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

Molecular Mechanisms of Bacterial Communication and Their Biocontrol

A bacterium's ability to colonize and adapt to an ecological niche is highly dependent on its capacity to perceive and analyze its environment and its ability to interact with its hosts and congeners [...].

Rhizopine biosensors for plant-dependent control of bacterial gene expression

Engineering signalling between plants and microbes could be exploited to establish host-specificity between plant-growth-promoting bacteria and target crops in the environment. We previously engineered rhizopine-signalling circuitry facilitating exclusive signalling between rhizopine-producing (RhiP) plants and model bacterial strains. Here, we conduct an in-depth analysis of rhizopine-inducible expression in bacteria. We characterize two rhizopine-inducible promoters and explore the bacterial host-range of rhizopine biosensor plasmids. By tuning the expression of rhizopine uptake genes, we also construct a new biosensor plasmid pSIR05 that has minimal impact on host cell growth in vitro and exhibits markedly improved stability of expression in situ on RhiP barley roots compared to the previously described biosensor plasmid pSIR02. We demonstrate that a sub-population of Azorhizobium caulinodans cells carrying pSIR05 can sense rhizopine and activate gene expression when colonizing RhiP barley roots. However, these bacteria were mildly defective for colonization of RhiP barley roots compared to the wild-type parent strain. This work provides advancement towards establishing more robust plant-dependent control of bacterial gene expression and highlights the key challenges remaining to achieve this goal.

Microbial mechanism of zinc fertilizer input on rice grain yield and zinc content of polished rice

Zinc is an essential minor element for rice growth and human health, which can also change the structure of the microorganisms. However, it remains unclear for the effects of zinc fertilizer on microbiome function in agricultural soils and crops. To solve this research gap, we investigated the relationship between improving rice (Oryza sativa L.) yield, Zn concentration, soil microbial community diversity, and function by the application of Zn fertilizer. The field trials included three rice varieties (Huanghuazhan, Nanjing9108, and Nuodao-9925) and two soil Zn levels (0 and 30 kg ha^-1) in Jiangsu province, China. As a test, we studied the variety of soil bacterial composition, diversity, and function using 16S rRNA gene sequencing. The results showed that soil Zn application reduced the diversity of microbial community, but the bacterial network was more closely linked, and the metabolic function of bacterial community was improved, which increased the grain yield (17.34-19.52%) and enriched the Zn content of polished rice (1.40-20.05%). Specifically, redundancy analysis (RDA) and Mantel's test results revealed soil total nitrogen (TN) was the primary driver that led to a community shift in the rice rhizosphere bacterial community, and soil organic carbon (SOC) was considered to have a strong influence on dominant phyla. Furthermore, network analysis indicated the most critical bacterial taxa were identified as Actinobacteria, Bacteroidetes, Proteobacteria, and Chloroflexi based on their topological roles of microorganisms. KEGG metabolic pathway prediction demonstrated that soil Zn application significantly (p < 0.05) improved lipid metabolism, amino acid metabolism, carbohydrate metabolism, and xenobiotic biodegradation. Overall, their positive effects were different among rice varieties, of which Nanjing-9108 (NJ9108) performed better. This study opens new avenues to deeply understand the plant and soil-microbe interactions by the application of fertilizer and further navigates the development of Zn-rich rice cultivation strategies.

Microbial Metabolites Beneficial to Plant Hosts Across Ecosystems

Plants are intimately connected with their associated microorganisms. Chemical interactions via natural products between plants and their microbial symbionts form an important aspect in host health and development, both in aquatic and terrestrial ecosystems. These interactions range from negative to beneficial for microbial symbionts as well as their hosts. Symbiotic microbes synchronize their metabolism with their hosts, thus suggesting a possible coevolution among them. Metabolites, synthesized from plants and microbes due to their association and coaction, supplement the already present metabolites, thus promoting plant growth, maintaining physiological status, and countering various biotic and abiotic stress factors. However, environmental changes, such as pollution and temperature variations, as well as anthropogenic-induced monoculture settings, have a significant influence on plant-associated microbial community and its interaction with the host. In this review, we put the prominent microbial metabolites participating in plant-microbe interactions in the natural terrestrial and aquatic ecosystems in a single perspective and have discussed commonalities and differences in these interactions for adaptation to surrounding environment and how environmental changes can alter the same. We also present the status and further possibilities of employing chemical interactions for environment remediation. Our review thus underlines the importance of ecosystem-driven functional adaptations of plant-microbe interactions in natural and anthropogenically influenced ecosystems and their possible applications.

