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

Role of bacterial quorum sensing in plant growth promotion

Quorum sensing (QS) also known as bacterial cell-cell communication or bacterial crosstalk is a phenomenon regulating various bacterial traits that can affect plant growth and defence. Similarities in the structure of root exudates and bacterial signalling molecules have tremendous implications governing the plant heath. The rhizosphere ecosystem being an excellent example of plant-microbe and microbe-microbe interactions harbours a variety of microorganisms exhibiting quorum sensing. Phytochemicals present in plant root exudates and QS signal molecules as well as volatile organic compounds (VOCs) produced by microorganisms work in coordination to establish intra- and inter-species communications. Interestingly, a number of plant growth promoting rhziobacterial (PGPR) activities like effective/enhanced root colonization, nutrient uptake, nodulation, nitrogen fixation, production of plant hormones, antimicrobial compounds and induction of plant defences can be attributed directly or indirectly to their quorum sensing and quenching abilities. Although not completely understood, root development, stress tolerance and defence against phytopathogens are some of the implications of such abilities which might prove beneficial for sustainable agriculture. Deciphering the mechanism of these interactions would be instrumental in improving crop health. Plant beneficial microorganisms employing QS and QS inhibition (QSI) strategies have been discussed in this review.

Iron Deficiency in Tomatoes Reversed by Pseudomonas Strains: A Synergistic Role of Siderophores and Plant Gene Activation

An alkaline pH in soils reduces Fe availability, limiting Fe uptake, compromising plant growth, and showing chlorosis due to a decrease in chlorophyll content. To achieve proper Fe homeostasis, dicotyledonous plants activate a battery of strategies involving not only Fe absorption mechanisms, but also releasing phyto-siderophores and recruiting siderophore-producing bacterial strains. A screening for siderophore-producing bacterial isolates from the rhizosphere of Pinus pinea was carried out, resulting in two Pseudomonas strains, Z8.8 and Z10.4, with an outstanding in vitro potential to solubilize Fe, Mn, and Co. The delivery of each strain to 4-week-old iron-starved tomatoes reverted chlorosis, consistent with enhanced Fe contents up to 40%. Photosynthesis performance was improved, revealing different strategies. While Z8.8 increased energy absorption together with enhanced chlorophyll "a" content, followed by enhanced energy dissipation, Z10.4 lowered pigment contents, indicating a better use of absorbed energy, leading to a better survival rate. The systemic reprogramming induced by both strains reveals a lower expression of Fe uptake-related genes, suggesting that both strains have activated plant metabolism to accelerate Fe absorption faster than controls, consistent with increased Fe content in leaves (47% by Z8.8 and 42% by Z10.4), with the difference probably due to the ability of Z8.8 to produce auxins affecting root structure. In view of these results, both strains are effective candidates to develop biofertilizers.

Quorum sensing-related activities of beneficial and pathogenic bacteria have important implications for plant and human health

Eukaryotic organisms coevolved with microbes from the environment forming holobiotic meta-genomic units. Members of host-associated microbiomes have commensalic, beneficial/symbiotic, or pathogenic phenotypes. More than 100 years ago, Lorenz Hiltner, pioneer of soil microbiology, introduced the term 'Rhizosphere' to characterize the observation that a high density of saprophytic, beneficial, and pathogenic microbes are attracted by root exudates. The balance between these types of microbes decide about the health of the host. Nowadays we know, that for the interaction of microbes with all eukaryotic hosts similar principles and processes of cooperative and competitive functions are in action. Small diffusible molecules like (phyto)hormones, volatiles and quorum sensing signals are examples for mediators of interspecies and cross-kingdom interactions. Quorum sensing of bacteria is mediated by different autoinducible metabolites in a density-dependent manner. In this perspective publication, the role of QS-related activities for the health of hosts will be discussed focussing mostly on N-acyl-homoserine lactones (AHL). It is also considered that in some cases very close phylogenetic relations exist between plant beneficial and opportunistic human pathogenic bacteria. Based on a genome and system-targeted new understanding, sociomicrobiological solutions are possible for the biocontrol of diseases and the health improvement of eukaryotic hosts.

N- acyl homoserine lactones (AHLs) type signal molecules produced by rhizobacteria associated with plants that growing in a metal(oids) contaminated soil: A catalyst for plant growth

The present study explores the potential of rhizobacteria isolated from Baccharis linearis and Solidago chilensis in metal(loid)-contaminated soil for producing N-acyl-homoserine lactones (AHLs)-type signal molecules and promoting plant growth. A total of 42 strains were isolated, four demonstrating the production of AHL-type signal molecules. Based on 16S rRNA gene sequencing analyses and MALDI-TOF analyses, these four isolates were identified as belonging to the Pseudomonas genus, specifically P. brassicacearum, P. frederickberguensis, P. koreensis, and P. orientalis. The four AHL-producing strains were evaluated for metal(loid)s tolerance, their plant growth promotion traits, AHL quantification, and their impact on in vitro Lactuca sativa plant growth. The study found that four strains exhibited high tolerance to metal(loid)s, particularly As, Cu, and Zn. Additionally, plant growth-promoting traits were detected in AHL-producing bacteria, such as siderophore production, ammonia production, ACC deaminase activity, and P solubilization. Notably, AHL production varied among strains isolated from B. linearis, where C7-HSL and C9-HSL signal molecules were detected, and S. chilensis, where only C7-HSL signal molecules were observed. In the presence of copper, the production of C7-HSL and C9-HSL significantly decreased in B. linearis isolates, while in S. chilensis isolates, C7-HSL production was inhibited. Further, when these strains were inoculated on lettuce seeds and in vitro plants, a significant increase in germination and plant growth was observed. Mainly, the inoculation of P. brassicacearum and P. frederickberguensis led to extensive root hair development, significantly increasing length and root dry weight. Our results demonstrate that rhizospheric strains produce AHL molecules and stimulate plant growth, primarily through root development. However, the presence of copper reduces the production of these molecules, potentially affecting the root development of non-metalloid tolerant plants such as S. chilensis, which would explain its low population in this hostile environment.

