Plant Beneficial Microbes Research Articles

Co-Culture of Plant Beneficial Microbes as Source of Bioactive Metabolites

In microbial cultures the production of secondary metabolites is affected by experimental conditions, and the discovery of novel compounds is often prevented by the re-isolation of known metabolites. To limit this, it is possible to cultivate microorganisms by simulating naturally occurring interactions, where microbes co-exist in complex communities. In this work, co-culturing experiments of the biocontrol agent Trichoderma harzianum M10 and the endophyte Talaromyces pinophilus F36CF have been performed to elicit the expression of genes which are not transcribed in standard laboratory assays. Metabolomic analysis revealed that the co-culture induced the accumulation of siderophores for both fungi, while production of M10 harzianic and iso-harzianic acids was not affected by F36CF. Conversely, metabolites of the latter strain, 3-O-methylfunicone and herquline B, were less abundant when M10 was present. A novel compound, hereby named harziaphilic acid, was isolated from fungal co-cultures, and fully characterized. Moreover, harzianic and harziaphilic acids did not affect viability of colorectal cancer and healthy colonic epithelial cells, but selectively reduced cancer cell proliferation. Our results demonstrated that the co-cultivation of plant beneficial fungi may represent an effective strategy to modulate the production of bioactive metabolites and possibly identify novel compounds.

Genotype-specific responses to the effects of commercial Trichoderma formulations in lentil (Lens culinaris ssp. culinaris) in the presence and absence of the oomycete pathogen Aphanomyces euteiches

ABSTRACTMembers of the endophytic fungal genus Trichoderma have been established as plant-beneficial microbes and are most successful commercial biologicals in the form of bio-fertilisers, biocontrol agents, and growth stimulators. We report the variable interactions among different lentil genotypes and Trichoderma strains in both the presence and absence of biotic stress (root-rot pathogen Aphanomyces euteiches). Two commercial Trichoderma formulations, namely RootShield® (RS) and RootShield® Plus (RSP) based on T. harzianum T22 and T. virens G41, respectively, were evaluated for control of Aphanomyces root rot and plant growth promotion in 23 wild and cultivated lentil genotypes. No significant disease control was recorded with either formulation in any lentil genotype. Significant genotype-specific plant growth promotion was observed in terms of root and shoot development and leaf parameters in a genotype-specific manner. Genotypes of Lens culinaris and Lens tomentosus, both in the primary lentil gene pool, demonstrated the maximum response. The overall effect of Trichoderma treatment was markedly higher under biotically stressed conditions in comparison to unstressed conditions. In many cases, negative responses were recorded, particularly in the absence of root-rot disease. L. tomentosus PI 572390 exhibited positive responses for most of the tested parameters. Our findings clearly indicate that, in the case of lentil, plant genotype plays a major role in interactions among the tested Trichoderma strains and the plant. Moreover, the influence of Trichoderma was greater and more favourable under conditions of biotic stress vs. the absence of stress.

Genome-wide identification of bacterial plant colonization genes.

Diverse soil-resident bacteria can contribute to plant growth and health, but the molecular mechanisms enabling them to effectively colonize their plant hosts remain poorly understood. We used randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) in Pseudomonas simiae, a model root-colonizing bacterium, to establish a genome-wide map of bacterial genes required for colonization of the Arabidopsis thaliana root system. We identified 115 genes (2% of all P. simiae genes) with functions that are required for maximal competitive colonization of the root system. Among the genes we identified were some with obvious colonization-related roles in motility and carbon metabolism, as well as 44 other genes that had no or vague functional predictions. Independent validation assays of individual genes confirmed colonization functions for 20 of 22 (91%) cases tested. To further characterize genes identified by our screen, we compared the functional contributions of P. simiae genes to growth in 90 distinct in vitro conditions by RB-TnSeq, highlighting specific metabolic functions associated with root colonization genes. Our analysis of bacterial genes by sequence-driven saturation mutagenesis revealed a genome-wide map of the genetic determinants of plant root colonization and offers a starting point for targeted improvement of the colonization capabilities of plant-beneficial microbes.

Tiny Microbes, Big Yields: enhancing food crop production with biological solutions.

SummaryPlant‐associated microbiomes have tremendous potential to improve plant resilience and yields in farming systems. There is increasing evidence that biological technologies that use microbes or their metabolites can enhance nutrient uptake and yield, control pests and mitigate plant stress responses. However, to fully realize the potential of microbial technology, their efficacy and consistency under the broad range of real‐world conditions need to be improved. While the optimization of microbial biofertilizers and biopesticides is advancing rapidly to enable use in various soils, crop varieties and environments, crop breeding programmes have yet to incorporate the selection of beneficial plant–microbe interactions to breed ‘microbe‐optimized plants’. Emerging efforts exploring microbiome engineering could lead to microbial consortia that are better suited to support plants. The combination of all three approaches could be integrated to achieve maximum benefits and significantly improved crop yields to address food security.

