Beneficial microbes in the microbiome of plant roots improve plant health. Induced systemic resistance (ISR) emerged as an important mechanism by which selected plant growth-promoting bacteria and fungi in the rhizosphere prime the whole plant body for enhanced defense against a broad range of pathogens and insect herbivores. A wide variety of root-associated mutualists, including Pseudomonas, Bacillus, Trichoderma, and mycorrhiza species sensitize the plant immune system for enhanced defense without directly activating costly defenses. This review focuses on molecular processes at the interface between plant roots and ISR-eliciting mutualists, and on the progress in our understanding of ISR signaling and systemic defense priming. The central role of the root-specific transcription factor MYB72 in the onset of ISR and the role of phytohormones and defense regulatory proteins in the expression of ISR in aboveground plant parts are highlighted. Finally, the ecological function of ISR-inducing microbes in the root microbiome is discussed.

Heavy metal pollution of agricultural soils is one of main concerns causing some of the different ecological and environmental problems. Excess accumulation of these metals in soil has changed microbial community (e.g., structure, function, and diversity), deteriorated soil, decreased the growth and yield of plant, and entered into the food chain. Plants' tolerance to heavy metal stress needs to be improved in order to allow growth of crops with minimum or no accumulation of heavy metals in edible parts of plant that satisfy safe food demands for the world's rapidly increasing population. It is well known that PGPRs (plant growth-promoting rhizobacteria) enhance crop productivity and plant resistance to heavy metal stress. Many recent reports describe the application of heavy metal resistant-PGPRs to enhance agricultural yields without accumulation of metal in plant tissues. This review provides information about the mechanisms possessed by heavy metal resistant-PGPRs that ameliorate heavy metal stress to plants and decrease the accumulation of these metals in plant, and finally gives some perspectives for research on these bacteria in agriculture in the future.Copyright © 2017 Elsevier Inc. All rights reserved.

Krabbe disease (KD) is a neurodegenerative disorder caused by the lack of β- galactosylceramidase enzymatic activity and by widespread accumulation of the cytotoxic galactosyl-sphingosine in neuronal, myelinating and endothelial cells. Despite the wide use of Twitcher mice as experimental model for KD, the ultrastructure of this model is partial and mainly addressing peripheral nerves. More details are requested to elucidate the basis of the motor defects, which are the first to appear during KD onset. Here we use transmission electron microscopy (TEM) to focus on the alterations produced by KD in the lower motor system at postnatal day 15 (P15), a nearly asymptomatic stage, and in the juvenile P30 mouse. We find mild effects on motorneuron soma, severe ones on sciatic nerves and very severe effects on nerve terminals and neuromuscular junctions at P30, with peripheral damage being already detectable at P15. Finally, we find that the gastrocnemius muscle undergoes atrophy and structural changes that are independent of denervation at P15. Our data further characterize the ultrastructural analysis of the KD mouse model, and support recent theories of a dying-back mechanism for neuronal degeneration, which is independent of demyelination.

Krabbe disease (KD) is a neurodegenerative disorder caused by the lack of β- galactosylceramidase enzymatic activity and by widespread accumulation of the cytotoxic galactosyl-sphingosine in neuronal, myelinating and endothelial cells. Despite the wide use of Twitcher mice as experimental model for KD, the ultrastructure of this model is partial and mainly addressing peripheral nerves. More details are requested to elucidate the basis of the motor defects, which are the first to appear during KD onset. Here we use transmission electron microscopy (TEM) to focus on the alterations produced by KD in the lower motor system at postnatal day 15 (P15), a nearly asymptomatic stage, and in the juvenile P30 mouse. We find mild effects on motorneuron soma, severe ones on sciatic nerves and very severe effects on nerve terminals and neuromuscular junctions at P30, with peripheral damage being already detectable at P15. Finally, we find that the gastrocnemius muscle undergoes atrophy and structural changes that are independent of denervation at P15. Our data further characterize the ultrastructural analysis of the KD mouse model, and support recent theories of a dying-back mechanism for neuronal degeneration, which is independent of demyelination.

\n The nitrogen-fixing symbiont\n Sinorhizobium meliloti\n senses and responds to constantly changing environmental conditions as it makes its way through the soil in search of its leguminous plant host,\n Medicago sativa\n (alfalfa). As a result, this bacterium regulates various aspects of its physiology in order to respond appropriately to stress, starvation, and competition. For example, exopolysaccharide production, which has been shown to play an important role in the ability of\n S. meliloti\n to successfully invade its host, also helps the bacterium withstand osmotic changes and other environmental stresses. In an effort to further elucidate the intricate regulation of this important cell component, we set out to identify genetic factors that may affect its production. Here we characterize novel genes that encode a small protein (EmmA) and a putative two-component system (EmmB-EmmC). A mutation in any of these genes leads to increased production of the symbiotically important exopolysaccharide succinoglycan. In addition,\n emm\n mutants display membrane-associated defects, are nonmotile, and are unable to form an optimal symbiosis with alfalfa, suggesting that these novel genes may play a greater role in the overall fitness of\n S. meliloti\n both during the free-living stage and in its association with its host.\n