Microbiome-Mediated Protection against Pathogens in Woody Plants

Pathogens, especially invasive species, have caused significant global ecological, economic, and social losses in forests. Plant disease research has traditionally focused on direct interactions between plants and pathogens in an appropriate environment. However, recent research indicates that the microbiome can interact with the plant host and pathogens to modulate plant resistance or pathogen pathogenicity, thereby altering the outcome of plant-pathogen interactions. Thus, this presents new opportunities for studying the microbial management of forest diseases. Compared to parallel studies on human and crop microbiomes, research into the forest tree microbiome and its critical role in forest disease progression has lagged. The rapid development of microbiome sequencing and analysis technologies has resulted in the rapid accumulation of a large body of evidence regarding the association between forest microbiomes and diseases. These data will aid the development of innovative, effective, and environmentally sustainable methods for the microbial management of forest diseases. Herein, we summarize the most recent findings on the dynamic structure and composition of forest tree microbiomes in belowground and aboveground plant tissues (i.e., rhizosphere, endosphere, and phyllosphere), as well as their pleiotropic impact on plant immunity and pathogen pathogenicity, highlighting representative examples of biological control agents used to modulate relevant tree microbiomes. Lastly, we discuss the potential application of forest tree microbiomes in disease control as well as their future prospects and challenges.

Metabolic signatures of rhizobacteria-induced plant growth promotion

Various root-colonizing bacterial species can promote plant growth and trigger systemic resistance against aboveground leaf pathogens and herbivore insects. To date, the underlying metabolic signatures of these rhizobacteria-induced plant phenotypes are poorly understood. To identify core metabolic pathways that are targeted by growth-promoting rhizobacteria, we used combinations of three plant species and three rhizobacterial species and interrogated plant shoot chemistry by untargeted metabolomics. A substantial part (50%-64%) of the metabolites detected in plant shoot tissue was differentially affected by the rhizobacteria. Among others, the phenylpropanoid pathway was targeted by the rhizobacteria in each of the three plant species. Differential regulation of the various branches of the phenylpropanoid pathways showed an association with either plant growth promotion or growth reduction. Overall, suppression of flavonoid biosynthesis was associated with growth promotion, while growth reduction showed elevated levels of flavonoids. Subsequent assays with 12 Arabidopsis flavonoid biosynthetic mutants revealed that the proanthocyanidin branch plays an essential role in rhizobacteria-mediated growth promotion. Our study also showed that a number of pharmaceutically and nutritionally relevant metabolites in the plant shoot were significantly increased by rhizobacterial treatment, providing new avenues to use rhizobacteria to tilt plant metabolism towards the biosynthesis of valuable natural plant products.

Diversity and functions of quorum sensing bacteria in the root environment of the Suaeda glauca and Phragmites australis coastal wetlands

The quorum sensing (QS) system plays a significant role in the bacteria-bacteria or plant-bacteria relationships through signal molecules. However, little is known about the distribution and functional diversity of QS bacteria in the root environment of Suaeda glauca and Phragmites australis in coastal wetlands. We explored the bacterial community by amplicon sequencing and isolated 1050 strains from the rhizosphere soil and root tissues of S. glauca and P. australis in northern China to investigate the bacterial community and AHL producers. AHL activity was found in 76 isolates, and 22 distinct strains were confirmed by 16S rRNA gene sequencing. A substantial number of AHL producers clustered in rhizobiales and sphingomonadale, which derived from the root tissues. AHL producers in the rhizosphere soil mostly belonged to rhodobacterales. The different taxa of AHL producers in the rhizosphere soil and root tissues resulted in a variation of AHL profiles that C6-HSL dominated the AHL profiles in root bacteria compared to the C8-HSL in rhizobacteria, implying different ecological roles for AHL producers in the rhizosphere soil and root tissues. Many AHL producers may form biofilms, and some can degrade DMSP and oil, demonstrating that QS bacteria in the root environment have a wide ecological roles. In our study, for one of the first times here, we explore the distribution and functional variety of AHL producers in the root environment of S. glauca-P. australis. This study expands current knowledge of the relationship between QS bacteria and coastal plants (S. glauca and P. australis), and vital roles of QS bacterial in maintaining the health of coastal wetlands.

