely possess alternative degradation mechanism such as AHL-lactonase activity hydrolyzing the lactone ring of AHLs. The 16S rRNA gene sequence analysis results categorized these six AHL-degrading isolates into at least five genera, namely, Sphingomonas (Alphaproteobacteria), Diaphorobacter (Betaproteobacteria), Acidovorax (Betaproteobacteria), Stenotrophomonas (Gammaproteobacteria), and Mycobacterium (Actinobacteria); of these, Mycobacterium sp. M1 has never been known as QQ bacteria. Moreover, multiple β-lactam antibiotics showed high minimum inhibitory concentrations (MICs) when tested against all of isolates. These results strongly demonstrate that a wide variety of β-lactam antibiotic-resistant bacteria possess QQ activities. Although the genetic and enzymatic elements are yet unclear, this study may infer the functional and evolutionary correlation between β-lactam antibiotic resistance and QQ activities.

Deciphering Physiological Functions of AHL Quorum Quenching Acylases

N-Acylhomoserine lactone (AHL)-acylase (also known as amidase or amidohydrolase) is a class of enzyme that belongs to the Ntn-hydrolase superfamily. As the name implies, AHL-acylases are capable of hydrolysing AHLs, the most studied signaling molecules for quorum sensing in Gram-negative bacteria. Enzymatic degradation of AHLs can be beneficial in attenuating bacterial virulence, which can be exploited as a novel approach to fight infection of human pathogens, phytopathogens or aquaculture-related contaminations. Numerous acylases from both prokaryotic and eukaryotic sources have been characterized and tested for the interference of quorum sensing-regulated functions. The existence of AHL-acylases in a multitude of organisms from various ecological niches, raises the question of what the physiological roles of AHL-acylases actually are. In this review, we attempt to bring together recent studies to extend our understanding of the biological functions of these enzymes in nature.

Quorum Signal Inhibitors and Their Potential Use against Fish Diseases

Quorum sensing (QS) is a process of bacterial communication used to control group behaviors, including bioluminescence, virulence factor production, biofilm formation, and biofilm antimicrobial tolerance. Many aquatic bacterial pathogens such as Aeromonas, Vibrio, and Edwardsiella spp. use QS to regulate virulence factor production. The disruption of QS has been shown to be an effective strategy in the competition between higher organisms and bacteria and more recently between bacterial species. For this reason, QS disruption has been proposed as a strategy to prevent bacterial pathogenicity. In this review, we summarize the current literature and illustrate the value of QS inhibitors in controlling virulence production in aquatic bacterial pathogens. This represents a new, nonantibiotic strategy to combat fish diseases. Received August 11, 2015; accepted January 26, 2016.

Quorum Sensing: An Under-Explored Phenomenon in the Phylum Actinobacteria

Quorum sensing is known to play a major role in the regulation of secondary metabolite production, especially, antibiotics, and morphogenesis in the phylum Actinobacteria. Although it is one of the largest bacterial phylum, only 25 of the 342 genera have been reported to use quorum sensing. Of these, only nine have accompanying experimental evidence; the rest are only known through bioinformatic analysis of gene/genome sequences. It is evident that this important communication mechanism is not extensively explored in Actinobacteria. In this review, we summarize the different quorum sensing systems while identifying the limitations of the existing screening strategies and addressing the improvements that have taken place in this field in recent years. The γ-butyrolactone system turned out to be almost exclusively limited to this phylum. In addition, methylenomycin furans, AI-2 and other putative AHL-like signaling molecules are also reported in Actinobacteria. The lack of existing screening systems in detecting minute quantities and of a wider range of signaling molecules was a major reason behind the limited information available on quorum sensing in this phylum. However, recent improvements in screening strategies hold a promising future and are likely to increase the discovery of new signaling molecules. Further, the quorum quenching ability in many Actinobacteria has a great potential in controlling the spread of plant and animal pathogens. A systematic and coordinated effort is required to screen and exploit the enormous potential that quorum sensing in the phylum Actinobacteria has to offer for human benefit.

Synthesis and analysis of stable isotope-labelled N-acyl homoserine lactones

An easy, reliable manner to make suitable, deuterated standards of AHL-molecules belonging to all three important classes of AHLs is presented, starting from a cheap and commercially available deuterium source.

Extracellular Lipase and Protease Production from a Model Drinking Water Bacterial Community Is Functionally Robust to Absence of Individual Members

Bacteria secrete enzymes into the extracellular space to hydrolyze macromolecules into constituents that can be imported for microbial nutrition. In bacterial communities, these enzymes and their resultant products can be modeled as community property. Our goal was to investigate the impact of individual community member absence on the resulting community production of exoenzymes (extracellular enzymes) involved in lipid and protein hydrolysis. Our model community contained nine bacteria isolated from the potable water system of the International Space Station. Bacteria were grown in static conditions individually, all together, or in all combinations of eight species and exoproduct production was measured by colorimetric or fluorometric reagents to assess short chain and long chain lipases, choline-specific phospholipases C, and proteases. The exoenzyme production of each species grown alone varied widely, however, the enzyme activity levels of the mixed communities were functionally robust to absence of any single species, with the exception of phospholipase C production in one community. For phospholipase C, absence of Chryseobacterium gleum led to increased choline-specific phospholipase C production, correlated with increased growth of Burkholderia cepacia and Sphingomonas sanguinis. Because each individual species produced different enzyme activity levels in isolation, we calculated an expected activity value for each bacterial mixture using input levels or known final composition. This analysis suggested that robustness of each exoenzyme activity is not solely mediated by community composition, but possibly influenced by bacterial communication, which is known to regulate such pathways in many bacteria. We conclude that in this simplified model of a drinking water bacterial community, community structure imposes constraints on production and/or secretion of exoenzymes to generate a level appropriate to exploit a given nutrient environment.