Current agricultural practice depends on a wide use of pesticides, bactericides, and fungicides. Increased demand for organic products indicates consumer preference for reduced chemical use. Therefore, there is a need to develop novel sustainable strategies for crop protection and enhancement that do not rely on genetic modification and/or harmful chemicals. An increasing body of evidence indicates that bacterial and fungal microbial volatile organic compounds (MVOCs) might provide an alternative to the use of chemicals to protect plants from pathogens and provide a setting for better crop welfare. It is well known that MVOCs can modulate the physiology of plants and microorganisms and in this Opinion we propose that MVOCs can be exploited as an ecofriendly, cost-effective, and sustainable strategy for agricultural practices. Copyright © 2015 Elsevier Ltd. All rights reserved.

Metabolic capabilities of microorganisms include the production of secondary metabolites (e.g. antibiotics). The analysis of microbial volatile organic compounds (mVOCs) is an emerging research field with huge impact on medical, agricultural and biotechnical applied and basic science. The mVOC database (v1) has grown with microbiome research and integrated species information with data on emitted volatiles. Here, we present the mVOC 2.0 database with about 2000 compounds from almost 1000 species and new features to work with the database. The extended collection of compounds was augmented with data regarding mVOC-mediated effects on plants, fungi, bacteria and (in-)vertebrates. The mVOC database 2.0 now features a mass spectrum finder, which allows a quick mass spectrum comparison for compound identification and the generation of species-specific VOC signatures. Automatic updates, useful links and search for mVOC literature are also included. The mVOC database aggregates and refines available information regarding microbial volatiles, with the ultimate aim to provide a comprehensive and informative platform for scientists working in this research field. To address this need, we maintain a publicly available mVOC database at: http://bioinformatics.charite.de/mvoc.© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Twelve fungal species were screened for microbial volatile organic compounds (MVOCs): Aspergillus fumigatus, A. versicolor, A. niger, A. ochraceus, Trichoderma harzianum, T. pseudokoningii, Penicillium brevicompactum, P. chrysogenum, P. claviforme, P. expansum, Fusarium solani and Mucor sp. More than 150 volatile substances derived from fungal cultures have been analysed by head-space solid-phase microextraction (HS-SPME). Each species had a defined MVOC profile which may be subjected to considerable modification in response to external factors such as cultivation on different substrata. The cultivation on different substrata changes the number and concentration of MVOCs. Species-specific volatiles may serve as marker compounds for the selective detection of fungal species in indoor environments. Examination of MVOCs from indoor air samples may become an important method in indoor air hygiene for the detection of type and intensity of masked contamination by moulds.

Microbial volatile organic compounds (MVOCs) are produced by a wide array of microorganisms ranging from bacteria to fungi. A growing body of evidence indicates that MVOCs are ecofriendly and can be exploited as a cost-effective sustainable strategy for use in agricultural practice as agents that enhance plant growth, productivity, and disease resistance. As naturally occurring chemicals, MVOCs have potential as possible alternatives to harmful pesticides, fungicides, and bactericides as well as genetic modification. Recent studies performed under open field conditions demonstrate that efficiently adopting MVOCs may contribute to sustainable crop protection and production. We review here the chemical diversity of MVOCs by describing microbial plants and microbial microbial interactions. Furthermore, we discuss MVOCs role in inducing phenotypic plant responses and their potential physiological effects on crops. Finally, we analyze potential and actual limitations for MVOC use and deployment in field conditions as a sustainable strategy for improving productivity and reducing pesticide use.

Certain plant growth-promoting rhizobacteria (PGPR) elicit induced systemic resistance (ISR) and plant growth promotion in the absence of physical contact with plants via volatile organic compound (VOC) emissions. In this article, we review the recent progess made by research into the interactions between PGPR VOCs and plants, focusing on VOC emission by PGPR strains in plants. Particular attention is given to the mechanisms by which these bacterial VOCs elicit ISR. We provide an overview of recent progress in the elucidation of PGPR VOC interactions from studies utilizing transcriptome, metabolome, and proteome analyses. By monitoring defense gene expression patterns, performing 2-dimensional electrophoresis, and studying defense signaling null mutants, salicylic acid and ethylene have been found to be key players in plant signaling pathways involved in the ISR response. Bacterial VOCs also confer induced systemic tolerance to abiotic stresses, such as drought and heavy metals. A review of current analytical approaches for PGPR volatile profiling is also provided with needed future developments emphasized. To assess potential utilization of PGPR VOCs for crop plants, volatile suspensions have been applied to pepper and cucumber roots and found to be effective at protecting plants against plant pathogens and insect pests in the field. Taken together, these studies provide further insight into the biological and ecological potential of PGPR VOCs for enhancing plant self-immunity and/or adaptation to biotic and abiotic stresses in modern agriculture.