Root Exudates: Mechanistic Insight of Plant Growth Promoting Rhizobacteria for Sustainable Crop Production

The breaking silence between the plant roots and microorganisms in the rhizosphere affects plant growth and physiology by impacting biochemical, molecular, nutritional, and edaphic factors. The components of the root exudates are associated with the microbial population, notably, plant growth-promoting rhizobacteria (PGPR). The information accessible to date demonstrates that PGPR is specific to the plant's roots. However, inadequate information is accessible for developing bio-inoculation/bio-fertilizers for the crop in concern, with satisfactory results at the field level. There is a need to explore the perfect candidate PGPR to meet the need for plant growth and yield. The functions of PGPR and their chemotaxis mobility toward the plant root are triggered by the cluster of genes induced by the components of root exudates. Some reports have indicated the benefit of root exudates in plant growth and productivity, yet a methodical examination of rhizosecretion and its consequences in phytoremediation have not been made. In the light of the afore-mentioned facts, in the present review, the mechanistic insight and recent updates on the specific PGPR recruitment to improve crop production at the field level are methodically addressed.

Rhizosphere Signaling: Insights into Plant-Rhizomicrobiome Interactions for Sustainable Agronomy

Rhizospheric plant-microbe interactions have dynamic importance in sustainable agriculture systems that have a reduced reliance on agrochemicals. Rhizosphere signaling focuses on the interactions between plants and the surrounding symbiotic microorganisms that facilitate the development of rhizobiome diversity, which is beneficial for plant productivity. Plant-microbe communication comprises intricate systems that modulate local and systemic defense mechanisms to mitigate environmental stresses. This review deciphers insights into how the exudation of plant secondary metabolites can shape the functions and diversity of the root microbiome. It also elaborates on how rhizosphere interactions influence plant growth, regulate plant immunity against phytopathogens, and prime the plant for protection against biotic and abiotic stresses, along with some recent well-reported examples. A holistic understanding of these interactions can help in the development of tailored microbial inoculants for enhanced plant growth and targeted disease suppression.

Molecular mechanisms of N-acyl homoserine lactone signals perception by plants

N-acyl homoserine lactones (AHLs) belong to the class of bacterial quorum sensing signal molecules involved in distance signal transduction between Gram-negative bacteria colonizers of the rhizosphere, as well as bacteria and plants. AHLs synchronize the activity of genes from individual cells, allowing the bacterial population to act as a multicellular organism, and establish a symbiotic or antagonistic relationship with the host plant. Although the effect of AHLs on plants has been studied for more than ten years, the mechanisms of plant perception of AHL signals are not fully understood. The specificity of the reactions caused by AHL indicates the existence of appropriate mechanisms for their perception by plants. In the current review, we summarize available data on the molecular mechanisms of AHL-signal perception in plants, its effect on plant growth, development, and stress resistance. We describe the latest research demonstrating direct (on plants) and indirect (on rhizosphere microflora) effects of AHLs, as well as the prospects of using these compounds in biotechnology to increase plant resistance to biotic and abiotic stresses.

Microbial Derived Compounds Are a Promising Approach to Mitigating Salinity Stress in Agricultural Crops

The use of microbial derived compounds is a technological approach currently gaining popularity among researchers, with hopes of complementing, supplementing and addressing key issues associated with use of microbial cells for enhancing plant growth. The new technology is a promising approach to mitigating effects of salinity stress in agricultural crops, given that these compounds could be less prone to effects of salt stress, are required in small quantities and are easier to store and handle than microbial cells. Microorganism derived compounds such as thuricin17, lipochitooligosaccharides, phytohormones and volatile organic compounds have been reported to mitigate the effects of salt stress in agricultural crops such as soybean and wheat. This mini-review compiles current knowledge regarding the use of microbe derived compounds in mitigating salinity stress in crops, the mechanisms they employ as well as future prospects.

Microbial Derived Compounds, a Step Toward Enhancing Microbial Inoculants Technology for Sustainable Agriculture

Sustainable agriculture remains a focus for many researchers, in an effort to minimize environmental degradation and climate change. The use of plant growth promoting microorganisms (PGPM) is a hopeful approach for enhancing plant growth and yield. However, the technology faces a number of challenges, especially inconsistencies in the field. The discovery, that microbial derived compounds can independently enhance plant growth, could be a step toward minimizing shortfalls related to PGPM technology. This has led many researchers to engage in research activities involving such compounds. So far, the findings are promising as compounds have been reported to enhance plant growth under stressed and non-stressed conditions in a wide range of plant species. This review compiles current knowledge on microbial derived compounds, taking a reader through a summarized protocol of their isolation and identification, their relevance in present agricultural trends, current use and limitations, with a view to giving the reader a picture of where the technology has come from, and an insight into where it could head, with some suggestions regarding the probable best ways forward.

Bioeffectors as Biotechnological Tools to Boost Plant Innate Immunity: Signal Transduction Pathways Involved

The use of beneficial rhizobacteria (bioeffectors) and their derived metabolic elicitors are efficient biotechnological alternatives in plant immune system elicitation. This work aimed to check the ability of 25 bacterial strains isolated from the rhizosphere of Nicotiana glauca, and selected for their biochemical traits from a group of 175, to trigger the innate immune system of Arabidopsis thaliana seedlings against the pathogen Pseudomonas syringae pv. tomato DC3000. The five strains more effective in preventing pathogen infection were used to elucidate signal transduction pathways involved in the plant immune response by studying the differential expression of Salicylic acid and Jasmonic acid/Ethylene pathway marker genes. Some strains stimulated both pathways, while others stimulated either one or the other. The metabolic elicitors of two strains, chosen for the differential expression results of the genes studied, were extracted using n-hexane, ethyl acetate, and n-butanol, and their capacity to mimic bacterial effect to trigger the plant immune system was studied. N-hexane and ethyl acetate were the most effective fractions against the pathogen in both strains, achieving similar protection rates although gene expression responses were different from that obtained by the bacteria. These results open an amount of biotechnological possibilities to develop biological products for agriculture.