Detection of Diverse N-Acyl Homoserine Lactone Signalling Molecules Among Bacteria Associated with Rice Rhizosphere

Bacterial communities communicate, regulate and coordinate their cooperative activities and physiological process by releasing, sensing and responding to small diffusible signal molecules such as acyl homoserine lactones (AHLs), auto-inducing oligo-peptides (AIPs) and autoinducer-2, a process referred to as Quorum sensing (QS). The QS mediated communication in rhizosphere associated bacterial communities significantly influence traits governing plant-microbe interactions. This study aimed to identify AHL-mediated QS signals in bacterial communities associated with rice rhizosphere using two AHL biosensors reporter strains Chromobacterium violaceum CV026 and Agrobacterium tumefaciens NTL4 (pZLR4). Approximately 375 bacterial isolates isolated from rice rhizosphere and screened using both the biosensors, detected 49 (13%) AHL positive isolates. The BOX-Polymerase Chain reaction (BOX-PCR) fingerprinting profiles of the 49 AHL positive isolates represented 11 distinct cluster groups. Subsequent 16S rRNA gene sequence analysis identified 11 different species affiliated to two different phyla; predominantly γ-proteobacteria, representing 5 genera and 1 genus in α-proteobacteria. Thin-layer chromatography (TLC) analysis detected diverse AHL profiles among the 11 AHL positive isolates with both substituted and unsubstituted acyl side chains of C4, C6 and C8 carbon. Further, AHL production in Acinetobacter lactucae, Aeromonas popoffii, Serratia oryzae, and Rhizobium wuzhouense is being reported for the first time. Detection of diverse AHLs from different groups of rhizobacteria associated with rice indicates that these signalling molecules may be involved in the regulation of rhizobacterial behaviour and symbiotic plant-microbe interactions. Future research on the role of AHLs in trans-kingdom communication particularly plant-microbe interaction using synthetic microbial community will enable in evaluating and developing potential plant specific bioproducts.

Quorum sensing in rhizobia isolated from the spores of the mycorrhizal symbiont Rhizophagus intraradices

Most beneficial services provided by arbuscular mycorrhizal fungi (AMF), encompassing improved crop performance and soil resource availability, are mediated by AMF-associated bacteria, showing key-plant growth-promoting (PGP) traits, i.e., the production of indole acetic acid, siderophores and antibiotics, and activities increasing the availability of plant nutrients by nitrogen fixation and phosphate mobilization. Such functions may be affected by the ability of AMF-associated bacteria to communicate through the production and secretion of extracellular small diffusible chemical signals, N-acyl homoserine lactone signal molecules (AHLs), that regulate bacterial behavior at the community level (quorum sensing, QS). This work investigated the occurrence and extent of QS among rhizobia isolated from AMF spores, using two different QS reporter strains, Agrobacterium tumefaciens NTL4 pZRL4 and Chromobacterium violaceum CV026. We also assessed the quorum quenching (QQ) activity among Bacillus isolated from the same AMF spores. Most rhizobia were found to be quorum-signaling positive, including six isolates producing very high levels of AHLs. The results were confirmed by microtiter plate assay, which detected 65% of the tested bacteria as medium/high AHL producers. A 16S rDNA sequence analysis grouped the rhizobia into two clusters, consistent with the QS phenotype. None of the tested bacteria showed QQ activity able to disrupt the QS signaling, suggesting the absence of antagonism among bacteria living in AMF sporosphere. Our results provide the first evidence of the ability of AMF-associated rhizobia to communicate through QS, suggesting further studies on the potential importance of such a behavior in association with key-plant growth-promoting functions.