In vitro effects of copper nanoparticles on plant pathogens, beneficial microbes and crop plants

Copper-based chemicals are effectively used as antimicrobials in agriculture. However, with respect to its nanoparticulate form there has been limited number of studies. In this investigation, in vitro tests on effect of copper nanoparticles (CuNPs) against plant pathogenic fungi, oomycete, bacteria, beneficial microbes Trichoderma harzianum and Rhizobium spp., and wheat seeds were conducted. Integration of CuNPs with non-nano copper like copper oxychloride (CoC) at 50 mg/L concentration each recorded 76% growth inhibition of the oomycete Phytophthora cinnamomi in vitro compared to the control. CuNPs also showed synergistic inhibitory effect with CoC on mycelial growth and sporulation of A. alternata. Pseudomonas syringae was inhibited at 200 mg/L of CuNPs. CuNPs were not significantly biocidal against Rhizobium spp. and Trichoderma harzianum compared to CoC. Evaluation of the effect of CuNP on wheat revealed that rate of germination of wheat seeds was higher in presence of CuNPs and CoC compared to control. Germination vigor index, root length, shoot dry weight and seed metabolic efficiency of wheat were negatively affected. At low concentration, CuNPs promoted the growth of the plant pathogenic fungi Botrytis fabae, Fusarium oxysporum f.sp. ciceris, F.oxysporum f.sp. melonis, Alternaria alternate and P. syringae, and sporulation of T. harzianum. Synergistic effect of CuNPs and CoC in inhibiting P. cinnamomi offers a possibility of developing new fungicide formulation for better control of the oomycetes. Non-biocidal effect of CuNPs against beneficial microbes indicates its potential use in the agri-ecosystem.

Change of growth promotion and disease resistant of wheat seedling by application of biocontrol bacterium Pseudochrobactrum kiredjianiae A4 under simulated microgravity

Plant disease control and prevention in microgravity are critical for space plant cultivation. This study investigated the effects of a biocontrol bacterium Pseudochrobactrum kiredjianiae A4 on growth development and antifungal potential of wheat seedlings under simulated microgravity. The growth, antioxidant status and plant immune hormone of both non-infected and infected wheat seedlings were detected before and after inoculation of A4 strains under simulated microgravity condition (μG) and ground condition (1G). Our results showed that bacteria A4 promoted wheat growth by increasing root length and biomass accumulation and meanwhile enhancing fungal disease resistance through improving the antioxidant enzyme activities and plant hormone secretion. Moreover, A4 exhibited a weaker promotion ability on wheat biomass accumulation and disease resistance under μG condition compared to that under 1G. These results not only expand our understanding of the impact of microgravity on plant-microbe interaction, but also provide valuable insights into using plant beneficial microbes for plant cultivation and crop protection in space.

Tritrophic Interactions: Microbe-Mediated Plant Effects on Insect Herbivores.

It is becoming abundantly clear that the microbes associated with plants and insects can profoundly influence plant-insect interactions. Here, we focus on recent findings and propose directions for future research that involve microbe-induced changes to plant defenses and nutritive quality as well as the consequences of these changes for the behavior and fitness of insect herbivores. Insect (herbivore and parasitoid)-associated microbes can favor or improve insect fitness by suppressing plant defenses and detoxifying defensive phytochemicals. Phytopathogens can influence or manipulate insect behavior and fitness by altering plant quality and defense. Plant-beneficial microbes can promote plant growth and influence plant nutritional and phytochemical composition that can positively or negatively influence insect fitness. Lastly, we suggest that entomopathogens have the potential to influence plant defenses directly as endophytes or indirectly by altering insect physiology.

Perspectives and Challenges of Microbial Application for Crop Improvement.

Global population increases and climate change pose a challenge to worldwide crop production. There is a need to intensify agricultural production in a sustainable manner and to find solutions to combat abiotic stress, pathogens, and pests. Plants are associated with complex microbiomes, which have an ability to promote plant growth and stress tolerance, support plant nutrition, and antagonize plant pathogens. The integration of beneficial plant-microbe and microbiome interactions may represent a promising sustainable solution to improve agricultural production. The widespread commercial use of the plant beneficial microorganisms will require a number of issues addressed. Systems approach using microscale information technology for microbiome metabolic reconstruction has potential to advance the microbial reproducible application under natural conditions.