AHL-priming for enhanced resistance as a tool in sustainable agriculture

Bacteria communicate with each other through quorum sensing (QS) molecules. N-acyl homoserine lactones (AHL) are one of the most extensively studied groups of QS molecules. The role of AHL molecules is not limited to interactions between bacteria; they also mediate inter-kingdom interaction with eukaryotes. The perception mechanism of AHL is well-known in bacteria and several proteins have been proposed as putative receptors in mammalian cells. However, not much is known about the perception of AHL in plants. Plants generally respond to short-chained AHL with modification in growth, while long-chained AHL induce AHL-priming for enhanced resistance. Since plants may host several AHL-producing bacteria and encounter multiple AHL at once, a coordinated response is required. The effect of the AHL combination showed relatively low impact on growth but enhanced resistance. Microbial consortium of bacterial strains that produce different AHL could therefore be an interesting approach in sustainable agriculture. Here, we review the molecular and genetical basis required for AHL perception. We highlight recent advances in the field of AHL-priming. We also discuss the recent discoveries on the impact of combination(s) of multiple AHL on crop plants and the possible use of this knowledge in sustainable agriculture.

Role of environmental factors in shaping the soil microbiome

The soil microbiome comprises one of the most important and complex components of all terrestrial ecosystems as it harbors millions of microbes including bacteria, fungi, archaea, viruses, and protozoa. Together, these microbes and environmental factors contribute to shaping the soil microbiome, both spatially and temporally. Recent advances in genomic and metagenomic analyses have enabled a more comprehensive elucidation of the soil microbiome. However, most studies have described major modulators such as fungi and bacteria while overlooking other soil microbes. This review encompasses all known microbes that may exist in a particular soil microbiome by describing their occurrence, abundance, diversity, distribution, communication, and functions. Finally, we examined the role of several abiotic factors involved in the shaping of the soil microbiome.

Growth-Stimulatory Effect of Quorum Sensing Signal Molecule N-Acyl-Homoserine Lactone-Producing Multi-Trait Aeromonas spp. on Wheat Genotypes Under Salt Stress

Salinity is one of the major threats to agricultural productivity worldwide. Soil and plant management practices, along with inoculation with plant-beneficial bacteria, play a key role in the plant’s tolerance toward salinity stress. The present study demonstrates the potential of acyl homoserine lactone (AHL)-producing plant growth promoting rhizobacteria (PGPR) strains of Aeromonas sp., namely, SAL-17 (accession no. HG763857) and SAL-21 (accession no. HG763858), for growth promotion of two wheat genotypes inherently different for salt tolerance potential. AHLs are the bacterial signal molecules that regulate the expression of various genes in bacteria and plants. Both Aeromonas spp., along with innate plant-growth-promoting (PGP) and salt tolerance traits, showed AHL production which was identified on tandem mass spectrometry as C6-HSL, 3-OH-C5-HSL, 3-OH-C6-HSL, 3-oxo-C7-HSL C10-HSL, 3-oxo-C10-HSL, 3-OH-C10-HSL, 3-oxo-C12-HSL and C6-HSL, and 3-oxo-C10-HSL. The exogenous application of purified AHLs (mix) significantly improved various root parameters at 200 mM NaCl in both salt-sensitive (SSG) and salt-tolerant (STG) genotypes, where the highest increase (≈80%) was observed where a mixture of both strains of AHLs was used. Confocal microscopic observations and root overlay assay revealed a strong root colonization potential of the two strains under salt stress. The inoculation response of both STG and SSG genotypes was evaluated with two AHL-producing strains (SAL-17 and SAL-21) and compared to non-AHL-producing Aeromonas sp. SAL-12 (accession no. HG763856) in saline (EC = 7.63 ms/cm²) and non-saline soil. The data reveal that plants inoculated with the bacterial consortium (SAL-21 + SAL-17) showed a maximum increase in leaf proline content, nitrate reductase activity, chlorophyll a/b, stomatal conductance, transpiration rate, root length, shoot length, and grain weight over non-inoculated plants grown in saline soil. Both STG and SSG showed relative effectiveness toward inoculation (percent increase for STG: 165–16%; SSG: 283–14%) and showed a positive correlation of grain yield with proline and nitrate reductase activity. Furthermore, principal component analysis (PCA) and categorical PCA analysis clearly showed an inoculation response in both genotypes, revealing the effectiveness of AHL-producing Aeromonas spp. than the non-AHL-producing strain. The present study documents that the consortium of salt-tolerant AHL-producing Aeromonas spp. is equally effective for sustaining the growth of STG as well as SSG wheat genotypes in saline soil, but biosafety should be fully ensured before field release.