Silencing the mob: disrupting quorum sensing as a means to fight plant disease

Bacteria are able to sense their population's density through a cell-cell communication system, termed 'quorum sensing' (QS). This system regulates gene expression in response to cell density through the constant production and detection of signalling molecules. These molecules commonly act as auto-inducers through the up-regulation of their own synthesis. Many pathogenic bacteria, including those of plants, rely on this communication system for infection of their hosts. The finding that the countering of QS-disrupting mechanisms exists in many prokaryotic and eukaryotic organisms offers a promising novel method to fight disease. During the last decade, several approaches have been proposed to disrupt QS pathways of phytopathogens, and hence to reduce their virulence. Such studies have had varied success in vivo, but most lend promising support to the idea that QS manipulation could be a potentially effective method to reduce bacterial-mediated plant disease. This review discusses the various QS-disrupting mechanisms found in both bacteria and plants, as well as the different approaches applied artificially to interfere with QS pathways and thus protect plant health.

Genome Sequence of the Quorum-Quenching Agrobacterium tumefaciens Strain WRT31

Agrobacterium tumefaciens strain WRT31 is a quorum-sensing signal-degrading bacterium that has been isolated from the rhizosphere of tobacco plants. This strain belongs to A. tumefaciens genomovar G1, is avirulent on various putative host plants, devoid of Ti plasmid, and contains the blcC gene encoding a gamma-butyrolactonase.

A metagenomic study highlights phylogenetic proximity of quorum-quenching and xenobiotic-degrading amidases of the AS-family

Quorum-sensing (QS) signals of the N-acylhomoserine lactone (NAHL) class are cleaved by quorum-quenching enzymes, collectively named NAHLases. Here, functional metagenomics allowed the discovery of a novel bacterial NAHLase in a rhizosphere that was treated with γ-caprolactone. As revealed by rrs-DGGE and rrs-pyrosequencing, this treatment increased the percentage of the NAHL-degrading bacteria and strongly biased the structure of the bacterial community, among which Azospirillum dominated. Among the 29 760 fosmids of the metagenomic library, a single one was detected that expressed the qsdB gene conferring NAHL-degradation upon E. coli and decreased QS-regulated virulence in Pectobacterium. Phylogenetic analysis of the 34 orfs of the fosmid suggested that it would belong to an unknown Proteobacterium - probably a γ-proteobacterium. qPCR quantification of the NAHLase-encoding genes attM, qsdA, and qsdB revealed their higher abundance in the γ-caprolactone-treated rhizosphere as compared to an untreated control. The purified QsdB enzyme exhibited amidase activity. QsdB is the first amidase signature (AS) family member exhibiting NAHLase-activity. Point mutations in the AS-family catalytic triad K-S-S abolished the NAHLase activity of QsdB. This study extends the diversity of NAHLases and highlights a common phylogenic origin of AS-family enzymes involved in the degradation of natural compounds, such as NAHLs, and xenobiotics, such as nylon and linuron.

Efficient biostimulation of native and introduced quorum-quenching Rhodococcus erythropolis populations is revealed by a combination of analytical chemistry, microbiology, and pyrosequencing

Degradation of the quorum-sensing (QS) signals known as N-acylhomoserine lactones (AHL) by soil bacteria may be useful as a beneficial trait for protecting crops, such as potato plants, against the worldwide pathogen Pectobacterium. In this work, analytical chemistry and microbial and molecular approaches were combined to explore and compare biostimulation of native and introduced AHL-degrading Rhodococcus erythropolis populations in the rhizosphere of potato plants cultivated in farm greenhouses under hydroponic conditions. We first identified gamma-heptalactone (GHL) as a novel biostimulating agent that efficiently promotes plant root colonization by AHL-degrading R. erythropolis population. We also characterized an AHL-degrading biocontrol R. erythropolis isolate, R138, which was introduced in the potato rhizosphere. Moreover, root colonization by AHL-degrading bacteria receiving different combinations of GHL and R138 treatments was compared by using a cultivation-based approach (percentage of AHL-degrading bacteria), pyrosequencing of PCR-amplified rrs loci (total bacterial community), and quantitative PCR (qPCR) of the qsdA gene, which encodes an AHL lactonase in R. erythropolis. Higher densities of the AHL-degrading R. erythropolis population in the rhizosphere were observed when GHL treatment was associated with biocontrol strain R138. Under this condition, the introduced R. erythropolis population displaced the native R. erythropolis population. Finally, chemical analyses revealed that GHL, gamma-caprolactone (GCL), and their by-products, gamma-hydroxyheptanoic acid and gamma-hydroxycaproic acid, rapidly disappeared from the rhizosphere and did not accumulate in plant tissues. This integrative study highlights biostimulation as a potential innovative approach for improving root colonization by beneficial bacteria.