Understanding and exploiting plant beneficial microbes

Understanding and exploiting plant beneficial microbes

Role of salt precursors for the synthesis of zinc oxide nanoparticles and in imparting variable antimicrobial activity

Synthesis of nanoparticles (NPs) having unique potentials and properties is of great importance in nanotechnology. The NP synthesis techniques may include the wet chemistry to microbial incubation reduction methods. This work reports generation of ZnO NPs by identical preparation including incubation of different zinc salts i.e. zinc acetate, zinc chloride and zinc sulphate as precursors with cell free extracts of Bacillus circulans MTCC 7906 (Bc7906) and Pleurotus florida (Pf). The synthesized NPs exhibited variation in their absorption peaks in UV-Vis spectra which appeared at 275 nm, 325 nm and 375 nm with P. florida for the three salt precursors respectively while the Bc7906 generated ZnO NPs showed peaks between 300-350 nm. A variation in ZnO NP morphology ranged from 50 to 120 nm in size and spherical, oval, cylindrical to trigonal anisotropic in shape by transmission EM. Further, the rough and corrugated surface topography of ZnO NPs was observed in Scanning EM. The % weight for Zn element surface composition as recorded by SEM-EDS was observed to be highest for zinc acetate (2.34%) and zinc sulphate (7.54 %) on microbial synthesis from Bc7906 and Pf respectively. The antimicrobial potential of the synthesized ZnO NPs on human pathogenic and plant beneficial bacteria was tested and it was observed to be highest for microbially synthesized ZnO NPs using zinc acetate (15 mm) and zinc sulphate (14 mm) as salt precursors @ 10 ppm. This is the first report on differential antimicrobial behavior of ZnO NPs on human pathogenic and plant beneficial microbes.

Optimizing Chemically Induced Resistance in Tomato Against Botrytis cinerea.

Resistance-inducing chemicals can offer broad-spectrum disease protection in crops, but can also affect plant growth and interactions with plant-beneficial microbes. We have evaluated different application methods of β-aminobutyric acid (BABA) and jasmonic acid (JA) for long-lasting induced resistance in tomato against Botrytis cinerea. In addition, we have studied nontarget effects on plant growth and root colonization by arbuscular mycorrhizal fungi (AMF). Germinating seeds for 1 week in BABA- or JA-containing solutions promoted seed germination efficiency, did not affect plant growth, and induced resistance in 4-week-old plants. When formulating BABA and JA in carboxymethyl cellulose seed coating, only BABA was able to induce resistance in 4-week-old plants. Root treatment of 1-week-old seedlings with BABA or JA also induced resistance in 4-week-old plants. However, this seedling treatment repressed plant growth at higher concentrations of the chemicals, which was particularly pronounced in hydroponically grown plants after BABA treatment. Both seed coating with BABA, and seedling treatments with BABA or JA, did not affect AMF root colonization in soil-grown tomato. Our study has identified commercially feasible application methods of BABA and JA, which induce durable disease resistance in tomato without concurrent impacts on plant growth or colonization by plant-beneficial AMF.

A perspective on inter-kingdom signaling in plant-beneficial microbe interactions.

Recent work has shown that the rhizospheric and phyllospheric microbiomes of plants are composed of highly diverse microbial species. Though the information pertaining to the diversity of the aboveground and belowground microbes associated with plants is known, an understanding of the mechanisms by which these diverse microbes function is still in its infancy. Plants are sessile organisms, that depend upon chemical signals to interact with the microbiota. Of late, the studies related to the impact of microbes on plants have gained much traction in the research literature, supporting diverse functional roles of microbes on plant health. However, how these microbes interact as a community to confer beneficial traits to plants is still poorly understood. Recent advances in the use of "biologicals" as bio-fertilizers and biocontrol agents for sustainable agricultural practices is promising, and a fundamental understanding of how microbes in community work on plants could help this approach be more successful. This review attempts to highlight the importance of different signaling events that mediate a beneficial plant microbe interaction. Fundamental research is needed to understand how plants react to different benign microbes and how these microbes are interacting with each other. This review highlights the importance of chemical signaling, and biochemical and genetic events which determine the efficacy of benign microbes to promote the development of beneficial traits in plants.

Insight into the Interaction between Plants and Associated FluorescentPseudomonasspp.

FluorescentPseudomonasare known for their plant growth promoting and disease protection abilities. In past years, a number of studies have focused on how these bacteria suppress disease and induce resistance. They are known to produce antibiotics and siderophores, promote growth, and induce systemic resistance in the host plant. This bacterium has come out as a model organism for ecological studies going on in rhizosphere and for studying plant-beneficial microbe interaction. This review focuses on the current state of knowledge on biocontrol potential of fluorescentPseudomonasstrains and the mechanisms adopted by them.