Interspecies interactions are an integral determinant of microbial community dynamics

This study investigated the factors that determine the dynamics of bacterial communities in a complex system using multidisciplinary methods. Since natural and engineered microbial ecosystems are too complex to study, six types of synthetic microbial ecosystems (SMEs) were constructed under chemostat conditions with phenol as the sole carbon and energy source. Two to four phenol-degrading, phylogenetically and physiologically different bacterial strains were used in each SME. Phylogeny was based on the nucleotide sequence of 16S rRNA genes, while physiologic traits were based on kinetic and growth parameters on phenol. Two indices, J parameter and “interspecies interaction,” were compared to predict which strain would become dominant in an SME. The J parameter was calculated from kinetic and growth parameters. On the other hand, “interspecies interaction,” a new index proposed in this study, was evaluated by measuring the specific growth activity, which was determined on the basis of relative growth of a strain with or without the supernatant prepared from other bacterial cultures. Population densities of strains used in SMEs were enumerated by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase and were compared to predictions made from J parameter and interspecies interaction calculations. In 4 of 6 SEMs tested the final dominant strain shown by real-time qPCR analyses coincided with the strain predicted by both the J parameter and the interspecies interaction. However, in SMEII-2 and SMEII-3 the final dominant Variovorax strains coincided with prediction of the interspecies interaction but not the J parameter. These results demonstrate that the effects of interspecies interactions within microbial communities contribute to determining the dynamics of the microbial ecosystem.

Biotic inactivation of the Pseudomonas aeruginosa quinolone signal molecule

In Pseudomonas aeruginosa, quorum sensing (QS) regulates the production of secondary metabolites, many of which are antimicrobials that impact on polymicrobial community composition. Consequently, quenching QS modulates the environmental impact of P. aeruginosa. To identify bacteria capable of inactivating the QS signal molecule 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS), a minimal medium containing PQS as the sole carbon source was used to enrich a Malaysian rainforest soil sample. This yielded an Achromobacter xylosoxidans strain (Q19) that inactivated PQS, yielding a new fluorescent compound (I-PQS) confirmed as PQS-derived using deuterated PQS. The I-PQS structure was elucidated using mass spectrometry and nuclear magnetic resonance spectroscopy as 2-heptyl-2-hydroxy-1,2-dihydroquinoline-3,4-dione (HHQD). Achromobacter xylosoxidans Q19 oxidized PQS congeners with alkyl chains ranging from C1 to C5 and also N-methyl PQS, yielding the corresponding 2-hydroxy-1,2-dihydroquinoline-3,4-diones, but was unable to inactivate the PQS precursor HHQ. This indicates that the hydroxyl group at position 3 in PQS is essential and that A. xylosoxidans inactivates PQS via a pathway involving the incorporation of oxygen at C2 of the heterocyclic ring. The conversion of PQS to HHQD also occurred on incubation with 12/17 A. xylosoxidans strains recovered from cystic fibrosis patients, with P. aeruginosa and with Arthrobacter, suggesting that formation of hydroxylated PQS may be a common mechanism of inactivation.

Design, synthesis and biological evaluation of novel unsymmetrical azines as quorum sensing inhibitors

In this report, novel unsymmetrical azines have been designed and synthesised by using one pot approach. Further, they were evaluated as quorum sensing inhibitors.

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.

Metagenomic approaches to understanding phylogenetic diversity in quorum sensing

Quorum sensing, a form of cell-cell communication among bacteria, allows bacteria to synchronize their behaviors at the population level in order to control behaviors such as luminescence, biofilm formation, signal turnover, pigment production, antibiotics production, swarming, and virulence. A better understanding of quorum-sensing systems will provide us with greater insight into the complex interaction mechanisms used widely in the Bacteria and even the Archaea domain in the environment. Metagenomics, the use of culture-independent sequencing to study the genomic material of microorganisms, has the potential to provide direct information about the quorum-sensing systems in uncultured bacteria. This article provides an overview of the current knowledge of quorum sensing focused on phylogenetic diversity, and presents examples of studies that have used metagenomic techniques. Future technologies potentially related to quorum-sensing systems are also discussed.