N-3-oxo-hexanoyl-homoserine lactone, a bacterial quorum sensing signal, enhances salt tolerance in Arabidopsis and wheat

BACKGROUND

N-acyl-homoserine lactones (AHLs) are the quorum sensing (QS) signal molecules to coordinate the collective behavior in a population in Gram-negative bacteria. Recent evidences demonstrate their roles in plant growth and defense responses.

RESULTS

In present study, we show that the treatment of plant roots with N-3-oxo-hexanoyl-homoserine lactone (3OC6-HSL), one molecule of AHLs family, resulted in enhanced salt tolerance in Arabidopsis and wheat. We found that the growth inhibition phenotype including root length, shoot length and fresh weight were significantly improved by 3OC6-HSL under salt stress condition. The physiological and biochemical analysis revealed that the contents of chlorophyll and proline were increased and the contents of MDA and Na⁺ and Na⁺/K⁺ ratios were decreased after 3OC6-HSL treatment in Arabidopsis and wheat under salt stress condition. Molecular analysis showed that 3OC6-HSL significantly upregulated the expression of salt-responsive genes including ABA-dependent osmotic stress responsive genes COR15a, RD22, ADH and P5CS1, ABA-independent gene ERD1, and ion-homeostasis regulation genes SOS1, SOS2 and SOS3 in Arabidopsis under salt stress condition.

CONCLUSIONS

These results indicated that 3OC6-HSL enhanced plant salt tolerance and ABA-dependent and ABA-independent signal pathways and SOS signaling might be involved in the induction of salt resistance by 3OC6-HSL in plants. Our data provide a new insight into the plant-microbe inter-communication.

Review: Phytostimulation and root architectural responses to quorum-sensing signals and related molecules from rhizobacteria

Bacteria rely on chemical communication to sense the environment and to retrieve information on their population densities. Accordingly, a vast repertoire of molecules is released, which synchronizes expression of genes, coordinates behavior through a process termed quorum-sensing (QS), and determines the relationships with eukaryotic species. Already identified QS molecules from Gram negative bacteria can be grouped into two main classes, N-acyl-L-homoserine lactones (AHLs) and cyclodipeptides (CDPs), with roles in biofilm formation, bacterial virulence or symbiotic interactions. Noteworthy, plants detect each of these molecules, change their own gene expression programs, re-configurate root architecture, and activate defense responses, improving in this manner their adaptation to natural and agricultural ecosystems. AHLs may act as alarm signals, pathogen and/or microbe-associated molecular patterns, whereas CDPs function as hormonal mimics for plants via their putative interactions with the auxin receptor Transport Inhibitor Response1 (TIR1). A major challenge is to identify the molecular pathways of QS-mediated crosstalk and the plant receptors and interacting proteins for AHLs, CDPs and related signals.

Role of quorum sensing and chemical communication in fungal biotechnology and pathogenesis

Microbial cells do not live in isolation in their environment, but rather they communicate with each other using chemical signals. This sophisticated mode of cell-to-cell signalling, known as quorum sensing, was first discovered in bacteria, and coordinates the behaviour of microbial population behaviour in a cell-density-dependent manner. More recently, these mechanisms have been described in eukaryotes, particularly in fungi, where they regulate processes such as pathogenesis, morphological differentiation, secondary metabolite production and biofilm formation. In this manuscript, we review the information available to date on these processes in yeast, dimorphic fungi and filamentous fungi. We analyse the diverse chemical 'languages' used by different groups of fungi, their possible cross-talk and interkingdom interactions with other organisms. We discuss the existence of these mechanisms in multicellular organisms, the ecophysiological role of QS in fungal colonisation and the potential applications of these mechanisms in biotechnology and pathogenesis.

In Silico Analysis of the Quorum Sensing Metagenome in Environmental Biofilm Samples

Quorum sensing (QS) is a sophisticated cell to cell signaling mechanism mediated by small diffusible molecules called “autoinducers.” This phenomenon is well studied in bacteria, where different QS systems are described that differ between Gram-negative and Gram-positive bacteria. However, a common system to these groups was discovered, the autoinducer 2. QS has implications in biofilm formation, where the application of metagenomic techniques to study these phenomena may be useful to understand the communication networks established by the different components of the community, and to discover new targets for microbial control. Here we present an in silico screening of QS proteins in all publicly available biofilm metagenomes from the JGI database. We performed sequence, conserved motifs, phylogenetic, and three-dimensional structure analyses of the candidates, resulting in an effective strategy to search QS proteins in metagenomes sequences. The number of QS proteins present in each sample, and its phylogenetic affiliation, was clearly related to the bacterial diversity and the origin of the biofilm. The samples isolated from natural habitats presented clear differences with those from artificial habitats. Interesting findings have been made in the abundance of LuxR-like proteins finding an unbalanced ratio between the synthases and the receptor proteins in Bacteroidetes bacteria, pointing out the existence of “cheaters” in this group. Moreover, we have shown the presence of the LuxI/R QS system in bacteria from the Nitrospira taxonomic group. Finally, some undescribed proteins from the HdtS family have been found in Gamma-proteobacteria.

