Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria

Fine-Tuning of Arabidopsis thaliana Response to Endophytic Colonization by Gluconacetobacter diazotrophicus PAL5 Revealed by Transcriptomic Analysis

Gluconacetobacter diazotrophicus is a diazotrophic endophytic bacterium that promotes the growth and development of several plant species. However, the molecular mechanisms activated during plant response to this bacterium remain unclear. Here, we used the RNA-seq approach to understand better the effect of G. diazotrophicus PAL5 on the transcriptome of shoot and root tissues of Arabidopsis thaliana. G. diazotrophicus colonized A. thaliana roots and promoted growth, increasing leaf area and biomass. The transcriptomic analysis revealed several differentially expressed genes (DEGs) between inoculated and non-inoculated plants in the shoot and root tissues. A higher number of DEGs were up-regulated in roots compared to shoots. Genes up-regulated in both shoot and root tissues were associated with nitrogen metabolism, production of glucosinolates and flavonoids, receptor kinases, and transcription factors. In contrast, the main groups of down-regulated genes were associated with pathogenesis-related proteins and heat-shock proteins in both shoot and root tissues. Genes encoding enzymes involved in cell wall biogenesis and modification were down-regulated in shoots and up-regulated in roots. In contrast, genes associated with ROS detoxification were up-regulated in shoots and down-regulated in roots. These results highlight the fine-tuning of the transcriptional regulation of A. thaliana in response to colonization by G. diazotrophicus PAL5.

Exploring the potential of endophyte-plant interactions for improving crop sustainable yields in a changing climate

Climate change poses a major threat to global food security, significantly reducing crop yields as cause of abiotic stresses, and for boosting the spread of new and old pathogens and pests. Sustainable crop management as a route to mitigation poses the challenge of recruiting an array of solutions and tools for the new aims. Among these, the deployment of positive interactions between the micro-biotic components of agroecosystems and plants can play a highly significant role, as part of the agro-ecological revolution. Endophytic microorganisms have emerged as a promising solution to tackle this challenge. Among these, Arbuscular Mycorrhizal Fungi (AMF) and endophytic bacteria and fungi have demonstrated their potential to alleviate abiotic stresses such as drought and heat stress, as well as the impacts of biotic stresses. They can enhance crop yields in a sustainable way also by other mechanisms, such as improving the nutrient uptake, or by direct effects on plant physiology. In this review we summarize and update on the main types of endophytes, we highlight several studies that demonstrate their efficacy in improving sustainable yields and explore possible avenues for implementing crop-microbiota interactions. The mechanisms underlying these interactions are highly complex and require a comprehensive understanding. For this reason, omic technologies such as genomics, transcriptomics, proteomics, and metabolomics have been employed to unravel, by a higher level of information, the complex network of interactions between plants and microorganisms. Therefore, we also discuss the various omic approaches and techniques that have been used so far to study plant-endophyte interactions.

Multispecies Bacterial Bio-Input: Tracking and Plant-Growth-Promoting Effect on Lettuce var. sagess

The use of multispecies bacterial bio-inputs is a promising strategy for sustainable crop production over the use of single-species inoculants. Studies of the use of multispecies bio-inputs in horticultural crops are scarce, not only on the growth-promoting effects of each bacterium within the formulation, but also on their compatibility and persistence in the root environment. In this work, we described that a multispecies bacterial bio-input made up of Azospirillum argentinense Az39, Gluconacetobacter diazotrophicus PAL-5, Pseudomonas protegens Pf-5 and Bacillus sp. Dm-B10 improved lettuce plant growth more effectively than when these strains were inoculated as single-species bio-inputs. Bacteria persisted together (were compatible) and also colonized seedling roots of lettuce plants grown in controlled conditions. Interestingly, colonization was highly related to an early and enhanced growth of seedlings grown in the nursery. A similar effect on plant growth was found in lettuce plants in a commercial greenhouse production in the peri-urban area of La Plata City, Buenos Aires, Argentina. To our knowledge, this is the first study demonstrating that a synthetic mixture of bacteria can colonize and persist on lettuce plants, and also showing their synergistic beneficial effect both in the nursery greenhouse as well as the commercial production farm.

Understanding plant-microbe interaction of rice and soybean with two contrasting diazotrophic bacteria through comparative transcriptome analysis