AidC, a novel N-acylhomoserine lactonase from the potato root-associated cytophaga-flavobacteria-bacteroides (CFB) group bacterium Chryseobacterium sp. strain StRB126

N-acylhomoserine lactones (AHLs) are used as quorum-sensing (QS) signal molecules by many gram-negative bacteria. We have reported that Chryseobacterium sp. strain StRB126, which was isolated from the root surface of potato, has AHL-degrading activity. In this study, we cloned and characterized the aidC gene from the genomic library of StRB126. AidC has AHL-degrading activity and shows homology to several metallo-β-lactamase proteins from Bacteroidetes, although not to any known AHL-degrading enzymes. Purified AidC, as a maltose-binding fusion protein, showed high degrading activity against all tested AHLs, whether short- or long-chain forms, with or without substitution at carbon 3. High-performance liquid chromatography (HPLC) analysis revealed that AidC functions as an AHL lactonase catalyzing AHL ring opening by hydrolyzing lactones. An assay to determine the effects of covalent and ionic bonding showed that Zn(2+) is important to AidC activity both in vitro and in vivo. In addition, the aidC gene could also be PCR amplified from several other Chryseobacterium strains. In conclusion, this study indicated that the aidC gene, encoding a novel AHL lactonase, may be widespread throughout the genus Chryseobacterium. Our results extend the diversity and known bacterial hosts of AHL-degrading enzymes.

Quenching the quorum sensing system: potential antibacterial drug targets

Emergence of antibiotic and multi-drug resistant pathogenic bacteria has created the need for new drugs and drug targets. During pathogenesis bacteria release signals which regulate virulence and pathogenicity related genes. Such bacteria co-ordinate their virulent behaviour in a cell density dependent phenomenon termed as quorum sensing (QS). In contrast, microbes interfere with QS system by quenching the signals, termed quorum quenching (QQ). As a consequence of disrupted QS, pathogens become susceptible to antibiotics and drugs. In this article, the biodiversity of organisms with potential to quench QS signals and the use of QQ molecules as antibacterial drugs have been reviewed.

Complete genome sequence of the metabolically versatile plant growth-promoting endophyte Variovorax paradoxus S110

Variovorax paradoxus is a microorganism of special interest due to its diverse metabolic capabilities, including the biodegradation of both biogenic compounds and anthropogenic contaminants. V. paradoxus also engages in mutually beneficial interactions with both bacteria and plants. The complete genome sequence of V. paradoxus S110 is composed of 6,754,997 bp with 6,279 predicted protein-coding sequences within two circular chromosomes. Genomic analysis has revealed multiple metabolic features for autotrophic and heterotrophic lifestyles. These metabolic diversities enable independent survival, as well as a symbiotic lifestyle. Consequently, S110 appears to have evolved into a superbly adaptable microorganism that is able to survive in ever-changing environmental conditions. Based on our findings, we suggest V. paradoxus S110 as a potential candidate for agrobiotechnological applications, such as biofertilizer and biopesticide. Because it has many associations with other biota, it is also suited to serve as an additional model system for studies of microbe-plant and microbe-microbe interactions.

Rapid degradation of N-3-oxo-acylhomoserine lactones by a Bacillus cereus isolate from Malaysian rainforest soil

A bacterial strain, KM1S, was isolated from a Malaysian rainforest soil sample by using a defined enrichment medium that specifically facilitates selection of quorum quenching bacteria. KM1S was clustered closely to Bacillus cereus by 16S ribosomal DNA sequence analysis. It degraded N-3-oxo-hexanoyl homoserine lactone and N-3-oxo-octanoyl homoserine lactone in vitro rapidly at 4.98 and 6.56 microg AHL h(-1) per 10(9) CFU/ml, respectively, as determined by the Rapid Resolution Liquid Chromatography. The aiiA homologue, encoding an autoinducer inactivation enzyme catalyzing the degradation of N-acylhomoserine lactones, of KM1S was amplified and cloned. Sequence analysis indicated the presence of the motif (106)HXDH-59 amino acids-H(169)-21 amino acids-D(191) for N-acylhomoserine lactone lactonases.

A synthetic genetic edge detection program

Edge detection is a signal processing algorithm common in artificial intelligence and image recognition programs. We have constructed a genetically encoded edge detection algorithm that programs an isogenic community of E. coli to sense an image of light, communicate to identify the light-dark edges, and visually present the result of the computation. The algorithm is implemented using multiple genetic circuits. An engineered light sensor enables cells to distinguish between light and dark regions. In the dark, cells produce a diffusible chemical signal that diffuses into light regions. Genetic logic gates are used so that only cells that sense light and the diffusible signal produce a positive output. A mathematical model constructed from first principles and parameterized with experimental measurements of the component circuits predicts the performance of the complete program. Quantitatively accurate models will facilitate the engineering of more complex biological behaviors and inform bottom-up studies of natural genetic regulatory networks.

Membrane bioreactor treatment of a simulated metalworking fluid wastewater containing ethylenediaminetetraacetic acid and dicyclohexylamine

Membrane bioreactors (MBRs) have been installed at automotive plants to treat metalworking fluid (MWF) wastewaters, which are known to contain toxic and/or recalcitrant organic compounds. A laboratory study was conducted to evaluate treatment of a simulated wastewater prepared from a semisynthetic MWF, which contains two such compounds, dicyclohexylamine (DCHA) and ethylenediaminetetraacetic acid (EDTA). Primary findings were as follows: During stable operating periods, almost all chemical oxygen demand (COD), total Kjeldahl nitrogen (TKN), and EDTA were removed (by > 96%). During somewhat unstable periods, COD removal was still extremely robust, but removal of EDTA and TKN were sensitive to prolonged episodes of low dissolved oxygen. Nitrogen mass balance suggested 30 to 40% TKN removal by assimilation and 60 to 70% by nitrification (including up to 34% TKN removal via subsequent denitrification). Dicyclohexylamine appeared to be readily biodegraded. Maximum DCHA and EDTA degradation rates between pH 7 and 8 were found. An Arthrobacter sp. capable of growth on DCHA as the sole source of carbon and energy was isolated.