Plant-microbial interactions in agriculture and the use of farming systems to improve diversity and productivity

A thorough understanding of the services provided by microorganisms to the agricultural ecosystem is integral to understanding how management systems can improve or deteriorate soil health and production over the long term. Yet it is hampered by the difficulty in measuring the intersection of plant, microbe, and environment, in no small part because of the situational specificity to some plant-microbial interactions, related to soil moisture, nutrient content, climate, and local diversity. Despite this, perspective on soil microbiota in agricultural settings can inform management practices to improve the sustainability of agricultural production.

Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies

Abiotic stresses are the foremost limiting factors for agricultural productivity. Crop plants need to cope up adverse external pressure created by environmental and edaphic conditions with their intrinsic biological mechanisms, failing which their growth, development, and productivity suffer. Microorganisms, the most natural inhabitants of diverse environments exhibit enormous metabolic capabilities to mitigate abiotic stresses. Since microbial interactions with plants are an integral part of the living ecosystem, they are believed to be the natural partners that modulate local and systemic mechanisms in plants to offer defense under adverse external conditions. Plant-microbe interactions comprise complex mechanisms within the plant cellular system. Biochemical, molecular and physiological studies are paving the way in understanding the complex but integrated cellular processes. Under the continuous pressure of increasing climatic alterations, it now becomes more imperative to define and interpret plant-microbe relationships in terms of protection against abiotic stresses. At the same time, it also becomes essential to generate deeper insights into the stress-mitigating mechanisms in crop plants for their translation in higher productivity. Multi-omics approaches comprising genomics, transcriptomics, proteomics, metabolomics and phenomics integrate studies on the interaction of plants with microbes and their external environment and generate multi-layered information that can answer what is happening in real-time within the cells. Integration, analysis and decipherization of the big-data can lead to a massive outcome that has significant chance for implementation in the fields. This review summarizes abiotic stresses responses in plants in-terms of biochemical and molecular mechanisms followed by the microbe-mediated stress mitigation phenomenon. We describe the role of multi-omics approaches in generating multi-pronged information to provide a better understanding of plant-microbe interactions that modulate cellular mechanisms in plants under extreme external conditions and help to optimize abiotic stresses. Vigilant amalgamation of these high-throughput approaches supports a higher level of knowledge generation about root-level mechanisms involved in the alleviation of abiotic stresses in organisms.

Quorum-Sensing Mechanisms Mediated by Farnesol in Ophiostoma piceae: Effect on Secretion of Sterol Esterase

Ophiostoma piceae CECT 20416 is a dimorphic wood-staining fungus able to produce an extracellular sterol-esterase/lipase (OPE) that is of great biotechnological interest. In this work, we have studied the morphological change of this fungus from yeast to hyphae, which is associated with the cell density-related mechanism known as quorum sensing (QS), and how this affects the secretion of OPE. The data presented here confirm that the molecule E,E-farnesol accumulates as the cell number is growing within the population. The exogenous addition of this molecule or spent medium to the cultures increased the extracellular activity of OPE 2.5 times. This fact was related not to an increase in microbial biomass or in the expression of the gene coding for OPE but to a marked morphological transition in the cultures. Moreover, the morphological transition also occurred when a high cell density was inoculated into the medium. The results suggest that E,E-farnesol regulates through QS mechanisms the morphological transition in the dimorphic fungus O. piceae and that it is associated with a higher extracellular esterase activity. Furthermore, identification and transcriptional analysis of genes tup1 and cyr1, which are involved in the response, was carried out. Here we report enhanced production of a sterol-esterase/lipase of biotechnological interest by means of QS mechanisms. These results may be useful in increasing the production of secreted enzymes of other dimorphic fungi of biotechnological interest.

Plant growth-promoting bacteria facilitate the growth of barley and oats in salt-impacted soil: implications for phytoremediation of saline soils

Plant growth-promoting bacteria (PGPB) strains that contain the enzyme 1-amino-cyclopropane-1-carboxylate (ACC) deaminase can lower stress ethylene levels and improve plant growth. In this study, ACC deaminase-producing bacteria were isolated from a ) salt-impacted ( 50 dS/m) farm field, and their ability to promote plant growth of barley 1): and oats in saline soil was investigated in pouch assays (1% NaCI), greenhouse trials (9.4 dS/m), and field trials (6-24 dS/m). A mix of previously isolated PGPB strains UW3 (Pseudomonas sp.) and UW4 (P. sp.) was also tested for comparison. Rhizobacterial isolate CMH3 (P. corrugata) and UW3+UW4 partially alleviated plant salt stress in growth pouch assays. In greenhouse trials, CMH3 enhanced root biomass of barley and oats by 200% and 50%, respectively. UW3+UW4, CMH3 and isolate CMH2 also enhanced barley and oat shoot growth by 100%-150%. In field tests, shoot biomass of oats tripled when treated with UW3+UW4 and doubled with CHM3 compared with that of untreated plants. PGPB treatment did not affect salt uptake on a per mass basis; higher plant biomass led to greater salt uptake, resulting in decreased soil salinity. This study demonstrates a method for improving plant growth in marginal saline soils. Associated implications for salt

Microbe associated molecular patterns from rhizosphere bacteria trigger germination and Papaver somniferum metabolism under greenhouse conditions