Fungal endophyte infection of ryegrass reprograms host metabolism and alters development.

Summary Beneficial associations between plants and microbes play an important role in both natural and agricultural ecosystems. For example, associations between fungi of the genus Epichloë, and cool‐season grasses are known for their ability to increase resistance to insect pests, fungal pathogens and drought. However, little is known about the molecular changes induced by endophyte infection.To study the impact of endophyte infection, we compared the expression profiles, based on RNA sequencing, of perennial ryegrass infected with Epichloë festucae with noninfected plants.We show that infection causes dramatic changes in the expression of over one third of host genes. This is in stark contrast to mycorrhizal associations, where substantially fewer changes in host gene expression are observed, and is more similar to pathogenic interactions. We reveal that endophyte infection triggers reprogramming of host metabolism, favouring secondary metabolism at a cost to primary metabolism. Infection also induces changes in host development, particularly trichome formation and cell wall biogenesis.Importantly, this work sheds light on the mechanisms underlying enhanced resistance to drought and super‐infection by fungal pathogens provided by fungal endophyte infection. Finally, our study reveals that not all beneficial plant–microbe associations behave the same in terms of their effects on the host.

Unearthing the genomes of plant-beneficial Pseudomonas model strains WCS358, WCS374 and WCS417.

BackgroundPlant growth-promoting rhizobacteria (PGPR) can protect plants against pathogenic microbes through a diversity of mechanisms including competition for nutrients, production of antibiotics, and stimulation of the host immune system, a phenomenon called induced systemic resistance (ISR). In the past 30 years, the Pseudomonas spp. PGPR strains WCS358, WCS374 and WCS417 of the Willie Commelin Scholten (WCS) collection have been studied in detail in pioneering papers on the molecular basis of PGPR-mediated ISR and mechanisms of biological control of soil-borne pathogens via siderophore-mediated competition for iron.ResultsThe genomes of the model WCS PGPR strains were sequenced and analyzed to unearth genetic cues related to biological questions that surfaced during the past 30 years of functional studies on these plant-beneficial microbes. Whole genome comparisons revealed important novel insights into iron acquisition strategies with consequences for both bacterial ecology and plant protection, specifics of bacterial determinants involved in plant-PGPR recognition, and diversity of protein secretion systems involved in microbe-microbe and microbe-plant communication. Furthermore, multi-locus sequence alignment and whole genome comparison revealed the taxonomic position of the WCS model strains within the Pseudomonas genus. Despite the enormous diversity of Pseudomonas spp. in soils, several plant-associated Pseudomonas spp. strains that have been isolated from different hosts at different geographic regions appear to be nearly isogenic to WCS358, WCS374, or WCS417. Interestingly, all these WCS look-a-likes have been selected because of their plant protective or plant growth-promoting properties.ConclusionsThe genome sequences of the model WCS strains revealed that they can be considered representatives of universally-present plant-beneficial Pseudomonas spp. With their well-characterized functions in the promotion of plant growth and health, the fully sequenced genomes of the WCS strains provide a genetic framework that allows for detailed analysis of the biological mechanisms of the plant-beneficial traits of these PGPR. Considering the increasing focus on the role of the root microbiome in plant health, functional genomics of the WCS strains will enhance our understanding of the diversity of functions of the root microbiome.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1632-z) contains supplementary material, which is available to authorized users.

Paenibacillus yonginensis DCY84T induces changes in Arabidopsis thaliana gene expression against aluminum, drought, and salt stress

Current agricultural production methods, for example the improper use of chemical fertilizers and pesticides, create many health and environmental problems. Use of plant growth-promoting bacteria (PGPB) for agricultural benefits is increasing worldwide and also appears to be a trend for the future. There is possibility to develop microbial inoculants for use in agricultural biotechnology, based on these beneficial plant–microbe interactions. For this study, ten bacterial strains were isolated from Yongin forest soil for which in vitro plant-growth promoting trait screenings, such as indole acetic acid (IAA) production, a phosphate solubilization test, and a siderophore production test were used to select two PGPB candidates. Arabidopsis thaliana plants were inoculated with Paenibacillus yonginensis DCY84T and Micrococcus yunnanensis PGPB7. Salt stress, drought stress and heavy metal (aluminum) stress challenges indicated that P. yonginensis DCY84T-inoculated plants were more resistant than control plants. AtRSA1, AtVQ9 and AtWRKY8 were used as the salinity responsive genes. The AtERD15, AtRAB18, and AtLT178 were selected to check A. thaliana responses to drought stress. Aluminum stress response was checked using AtAIP, AtALS3 and AtALMT1. The qRT-PCR results indicated that P. yonginensis DCY84T can promote plant tolerance against salt, drought, and aluminum stress. P. yonginensis DCY84T also showed positive results during in vitro compatibility testing and virulence assay against X. oryzae pv. oryzae Philippine race 6 (PXO99). Better germination rates and growth parameters were also recorded for the P. yonginensis DCY84T Chuchung cultivar rice seed which was grown on coastal soil collected from Suncheon. Based on these results, P. yonginensis DCY84T can be used as a promising PGPB isolate for crop improvement.