Mini-review: quorum sensing in the marine environment and its relationship to biofouling

Bacterial quorum sensing (QS) is a cell-cell communication and gene regulatory mechanism that allows bacteria to coordinate swarming, biofilm formation, stress resistance, and production of toxins and secondary metabolites in response to threshold concentrations of QS signals that accumulate within a diffusion-limited environment. This review focuses on the role of QS signaling and QS inhibition in marine bacteria by compounds derived from marine organisms. Since the formation of a biofilm is considered to be an initial step in the development of fouling, direct and indirect effects of QS signals and inhibitors on the process of marine biofouling are discussed. Directions for future investigations and QS-related biotechnological applications are highlighted.

Two dissimilar N-acyl-homoserine lactone acylases of Pseudomonas syringae influence colony and biofilm morphology

Plant aerial surfaces comprise a complex habitat for microorganisms, and many plant-associated bacteria, such as the pathogen Pseudomonas syringae, exhibit density-dependent survival on leaves by utilizing quorum sensing (QS). QS is often mediated by diffusible signals called N-acyl-homoserine lactones (AHLs), and P. syringae utilizes N-3-oxo-hexanoyl-dl-homoserine lactone (3OC6HSL) to control traits influencing epiphytic fitness and virulence. The P. syringae pathovar syringae B728a genome sequence revealed two putative AHL acylases, termed HacA (Psyr_1971) and HacB (Psyr_4858), which are N-terminal nucleophile hydrolases that inactivate AHLs by cleaving their amide bonds. HacA is a secreted AHL acylase that degrades only long-chain (C > or = 8) AHLs, while HacB is not secreted and degrades all tested AHLs. Targeted disruptions of hacA, hacB, and hacA and hacB together do not alter endogenous 3OC6HSL levels under the tested conditions. Surprisingly, targeted disruptions of hacA alone and hacA and hacB together confer complementable phenotypes that are very similar to autoaggregative phenotypes seen in other species. While AHL acylases might enable P. syringae B728a to degrade signals of competing species and block expression of their QS-dependent traits, these enzymes also play fundamental roles in biofilm formation.

Rhizosphere Bacterial Signalling: A Love Parade Beneath Our Feet

Plant roots support the growth and activities of a wide variety of microorganisms that may have a profound effect on the growth and/or health of plants. Among these microorganisms, a high diversity of bacteria have been identified and categorized as deleterious, beneficial, or neutral with respect to the plant. The beneficial bacteria, termed plant growth-promoting rhizobacteria (PGPR), are widely studied by microbiologists and agronomists because of their potential in plant production. Azospirillum, a genus of versatile PGPR, is able to enhance the plant growth and yield of a wide range of economically important crops in different soils and climatic regions. Plant beneficial effects of Azospirillum have mainly been attributed to the production of phytohormones, nitrate reduction, and nitrogen fixation, which have been subject of extensive research throughout the years. These elaborate studies made Azospirillum one of the best-characterized genera of PGPR. However, the genetic and molecular determinants involved in the initial interaction between Azospirillum and plant roots are not yet fully understood. This review will mainly highlight the current knowledge on Azospirillum plant root interactions, in the context of preceding and ongoing research on the association between plants and plant growth-promoting rhizobacteria.

Purification and characterization of a novel esterase (beta-hydroxypalmitate methyl ester hydrolase) and prevention of the expression of virulence by Ralstonia solanacearum

AIMS

To screen novel micro-organisms and enzymes capable of degrading 3-hydroxypalmitic acid methyl ester (3-OH PAME), the quorum-sensing signal molecule (quormone), which regulates the virulence of Ralstonia solanacearum.

METHODS AND RESULTS

Ideonella sp. 0-0013, a betaproteobacterium isolated from soil using the selective-enrichment culture method, was grown on plates containing 3-OH PAME as its main carbon source. beta-Hydroxypalmitate methyl ester hydrolase (betaHPMEH) purified from the supernatant of the Ideonella sp. 0-0013 culture exhibited high hydrolysing activity towards the ester bond of 3-OH PAME and eliminated the 3-OH PAME activity, thereby reducing the virulence of R. solanacearum. An Escherichia coli transformant of the betahpmeh gene expression vector degraded 3-OH PAME, and the crude enzyme from the transformant inhibited in vitro production of the R. solanacearum exopolysaccharide (EPS).

CONCLUSIONS

The ability of betaHPMEH to hydrolyse 3-OH PAME inhibited the production of EPS by the R. solanacearum wild-type strain, indicating that betaHPMEH inhibits the effects of activation of virulence genes. This ability will be potentially useful for pest control of the wilt disease caused by this bacterium.