Root colonization of plants with certain rhizobacteria, such as Pseudomonas chlororaphis O6, induces tolerance to biotic and abiotic stresses. Tolerance to drought was correlated with reduced water loss in P. chlororaphis O6-colonized plants and with stomatal closure, indicated by size of stomatal aperture and percentage of closed stomata. Stomatal closure and drought resistance were mediated by production of 2R,3R-butanediol, a volatile metabolite of P. chlororaphis O6. Root colonization with bacteria deficient in 2R,3R-butanediol production showed no induction of drought tolerance. Studies with Arabidopsis mutant lines indicated that induced drought tolerance required the salicylic acid (SA)-, ethylene-, and jasmonic acid-signaling pathways. Both induced drought tolerance and stomatal closure were dependent on Aba-1 and OST-1 kinase. Increases in free SA after drought stress of P. chlororaphis O6-colonized plants and after 2R,3R-butanediol treatment suggested a primary role for SA signaling in induced drought tolerance. We conclude that the bacterial volatile 2R,3R-butanediol was a major determinant in inducing resistance to drought in Arabidopsis through an SA-dependent mechanism.

Infection of plants by necrotizing pathogens or colonization of plant roots with certain beneficial microbes causes the induction of a unique physiological state called "priming." The primed state can also be induced by treatment of plants with various natural and synthetic compounds. Primed plants display either faster, stronger, or both activation of the various cellular defense responses that are induced following attack by either pathogens or insects or in response to abiotic stress. Although the phenomenon has been known for decades, most progress in our understanding of priming has been made over the past few years. Here, we summarize the current knowledge of priming in various induced-resistance phenomena in plants.

Elevated sodium (Na(+)) decreases plant growth and, thereby, agricultural productivity. The ion transporter high-affinity K(+) transporter (HKT)1 controls Na(+) import in roots, yet dysfunction or overexpression of HKT1 fails to increase salt tolerance, raising questions as to HKT1's role in regulating Na(+) homeostasis. Here, we report that tissue-specific regulation of HKT1 by the soil bacterium Bacillus subtilis GB03 confers salt tolerance in Arabidopsis thaliana. Under salt stress (100 mM NaCl), GB03 concurrently down- and upregulates HKT1 expression in roots and shoots, respectively, resulting in lower Na(+) accumulation throughout the plant compared with controls. Consistent with HKT1 participation in GB03-induced salt tolerance, GB03 fails to rescue salt-stressed athkt1 mutants from stunted foliar growth and elevated total Na(+) whereas salt-stressed Na(+) export mutants sos3 show GB03-induced salt tolerance with enhanced shoot and root growth as well as reduced total Na(+). These results demonstrate that tissue-specific regulation of HKT1 is critical for managing Na(+) homeostasis in salt-stressed plants, as well as underscore the breadth and sophistication of plant-microbe interactions.

Microbial lifeforms associated with land plants represent a rich source for crop growth-and health-promoting microorganisms and biocontrol agents. Volatile organic compounds (VOCs) produced by the plant microbiota have been demonstrated to elicit plant defenses and inhibit the growth and development of numerous plant pathogens. Therefore, these molecules are prospective alternatives to synthetic pesticides and the determination of their bioactivities against plant threats could contribute to the development of control strategies for sustainable agriculture. In our previous study we investigated the inhibitory impact of volatiles emitted by Pseudomonas species isolated from a potato field against the late blight-causing agent Phytophthora infestans. Besides the well-documented emission of hydrogen cyanide, other Pseudomonas VOCs impeded P infestans mycelial growth and sporangia germination. Current advances in the field support the emerging concept that the microbial volatilome contains unexploited, eco-friendly chemical resources that could help select for efficient biocontrol strategies and lead to a greener chemical disease management in the field.

The generation of novel secondary metabolites by reengineering or refactoring biochemical pathways is a rewarding but also challenging goal of synthetic biology. For this, the development of tools for the reconstruction of secondary metabolite gene clusters as well as the challenge of understanding the obstacles in this process is of great interest. The artificial gene operon assembly system (AGOS) is a plug-and-play method developed as a tool to consecutively assemble artificial gene operons into a destination vector and subsequently express them under the control of a de-repressed promoter in a Streptomyces host strain. AGOS was designed as a set of entry plasmids for the construction of artificial gene operons and a SuperCos1 based destination vector, into which the constructed operons can be assembled by Red/ET-mediated recombination. To provide a proof-of-concept of this method, we disassembled the well-known novobiocin biosynthetic gene cluster into four gene operons, encoding for the different moieties of novobiocin. We then genetically reorganized these gene operons with the help of AGOS to finally obtain the complete novobiocin gene cluster again. The production of novobiocin precursors and of novobiocin could successfully be detected by LC-MS and LC-MS/MS. Furthermore, we demonstrated that the omission of terminator sequences only had a minor impact on product formation in our system.