Root-feeding insects and their interactions with organisms in the rhizosphere.

Root-feeding insects are an increasingly studied group of herbivores whose impacts on plant productivity and ecosystem processes are widely recognized. Their belowground habitat has hitherto hindered our understanding of how they interact with other organisms that share the rhizosphere. A surge in research in this area has now shed light on these interactions. We review key interactions between root-feeding insects and other rhizospheric organisms, including beneficial plant microbes (mycorrhizal fungi, nitrogen-fixing bacteria), antagonists/pathogens of root herbivores (arthropod predators, entomopathogenic nematodes/fungi, and bacterial pathogens), competitors, symbiotic microbes, and detritivores. Patterns for these interactions are emerging. The negative impacts of mycorrhizal fungi on root herbivores, for instance, raise the intriguing prospect that these fungi could be used for pest management. Moreover, a better understanding of symbiotic microbes in root herbivores, especially those underpinning digestion, could prove useful in industries such as biofuel production.

21st century agriculture: integration of plant microbiomes for improved crop production and food security.

21st century agriculture: integration of plant microbiomes for improved crop production and food security.

Understanding and engineering beneficial plant-microbe interactions: plant growth promotion in energy crops.

Plant production systems globally must be optimized to produce stable high yields from limited land under changing and variable climates. Demands for food, animal feed, and feedstocks for bioenergy and biorefining applications, are increasing with population growth, urbanization and affluence. Low-input, sustainable, alternatives to petrochemical-derived fertilizers and pesticides are required to reduce input costs and maintain or increase yields, with potential biological solutions having an important role to play. In contrast to crops that have been bred for food, many bioenergy crops are largely undomesticated, and so there is an opportunity to harness beneficial plant–microbe relationships which may have been inadvertently lost through intensive crop breeding. Plant–microbe interactions span a wide range of relationships in which one or both of the organisms may have a beneficial, neutral or negative effect on the other partner. A relatively small number of beneficial plant–microbe interactions are well understood and already exploited; however, others remain understudied and represent an untapped reservoir for optimizing plant production. There may be near-term applications for bacterial strains as microbial biopesticides and biofertilizers to increase biomass yield from energy crops grown on land unsuitable for food production. Longer term aims involve the design of synthetic genetic circuits within and between the host and microbes to optimize plant production. A highly exciting prospect is that endosymbionts comprise a unique resource of reduced complexity microbial genomes with adaptive traits of great interest for a wide variety of applications.

Transcriptional regulation of Arabidopsis thaliana WRKY genes under interaction with beneficial fungus Trichoderma atroviride

Plants are associated with a wide range of microorganisms, and these interactions induce changes in both the plant and microorganism. Transcription factors play an important role in the regulation of large numbers of genes associated to plant–microbe response. WRKY transcription factors have been involved in the responses to plant–pathogen interactions, but little is known about WRKY transcription factors in beneficial plant–microbe interactions. In this study, the expression patterns of Arabidopsis thalianaWRKY genes were evaluated during the interaction with the beneficial fungus Trichoderma atroviride. Eight WRKY genes, AtWRKY8, AtWRKY33, AtWRKY38, AtWRKY42, AtWRKY54, AtWRKY57, AtWRKY60 and AtWRKY70, were analyzed by quantitative RT-PCR. These WRKY genes were found differentially expressed in a time-dependent manner during T. atroviride interaction. Our data suggest that T. atroviride induces the expression of positive regulators in jasmonic acid-mediated pathway such as AtWRKY8, AtWRKY33, AtWRKY38, AtWRKY42 and AtWRKY60, while salicylic acid pathway regulated by AtWRKY70 and AtWRKY54, could be activated at later stages of the interaction, when the fungus is fully established in the plant roots. In addition, Trichoderma treatment regulates the expression of WRKY genes such as AtWRKY57, AtWRKY60 and AtWRKY33 related to response to abiotic stresses. In this sense, WRKY transcription factors regulation suggests a complex signaling network in this beneficial plant–microbe interaction.