SIGNIFICANCE AND IMPACT OF THE STUDY

This enzyme is the first protein that has been found to degrade a quormone other than N-acyl homoserine lactone.

Growth promotion of quorum-quenching bacteria in the rhizosphere of Solanum tuberosum

Among 17 molecules structurally related to N-acylhomoserine lactone (NAHL), gamma-caprolactone (GCL), 6-caprolactone (6CL) and 4-heptanolide (HTN) were found to stimulate the degradation of NAHL by bacterial communities recovered from bulk and rhizospheric soils. In the 6CL-, GCL- and HTN-treated bacterial consortia, the NAHL-degrading bacteria were more abundant than in control (mannitol-treated) consortia. Moreover, the GCL- and HTN-consortia showed a biocontrol activity against Pectobacterium atrosepticum in soft rot assays with tubers of Solanum tuberosum. When GCL was applied to hydroponic cultures of S. tuberosum, a significant increase of the ratio of NAHL-degrading bacteria among total cultivable bacteria was observed in several independent experiments. Most of these bacteria, the growth of which was stimulated by GCL amendment, were also able to use GCL as a sole carbon source. They belong to the Rhodococcus and Delftia genera. DGGE analysis revealed that GCL treatments affected the structure of bacterial communities. This work highlights the possibility to manage the NAHL-degrading bacteria in a complex environment such as rhizosphere.

Detection and characterization of bacteria from the potato rhizosphere degrading N-acyl-homoserine lactone

Quorum sensing plays a role in the regulation of soft rot diseases caused by the plant pathogenic bacterium Pectobacterium carotovorum subsp. carotovorum. The signal molecules involved in quorum sensing in P. carotovorum subsp. carotovorum belong to the group of N-acyl homoserine lactones (AHLs). In our study, we screened bacteria isolated from the potato rhizosphere for the ability to degrade AHLs produced by P. carotovorum subsp. carotovorum. Six isolates able to degrade AHLs were selected for further studies. According to 16S rDNA sequence analysis and fatty acid methyl ester profiling, the isolates belonged to the genera Ochrobactrum, Rhodococcus, Pseudomonas, Bacillus, and Delftia. For the genera Ochrobactrum and Delftia, for the first time AHL-degrading isolates were found. Data presented in this study revealed for the first time that Ochrobactrum sp. strain A44 showed the capacity to inactivate various synthetic AHL molecules; the substituted AHLs were inactivated with a lower efficiency than the unsubstituted AHLs. Compared with the other isolates, A44 was very effective in the degradation of AHLs produced by P. carotovorum subsp. carotovorum. It was verified by polymerase chain reaction, DNA-DNA hybridization, and a lactone ring reconstruction assay that Ochrobactrum sp. strain A44 did not possess AHL lactonase activity. AHL degradation in Ochrobactrum sp. strain A44 occurred intracellularly; it was not found in the culture supernatant. AHL-degrading activity of A44 was thermo sensitive. Experiments in planta revealed that Ochrobactrum sp. strain A44 significantly inhibited the maceration of potato tuber tissue. Since A44 did not produce antibiotics, the attenuation of the decay might be due to the quenching of quorum- sensing-regulated production of pectinolytic enzymes. The strain can potentially serve to control P. carotovorum subsp. carotovorum in potato.

Beyond quorum sensing: the complexities of prokaryotic parliamentary procedures

Bacterial quorum-sensing regulatory systems can be summarized in a simple model wherein an autoinducer molecule accumulates in cultures and stimulates regulatory changes in gene expression upon reaching a critical threshold concentration. Although quorum sensing was originally thought to be an isolated phenomenon governing the regulation of a handful of processes in only a few bacteria, it is now considered to be a widespread mechanism for coordinating bacterial gene expression. Over decades of research, investigations of autoinducer-mediated regulation have revealed that these systems are far more complicated than originally appreciated, and such discoveries have accelerated recently with the application of molecular and genomic tools. The focus of this review is to highlight recent advances describing complexities that go beyond the simple model of quorum sensing. These complexities include the regulation of autoinducer production and degradation, the presence of multiple quorum-sensing systems in individual bacteria that regulate diverse genes, often in coordination with other regulatory elements, and the influence of interorganismal interactions on quorum sensing.

Nocardioides kongjuensis sp. nov., an N-acylhomoserine lactone-degrading bacterium

A Gram-positive, rod- or coccoid-shaped andN-hexanoyl-l-homoserine lactone-degrading bacterial strain, A2-4T, was isolated from a soil in Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain A2-4Tgrew optimally at pH 7.0–8.0 and 30 °C without NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain A2-4Tis most closely related to members of the genusNocardioides. Strain A2-4Tpossessed chemotaxonomic properties indicative of members of the genusNocardioides; the cell-wall peptidoglycan type was based onll-diaminopimelic acid, MK-8(H4) was the predominant menaquinone and iso-C16 : 0was the predominant fatty acid. The DNA G+C content was 72.1 mol%. The 16S rRNA gene sequence of strain A2-4Twas 98.3–99.1 % similar to those of the type strains ofNocardioides simplex,Nocardioides aromaticivoransandNocardioides nitrophenolicusand 93.8–96.3 % similar to those of the type strains of otherNocardioidesspecies. Strain A2-4Tcould be distinguished from the three phylogenetic relatives,N. nitrophenolicus,N. aromaticivoransandN. simplex, by DNA–DNA relatedness (25–42 %) and by differences in some phenotypic characteristics. On the basis of the phenotypic, phylogenetic and genetic data, the strain represents a novel species of the genusNocardioides, for which the nameNocardioides kongjuensissp. nov. is proposed. The type strain is A2-4T(=KCTC 19054T=JCM 12609T).