Transgenic plants expressing the quorum quenching lactonase AttM do not significantly alter root-associated bacterial populations

The possible impact of genetically engineered plants that degrade the quorum sensing (QS) signal of the plant pathogen Pectobacterium carotovorum was evaluated on non-target plant-associated bacterial populations and communities using Nicotiana tabacum lines expressing the lactonase AttM that degrades QS signals (AttM), and the wild type (WT) parent line. Cell densities of total culturable bacteria and those of selected populations (pseudomonads, agrobacteria) isolated from plant rhizospheres and rhizoplanes were comparable whatever the genotype of the plants (AttM or WT). Similarly, cell densities of members of the bacterial communities relying upon acyl-homoserine-lactones (AHLs) to communicate, or naturally degrading AHL signals, were identical and independent of plant genotype. Bacterial populations isolated from the two plant genotypes were also analyzed irrespective of their culturability status. DGGE analyses targeting the rrs gene (16S rRNA gene) did not reveal any significant differences within these populations. All these data indicate that bacterial population changes that could have resulted from the genetic modification of the plants are non-existent or very limited, as no changes linked to the plant genotype were observed.

Gamma-caprolactone stimulates growth of quorum-quenching Rhodococcus populations in a large-scale hydroponic system for culturing Solanum tuberosum

Bacteria degrading quorum sensing (QS) signals have been proposed as biocontrol agents able to quench QS-dependent expression of virulence symptoms caused by Pectobacterium on potato plants. We report here that gamma-caprolactone (GCL) treatment stimulated growth of the native QS-degrading bacterial community in an industrial plant hydroponic system for culturing Solanum tuberosum. Post-GCL treatment, QS-degrading bacteria were mainly identified as Rhodococcus isolates, while Agrobacterium isolates dominated under similar untreated conditions. Most of the assayed Rhodococcus isolates exhibited efficient biocontrol activity for protecting potato tubers. Analytical chemistry approach revealed the rapid degradation of GCL introduced in the plant cultures.

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.

Do transgenic plants affect rhizobacteria populations?

Plant genetic manipulation has led to the development of genetically modified plants (GMPs) expressing various traits. Since their first commercial use in 1996, GMPs have been increasingly used, reaching a global cultivating production area of 114.3 million hectares in 2007. The rapid development of agricultural biotechnology and release of GMPs have provided many agronomic and economic benefits, but has also raised concerns over the potential impact these plants might have on the environment. Among these environmental concerns, the unintentional impact that GMPs might have on soil‐associated microbes, especially rhizosphere‐inhabiting bacteria or rhizobacteria, represents one of the least studied and understood areas. As rhizobacteria are responsible for numerous key functions including nutrient cycling and decomposition, they have been defined as good indicator organisms to assess the general impact that GMPs might have on the soil environment. This minireview summarizes the results of various experiments that have been conducted to date on the impact of GMPs on rhizobacteria. Both biological and technical parameters are discussed and an attempt is made to determine if specific rhizobacterial responses exist for the different categories of GMPs developed to date.

Transgenic tomato plants alter quorum sensing in plant growth-promoting rhizobacteria