Ten PGPR from different backgrounds were assayed on Papaver somniferum var. Madrigal to evaluate their potential as biotic elicitors to increase alkaloid content under the rationale that some microbe associated molecular patterns (MAMPs) are able to trigger plant metabolism. First, the 10 strains and their culture media at two different concentrations were tested for their ability to trigger seed germination. Then, the best three strains were tested for their ability to increase seedling growth and alkaloid levels under greenhouse conditions. Only three strains and their culture media enhanced germination. Then, germination enhancing capacity of these best three strains, N5.18 Stenotrophomonas maltophilia, Aur9 Chryseobacterium balustinum and N21.4 Pseudomonas fluorescens was evaluated in soil. Finally, the three strains were applied on seedlings at two time points, by soil drench or by foliar spray. Photosynthesis was measured, plant height was recorded, capsules were weighted and alkaloids analyzed by HPLC. Only N5.18 delivered by foliar spray significantly increased plant height coupled to an increase in total alkaloids and a significant increase in opium poppy straw dry weight; these increases were supported by a better photosynthetic efficiency. The relative contents of morphine, thebaine, codeine and oripavine were affected by this treatment causing a significant increase in morphine coupled to a decrease in thebaine, demonstrating the effectivity of MAMPs from N5.18 in this plant species. Considering the increase in capsule biomass and alkaloids together with the acceleration of germination, strain N5.18 appears as a good candidate to elicit plant metabolism and consequently, to increase productivity of Papaver somniferum.

AHL-priming functions via oxylipin and salicylic acid

Collaborative action between the host plant and associated bacteria is crucial for the establishment of an efficient interaction. In bacteria, the synchronized behavior of a population is often achieved by a density-dependent communication called quorum sensing. This behavior is based on signaling molecules, which influence bacterial gene expression. N-acyl homoserine lactones (AHLs) are such molecules in many Gram-negative bacteria. Moreover, some AHLs are responsible for the beneficial effect of bacteria on plants, for example the long chain N-3-oxo-tetradecanoyl-L-homoserine lactone (oxo-C14-HSL) can prime Arabidopsis and barley plants for an enhanced defense. This AHL-induced resistance phenomenon, named AHL-priming, was observed in several independent laboratories during the last two decades. Very recently, the mechanism of priming with oxo-C14-HSL was shown to depend on an oxylipin and salicylic acid (SA). SA is a key element in plant defense, it accumulates during different plant resistance responses and is the base of systemic acquired resistance. In addition, SA itself can prime plants for an enhanced resistance against pathogen attack. On the other side, oxylipins, including jasmonic acid (JA) and related metabolites, are lipid-derived signaling compounds. Especially the oxidized fatty acid derivative cis-OPDA, which is the precursor of JA, is a newly described player in plant defense. Unlike the antagonistic effect of SA and JA in plant-microbe interactions, the recently described pathway functions through a synergistic effect of oxylipins and SA, and is independent of the JA signaling cascade. Interestingly, the oxo-C14-HSL-induced oxylipin/SA signaling pathway induces stomata defense responses and cell wall strengthening thus prevents pathogen invasion. In this review, we summarize the findings on AHL-priming and the related signaling cascade. In addition, we discuss the potential of AHL-induced resistance in new strategies of plant protection.

Quorum sensing and phytochemicals

Most infectious diseases are caused by bacteria, which proliferate within quorum sensing (QS)-mediated biofilms. Efforts to block QS in bacteria and disrupt biofilms have enabled the identification of bioactive molecules that are also produced by plants. This mini review primarily focuses on natural QS inhibitors, which display potential for treating bacterial infections and also enhance the safety of food supply.

Quorum sensing of bacteria and trans-kingdom interactions of N-acyl homoserine lactones with eukaryotes

Many environmental and interactive important traits of bacteria, such as antibiotic, siderophore or exoenzyme (like cellulose, pectinase) production, virulence factors of pathogens, as well as symbiotic interactions, are regulated in a population density-dependent manner by using small signaling molecules. This phenomenon, called quorum sensing (QS), is widespread among bacteria. Many different bacterial species are communicating or "speaking" through diffusible small molecules. The production often is sophisticatedly regulated via an autoinducing mechanism. A good example is the production of N-acyl homoserine lactones (AHL), which occur in many variations of molecular structure in a wide variety of Gram-negative bacteria. In Gram-positive bacteria, other compounds, such as peptides, regulate cellular activity and behavior by sensing the cell density. The degradation of the signaling molecule--called quorum quenching--is probably another important integral part in the complex quorum sensing circuit. Most interestingly, bacterial quorum sensing molecules also are recognized by eukaryotes that are colonized by QS-active bacteria. In this case, the cross-kingdom interaction can lead to specific adjustment and physiological adaptations in the colonized eukaryote. The responses are manifold, such as modifications of the defense system, modulation of the immune response, or changes in the hormonal status and growth responses. Thus, the interaction with the quorum sensing signaling molecules of bacteria can profoundly change the physiology of higher organisms too. Higher organisms are obligatorily associated with microbial communities, and these truly multi-organismic consortia, which are also called holobionts, can actually be steered via multiple interlinked signaling substances that originate not only from the host but also from the associated bacteria.