Utilization of capsaicin and vanillylamine as growth substrates by Capsicum (hot pepper)-associated bacteria

Capsaicin contributes to the organoleptic attributes of hot peppers. Here, we show that capsaicin is utilized as a growth nutrient by certain bacteria. Enrichment cultures utilizing capsaicin were successfully initiated using Capsicum-derived plant material or leaves of tomato (a related Solanaceae) as inocula. No other sources of inoculum examined yielded positive enrichments. Of 25 isolates obtained from enrichments: all utilized 8-methylnonanoic acid; nine were found capable of degrading capsaicin as sole carbon and energy source; 11 were found capable of utilizing vanillylamine; but only two strains could use either of these latter two compounds as sole nitrogen source. Phylogenetic analysis of capsaicin degraders revealed them to be strains of Variovorax and Ralstonia, whereas the vanillylamine degraders were strains of Pseudomonas and Variovorax. Neither of the two strains isolated from one enrichment culture originally inoculated with dried pepper fruit was capable of using capsaicin as sole carbon and nitrogen source. However, good growth was achieved under such conditions when the two isolates, a strain of Variovorax paradoxusThat degraded capsaicin when provided with ammonium, and a vanillylamine degrading strain of Pseudomonas putida, were cultured together. A cross-feeding of capsaicin-derived carbon and nitrogen between members of pepper-associated consortia is proposed.

Identification of QuiP, the product of gene PA1032, as the second acyl-homoserine lactone acylase of Pseudomonas aeruginosa PAO1

The relevance of the acyl homoserine lactone (acyl-HSL) quorum signals N-3-oxododecanoyl-homoserine lactone (3OC12HSL) and N-butanoyl-homoserine lactone to the biology and virulence of Pseudomonas aeruginosa is well investigated. Previously, P. aeruginosa was shown to degrade long-chain, but not short-chain, acyl-HSLs as sole carbon and energy sources (J. J. Huang, J.-I. Han, L.-H. Zhang, and J. R. Leadbetter, Appl. Environ. Microbiol. 69:5941-5949, 2003). A gene encoding an enzyme with acyl-HSL acylase activity, pvdQ (PA2385), was identified, but it was not required for acyl-HSL utilization. This indicated that P. aeruginosa encodes another acyl-HSL acylase, which we identify here. A comparison of total cell proteins of cultures grown with long-acyl acyl-HSLs versus other substrates implicated the involvement of a homolog of PvdQ, the product of gene PA1032, for which we propose the name QuiP. Transposon mutants of quiP were defective for growth when P. aeruginosa was cultured in medium containing decanoyl-HSL as a sole carbon and energy source. Complementation with a functional copy of quiP rescued this growth defect. When P. aeruginosa was grown in buffered lysogeny broth, constitutive expression of QuiP in P. aeruginosa led to decreased accumulations of the quorum signal 3OC12HSL, relative to the wild type. Heterologous expression of QuiP was sufficient to confer long-chain acyl-HSL acylase activity upon Escherichia coli. Examination of gene expression patterns during acyl-HSL-dependent growth of P. aeruginosa further supported the involvement of quiP in signal decay and revealed other genes also possibly involved. It is not yet known under which "natural" conditions quiP is expressed or how P. aeruginosa balances the expression of its quorum-sensing systems with the expression of its acyl-HSL acylase activities.

Utilization of homoserine lactone as a sole source of carbon and energy by soil Arthrobacter and Burkholderia species

Homoserine lactone (HSL) is a ubiquitous product of metabolism. It is generated by all known biota during the editing of certain mischarged aminoacyl-tRNA reactions, and is also released as a product of quorum signal degradation by bacterial species expressing acyl-HSL acylases. Little is known about its environmental fate over long or short periods of time. The mammalian enzyme paraoxonase, which has no known homologs in bacteria, has been reported to degrade HSL via a lactonase mechanism. Certain strains of Variovorax and Arthrobacter utilize HSL as a sole source of nitrogen, but not as a sole source of carbon or energy. In this study, the enrichment and isolation of four strains of soil bacteria capable of utilizing HSL as a carbon and energy source are described. Phylogenetic analysis of these isolates indicates that three are distinct members of the genus Arthrobacter, whereas the fourth clusters within the non-clinical Burkholderia. The optimal pH for growth of the isolates ranged from 6.0 to 6.5, at which their HSL-dependent doubling times ranged from 1.4 to 4 h. The biodegradation of HSL by these 4 isolates far outpaced its chemical decay. HSL degradation by soil bacteria has implications for the consortial mineralization of acyl-homoserine lactones by bacteria associated with quorum sensing populations.