Two Gram-negative, plant growth-promoting rhizobacteria (PGPRs), denominated as M12 and M14, were classified by 16S rDNA sequencing as Burkholderia graminis species. Both strains were shown to produce a variety of N-acyl-homoserine lactone (AHL) quorum sensing (QS) signalling molecules. The involvement of these molecules in plant growth promotion and the induction of protection against salt stress was examined. AHL production was evaluated in vitro by thin-layer chromatography using AHL biosensors, and the identity of the AHLs produced was determined by liquid chromatography-tandem mass spectrometry. The in situ production of AHLs by M12 and M14 in the rhizosphere of Arabidopsis thaliana plants was detected by co-inoculation with green fluorescent protein-based biosensor strains and confocal laser scanning microscopy. To determine whether plant growth promotion and protection against salt stress were mediated by QS, these PGPRs were assayed on wild-type tomato plants, as well as their corresponding transgenics expressing YenI (short-chain AHL producers) and LasI (long-chain AHL producers). In wild-type tomato plants, only M12 promoted plant growth, and this effect disappeared in both transgenic lines. In contrast, M14 did not promote growth in wild-type tomatoes, but did so in the LasI transgenic line. Resistance to salt stress was induced by M14 in wild-type tomato, but this effect disappeared in both transgenic lines. The strain M12, however, did not induce salt resistance in wild-type tomato, but did so in LasI tomato plants. These results reveal that AHL QS signalling molecules mediate the ability of both PGPR strains M12 and M14 to promote plant growth and to induce protection against salt stress.

A metagenomic analysis of soil bacteria extends the diversity of quorum-quenching lactonases

A metagenomic library of 10,121 clones, generated from bacteria inhabiting a pasture soil from France, was screened for the presence of fosmids conferring either N-acylhomoserine lactone (NAHL) synthesis or NAHL degradation ability upon their Escherichia coli host. No clone producing NAHLs was identified whereas one, containing a 31 972 bp insert in fosmid p2H8, allowed NAHL degradation. This led to the cloning and identification of a gene, qlcA, encoding an NAHL-lactonase activity, as judged by lactone-ring closure and HPLC/MS analyses of NAHL degradation products. The qlcA gene efficiently quenched quorum-sensing regulated pathogenic functions when expressed in Pectobacterium carotovorum. The QlcA peptide belongs to the family of zinc-dependent metallohydrolases and appears to be distantly related to other NAHL-lactonases discovered in Agrobacterium, Bacillus, Photorhabdus and Rhizobium. In-silico analysis of the metagenomic insert revealed the occurrence of 20 orf, with a constant GC% and codon usage, suggesting a unique bacterial origin. Nine out of these 20 orf were homologous to genes encoding biosynthesis of arginine; they were clustered with an unusual succession argFJADBCRGH. The fosmid p2H8 is able to complement the argA, argB and argC mutants in E. coli. Phylogenetic analysis showed that 9 orf out of 20 were related to sequences from members of the Acidobacteria, supporting the hypothesis that the analysed insert might be originated from an organism related to this phylum.

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.

Long- and short-chain plant-produced bacterial N-acyl-homoserine lactones become components of phyllosphere, rhizosphere, and soil

Two N-acyl-homoserine lactone (acyl-HSL) synthase genes, lasI from Pseudomonas aeruginosa and yenI from Yersinia enterocolitica, were introduced into tobacco, individually and in combination. Liquid chromatograph-tandem mass spectrometry and thin-layer chromatography confirmed products of lasI and yenI activity in single and cotransformants. Cotransformants expressing plastid-localized LasI and YenI synthases produced the major acyl-HSLs for each synthase in all tissues tested. Total acyl-HSL signals accumulated in leaf tissue up to 3 pmol/mg of fresh weight, half as much in stem tissue, and approximately 10-fold less in root tissues. Acyl-HSLs were present in aqueous leaf washes from greenhouse-grown transgenic plants. Transgenic lines grown for 14 days under axenic conditions produced detectable levels of acyl-HSLs in root exudates. Ethyl acetate extractions of rhizosphere and nonrhizosphere soil from transgenically grown plants contained active acyl-HSLs, whereas plant-free soil or rhizosphere and nonrhizosphere soil from wild-type plants lacked detectable amounts of acyl-HSLs. This work shows that bioactive acyl-HSLs are exuded from leaves and roots and accumulate in the phytosphere of plants engineered to produce acyl-HSLs. These data further suggest that plants that are bioengineered to synthesize acyl-HSLs can foster beneficial plant-bacteria communications or deter deleterious interactions. Therefore, it is feasible to use bioengineered plants to supplement soils with specific acyl-HSLs to modulate bacterial phenotypes and plant-associated bacterial community structures.

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.