Common features of environmental and potentially beneficial plant-associated Burkholderia

The genus Burkholderia comprises more than 60 species isolated from a wide range of niches. Although they have been shown to be diverse and ubiquitously distributed, most studies have thus far focused on the pathogenic species due to their clinical importance. However, the increasing number of recently described Burkholderia species associated with plants or with the environment has highlighted the division of the genus into two main clusters, as suggested by phylogenetical analyses. The first cluster includes human, animal, and plant pathogens, such as Burkholderia glumae, Burkholderia pseudomallei, and Burkholderia mallei, as well as the 17 defined species of the Burkholderia cepacia complex, while the other, more recently established cluster comprises more than 30 non-pathogenic species, which in most cases have been found to be associated with plants, and thus might be considered to be potentially beneficial. Several species from the latter group share characteristics that are of use when associating with plants, such as a quorum sensing system, the presence of nitrogen fixation and/or nodulation genes, and the ability to degrade aromatic compounds. This review examines the commonalities in this growing subgroup of Burkholderia species and discusses their prospective biotechnological applications.

Commonalities and differences in regulation of N-acyl homoserine lactone quorum sensing in the beneficial plant-associated burkholderia species cluster

The genus Burkholderia includes over 60 species isolated from a wide range of environmental niches and can be tentatively divided into two major species clusters. The first cluster includes pathogens such as Burkholderia glumae, B. pseudomallei, and B. mallei and 17 well-studied species of the Burkholderia cepacia complex. The other recently established cluster comprises at least 29 nonpathogenic species, which in most cases have been found to be associated with plants. It was previously established that Burkholderia kururiensis, a member of the latter cluster, possesses an N-acyl homoserine lactone (AHL) quorum-sensing (QS) system designated "BraI/R," which is found in all species of the plant-associated cluster. In the present study, two other BraI/R-like systems were characterized in B. xenovorans and B. unamae and were designated the BraI/R(XEN) and BraI/R(UNA) systems, respectively. Several phenotypes were analyzed, and it was determined that exopolysaccharide was positively regulated by the BraIR-like system in the species B. kururiensis, B. unamae, and B. xenovorans, highlighting commonality in targets. However, the three BraIR-like systems also revealed differences in targets since biofilm formation and plant colonization were differentially regulated. In addition, a second AHL QS system designated XenI2/R2 and an unpaired LuxR solo protein designated BxeR solo were also identified and characterized in B. xenovorans LB400(T). The two AHL QS systems of B. xenovorans are not transcriptionally regulating each other, whereas BxeR solo negatively regulated xenI2. The XenI2/R2 and BxeR solo proteins are not widespread in the Burkholderia species cluster. In conclusion, the present study represents an extensive analysis of AHL QS in the Burkholderia plant-associated cluster demonstrating both commonalities and differences, probably reflecting environmental adaptations of the various species.

Plant-rhizobacteria interactions alleviate abiotic stress conditions

Root-colonizing non-pathogenic bacteria can increase plant resistance to biotic and abiotic stress factors. Bacterial inoculates have been applied as biofertilizers and can increase the effectiveness of phytoremediation. Inoculating plants with non-pathogenic bacteria can provide 'bioprotection' against biotic stresses, and some root-colonizing bacteria increase tolerance against abiotic stresses such as drought, salinity and metal toxicity. Systematic identification of bacterial strains providing cross-protection against multiple stressors would be highly valuable for agricultural production in changing environmental conditions. For bacterial cross-protection to be an effective tool, a better understanding of the underlying morphological, physiological and molecular mechanisms of bacterially mediated stress tolerance, and the phenomenon of cross-protection is critical. Beneficial bacteria-mediated plant gene expression studies under non-stress conditions or during pathogenic rhizobacteria-plant interactions are plentiful, but only few molecular studies on beneficial interactions under abiotic stress situations have been reported. Thus, here we attempt an overview of current knowledge on physiological impacts and modes of action of bacterial mitigation of abiotic stress symptoms in plants. Where available, molecular data will be provided to support physiological or morphological observations. We indicate further research avenues to enable better use of cross-protection capacities of root-colonizing non-pathogenic bacteria in agricultural production systems affected by a changing climate.

The role of microbial signals in plant growth and development

Plant growth and development involves a tight coordination of the spatial and temporal organization of cell division, cell expansion and cell differentiation. Orchestration of these events requires the exchange of signaling molecules between the root and shoot, which can be affected by both biotic and abiotic factors. The interactions that occur between plants and their associated microorganisms have long been of interest, as knowledge of these processes could lead to the development of novel agricultural applications. Plants produce a wide range of organic compounds including sugars, organic acids and vitamins, which can be used as nutrients or signals by microbial populations. On the other hand, microorganisms release phytohormones, small molecules or volatile compounds, which may act directly or indirectly to activate plant immunity or regulate plant growth and morphogenesis. In this review, we focus on recent developments in the identification of signals from free-living bacteria and fungi that interact with plants in a beneficial way. Evidence has accumulated indicating that classic plant signals such as auxins and cytokinins can be produced by microorganisms to efficiently colonize the root and modulate root system architecture. Other classes of signals, including N-acyl-L-homoserine lactones, which are used by bacteria for cell-to-cell communication, can be perceived by plants to modulate gene expression, metabolism and growth. Finally, we discuss the role played by volatile organic compounds released by certain plant growth-promoting rhizobacteria in plant immunity and developmental processes. The picture that emerges is one in which plants and microbes communicate themselves through transkingdom signaling systems involving classic and novel signals.