Production of acylated homoserine lactones byAeromonasandPseudomonasstrains isolated from municipal activated sludge

Up to now, the production and role of N-acyl homoserine lactones (AHLs) in activated sludge have been poorly understood. In this study, cross-feeding assays with the reporter strains Agrobacterium tumefaciens NTL4 and Chromobacterium violaceum CV026 were used to investigate AHL signal production by municipal activated sludge samples. AHL signal production was consistently detected from municipal activated sludge when different samples were incubated on nutrient media. From one municipal activated sludge sample, 10 strains producing AHL-like auto inducers were isolated by an overlay technique. 16S rDNA-based phylogenetic analysis showed that eight of the isolates belonged to Aeromonas spp. and two to Pseudomonas spp. Box-PCR indicated that six of these Aeromonas isolates were different strains and the two Pseudomonas strains were identical. The production of AHL or AHL-like compounds by these strains was confirmed by thin layer chromatography and biosensor overlays. The six different Aeromonas strains were found to produce the same set of AHLs, including N-hexanoyl-L-homoserine lactone. These results may indicate the possible presence of AHLs in municipal activated sludge. The potential roles of AHL in this eco system are briefly discussed.Key words: municipal activated sludge, acylated homoserine lactones, Aeromonas spp., bioaggregates, Pseudomonas spp., AHL biosensors.

Diversity of N-acyl homoserine lactone-producing and -degrading bacteria in soil and tobacco rhizosphere

In Gram-negative bacteria, quorum-sensing (QS) communication is mostly mediated by N-acyl homoserine lactones (N-AHSL). The diversity of bacterial populations that produce or inactivate the N-AHSL signal in soil and tobacco rhizosphere was investigated by restriction fragment length polymorphism (RFLP) analysis of amplified 16S DNA and DNA sequencing. Such analysis indicated the occurrence of N-AHSL-producing strains among the alpha-, beta- and gamma-proteobacteria, including genera known to produce N-AHSL (Rhizobium, Sinorhizobium and Pseudomonas) and novel genera with no previously identified N-AHSL-producing isolates (Variovorax, Sphingomonas and Massilia). The diversity of N-AHSL signals was also investigated in relation to the genetic diversity of the isolates. However, N-AHSL-degrading strains isolated from soil samples belonged to the Bacillus genus, while strains isolated from tobacco rhizospheres belonged to both the Bacillus genus and to the alpha subgroup of proteobacteria, suggesting that diversity of N-AHSL-degrading strains may be modulated by the presence of the tobacco plant. Among these rhizospheric isolates, novel N-AHSL-degrading genera have been identified (Sphingomonas and Bosea). As the first simultaneous analysis of both N-AHSL-degrading and -producing bacterial communities in a complex environment, this study revealed the coexistence of bacterial isolates, belonging to the same genus or species that may produce or degrade N-AHSL.

Identification of large linear plasmids in Arthrobacter spp. encoding the degradation of quinaldine to anthranilate

Arthrobacter nitroguajacolicus Rü61a, which utilizes quinaldine as sole source of carbon and energy, was shown to contain a conjugative linear plasmid of approximately 110 kb, named pAL1. It exhibits similarities with other linear plasmids from Actinomycetales in that it has proteins covalently attached to its 5' ends. Southern hybridization with probes for the genes encoding quinaldine 4-oxidase and N-acetylanthranilate amidase indicated that pAL1 contains the gene cluster encoding the degradation of quinaldine to anthranilate. A mutant of strain Rü61a that had lost pAL1 indeed could not convert quinaldine, but was still able to grow on anthranilate. Conjugative transfer of pAL1 to the plasmid-less mutant of strain Rü61a and to Arthrobacter nicotinovorans DSM 420 (pAO1) occurred at frequencies of 5.4x10(-4) and 2.0x10(-4) per recipient, respectively, and conferred the ability to utilize quinaldine. Five other quinaldine-degrading Gram-positive strains were isolated from soil samples; 16S rDNA sequence analysis suggested the closest relationship to different Arthrobacter species. Except for strain K2-29, all isolates contained a pAL1-like linear plasmid carrying genes encoding quinaldine conversion. A 478 bp fragment that on pAL1 represents an intergenic region showed 100 % sequence identity in all isolates harbouring a pAL1-like plasmid, suggesting horizontal dissemination of the linear plasmid among the genus Arthrobacter.

Rapid acyl-homoserine lactone quorum signal biodegradation in diverse soils

Signal degradation impacts all communications. Although acyl-homoserine lactone (acyl-HSL) quorum-sensing signals are known to be degraded by defined laboratory cultures, little is known about their stability in nature. Here, we show that acyl-HSLs are biodegraded in soils sampled from diverse U.S. sites and by termite hindgut contents. When amended to samples at physiologically relevant concentrations, 14C-labeled acyl-HSLs were mineralized to 14CO2 rapidly and, at most sites examined, without lag. A lag-free turf soil activity was characterized in further detail. Heating or irradiation of the soil prior to the addition of radiolabel abolished mineralization, whereas protein synthesis inhibitors did not. Mineralization exhibited an apparent Km of 1.5 microM acyl-HSL, ca. 1,000-fold lower than that reported for a purified acyl-HSL lactonase. Under optimal conditions, acyl-HSL degradation proceeded at a rate of 13.4 nmol x h(-1) x g of fresh weight soil(-1). Bioassays established that the final extent of signal inactivation was greater than for its full conversion to CO2 but that the two processes were well coupled kinetically. A most probable number of 4.6 x 10(5) cells . g of turf soil(-1) degraded physiologically relevant amounts of hexanoyl-[1-14C]HSL to 14CO2. It would take chemical lactonolysis months to match the level of signal decay achieved in days by the observed biological activity. Rapid decay might serve either to quiet signal cross talk that might otherwise occur between spatially separated microbial aggregates or as a full system reset. Depending on the context, biological signal decay might either promote or complicate cellular communications and the accuracy of population density-based controls on gene expression in species-rich ecosystems.

Bacterial populations in the rhizosphere of tobacco plants producing the quorum-sensing signals hexanoyl-homoserine lactone and 3-oxo-hexanoyl-homoserine lactone

A tobacco line genetically modified to produce two N-acyl homoserine lactones and its non-transformed parental line were grown in non-sterile soil. Microbial populations inhabiting the bulk soil, and those colonizing the root system of the two tobacco lines, were analyzed using cultivation-independent (phospholipid fatty acid and denaturing gradient gel electrophoresis) and cultivation-based assays. The cell density of total cultivable bacteria, fluorescent pseudomonads, sporulated, and thermotolerant bacteria was also determined in a time-course experiment (15 weeks). A possible "rhizosphere effect" related to the development of the plant was seen. However, no dissimilarities in cell population densities or population ratios of the microbial groups were detected in the rhizosphere of the two plant lines. Similarly, bacterial communities that either produced N-acyl homoserine lactone or degraded the signal hexanoyl homoserine lactone were enumerated from the two plant lines. No noticeable differences were evidenced from one plant genotype to the other. Whilst the transgenic plants released detectable amounts of the quorum-sensing signal molecules and efficiently cross-talked with the surrounding microbial populations, the bias generated by these signals in the reported experimental conditions therefore appears to remain weak, if not non-existent.

Communications blackout? Do N-acylhomoserine-lactone-degrading enzymes have any role in quorum sensing?

A number of bacteria, including some significant pathogens, utilize N-acylhomoserine lactones (AHLs) as quorum sensing signals. There is considerable interest in the therapeutic potential of disrupting quorum sensing. Recently, a number of bacteria have been identified which are capable of enzymic inactivation of AHLs. These enzymes show considerable promise as ‘quenchers' of quorum sensing. However, the assumption that the natural function of these enzymes is to disrupt or modulate quorum sensing has yet to be established. This review surveys the progress made to date in this field and examines what implications these findings have for our understanding of the role played by these enzymes in vivo.

Fast screening method for detection of acyl-HSL-degrading soil isolates

A reliable method was developed for screening of bacteria isolates capable of degrading acyl-HSLs, the signal molecules in quorum-sensing-mediated processes of many Proteobacteria. The microtiter assay was based on the use of a GFP-marked Escherichia coli strain, which fluoresces upon the presence of acyl-HSLs. Measurement of GFP fluorescence with a Molecular Imager FX scanner (fluorometer) detected isolates capable of degrading acyl-HSLs. The potential of this method was demonstrated by isolation of different bacteria from a potato rhizosphere able to inactivate synthetic and natural acyl HSLs produced by Pectobacterium carotovorum subsp. carotovorum (Pcc) (Erwinia carotovora subsp. carotovora (Ecc)).

Quorum sensing and swarming migration in bacteria

Bacterial cells can produce and sense signal molecules, allowing the whole population to initiate a concerted action once a critical concentration (corresponding to a particular population density) of the signal has been reached, a phenomenon known as quorum sensing. One of the possible quorum sensing-regulated phenotypes is swarming, a flagella-driven movement of differentiated swarmer cells (hyperflagellated, elongated, multinucleated) by which bacteria can spread as a biofilm over a surface. The glycolipid or lipopeptide biosurfactants thereby produced function as wetting agent by reducing the surface tension. Quorum sensing systems are almost always integrated into other regulatory circuits. This effectively expands the range of environmental signals that influence target gene expression beyond population density. In this review, we first discuss the regulation of AHL-mediated surface migration and the involvement of other low-molecular-mass signal molecules (such as the furanosyl borate diester AI-2) in biosurfactant production of different bacteria. In addition, population density-dependent regulation of swarmer cell differentiation is reviewed. Also, several examples of interspecies signalling are reported. Different signal molecules either produced by bacteria (such as other AHLs and diketopiperazines) or excreted by plants (such as furanones, plant signal mimics) might influence the quorum sensing-regulated swarming behaviour in bacteria different from the producer. On the other hand, specific bacteria can reduce the local available concentration of signal molecules produced by others. In the last part, the role and regulation of a surface-associated movement in biofilm formation is discussed. Here we also describe how quorum sensing may disperse existing biofilms and control the interaction between bacteria and higher organisms (such as the Rhizobium-bean symbiosis).