Understanding the beneficial plant-microbe interactions is becoming extremely critical for deploying microbes imparting plant fitness and achieving sustainability in agriculture. Diazotrophic bacteria have the unique ability to survive without external sources of nitrogen and simultaneously promote host plant growth, but the mechanisms of endophytic interaction in cereals and legumes have not been studied extensively. We have studied the early interaction of two diazotrophic bacteria, Gluconacetobacter diazotrophicus (GAB) and Bradyrhizobium japonicum (BRH), in 15-day-old seedlings of rice and soybean up to 120 h after inoculation (hai) under low-nitrogen medium. Root colonization of GAB in rice was higher than that of BRH, and BRH colonization was higher in soybean roots as observed from the scanning electron microscopy at 120 hai. Peroxidase enzyme was significantly higher at 24 hai but thereafter was reduced sharply in soybean and gradually in rice. The roots of rice and soybean inoculated with GAB and BRH harvested from five time points were pooled, and transcriptome analysis was executed along with control. Two pathways, "Plant pathogen interaction" and "MAPK signaling," were specific to Rice-Gluconacetobacter (RG), whereas the pathways related to nitrogen metabolism and plant hormone signaling were specific to Rice-Bradyrhizobium (RB) in rice. Comparative transcriptome analysis of the root tissues revealed that several plant-diazotroph-specific differentially expressed genes (DEGs) and metabolic pathways of plant-diazotroph-specific transcripts, viz., chitinase, brassinosteroid, auxin, Myeloblastosis (MYB), nodulin, and nitrate transporter (NRT), were common in all plant-diazotroph combinations; three transcripts, viz., nitrate transport accessory protein (NAR), thaumatin, and thionin, were exclusive in rice and another three transcripts, viz., NAC (NAM: no apical meristem, ATAF: Arabidopsis thaliana activating factor, and CUC: cup-shaped cotyledon), ABA (abscisic acid), and ammonium transporter, were exclusive in soybean. Differential expression of these transcripts and reduction in pathogenesis-related (PR) protein expression show the early interaction. Based on the interaction, it can be inferred that the compatibility of rice and soybean is more with GAB and BRH, respectively. We propose that rice is unable to identify the diazotroph as a beneficial microorganism or a pathogen from an early response. So, it expressed the hypersensitivity-related transcripts along with PR proteins. The molecular mechanism of diazotrophic associations of GAB and BRH with rice vis-à-vis soybean will shed light on the basic understanding of host responses to beneficial microorganisms.

Tracking and plant growth-promoting effect of Paraburkholderia tropica MTo-293 applied to Solanum lycopersicum

Paraburkholderia tropica MTo-293 was applied as an experimental bio-input to Solanum lycopersicum (tomato) cv. Platense. Different plant growth systems and inoculation strategies were tested to evaluate P. tropica plant colonization at the seedling stage (growth chamber) using culture-dependent and -independent techniques. The effect of P. tropica on plant growth was evaluated in the growth chamber and greenhouse (productive stage) by biomass accumulation and fruit production, respectively. P. tropica was able to colonize the surface and inner root and stem of tomato seedlings regardless of the inoculation strategy-at sowing and/or before transplanting-showing the competitive nature of P. tropica in nonsterile substrate systems. A nested polymerase chain reaction was validated to track P. tropica in tomato plants even in the inner stem with endophytic P. tropica populations of less than 10²  CFU g^-1 of fresh weight. Efficient colonization of P. tropica correlated with a positive effect on tomato growth when applied at sowing and/or before transplanting: plant growth promotion was observed not only at the seedling stage but also at productive stages improving crop yield in two different seasons. To our knowledge, this report is the first to track and evaluate the plant growth-promoting effect of P. tropica MTo-293 in tomato plants grown in nonsterile substrate systems.

Gluconacetobacter diazotrophicus Inoculation of Two Lettuce Cultivars Affects Leaf and Root Growth under Hydroponic Conditions

The growth-promoting effects of Gluconacetobacter diazotrophicus inoculation on the leaf lettuce (Lactuca sativa L.) cultivars “Black Seeded Simpson” and “Bibb/Limestone” were investigated. Plants of each cultivar were grown hydroponically in Kratky jars in a growth chamber-controlled environment in a completely randomized factorial design with three or four replications. Each experiment was repeated once. Factors were (1) with or without inoculant and (2) seven levels of nitrogen (N) fertilization ranging from deficient (37.5 mg L−1 N) to excessive (172.5 mg L−1 N). The shoot, root, and total biomass accumulation, nitrogen density, and carbon/nitrogen (C/N) ratios were measured for each variety. Black Seeded Simpson demonstrated a shifting of production towards aerial tissues, with significantly greater shoot production and reduced root production. The observed increase in shoot biomass was greatest at the slightly deficient N rate of 105 mg L−1 N where inoculated plants produced 14.8% more than uninoculated plants. Lower N density and higher C/N ratios in inoculated shoot tissues indicate greater N use efficiency. Bibb/Limestone responded to inoculation with an average increase of 10.9% in shoot production and with greater root biomass. Bibb/Limestone also exhibited lower N density in inoculated shoot tissues with a corresponding increase in the C/N ratio. For growers looking to maximize lettuce yields, G. diaz inoculation may present a beneficial additive to the growing system by increasing leaf yields while not increasing N fertilizer requirements.

An endophytic Talaromyces omanensis enhances reproductive, physiological and anatomical characteristics of drought-stressed tomato

The effects of a newly discovered endophytic fungus, Talaromyces omanensis, on the drought tolerance of tomato is presented in this study. The fungus was obtained from a desert plant Rhazya stricta in Oman. Drought stress was induced by a 15% solution of Polyethylene glycol-6000 (PEG-6000). Several parameters were measured including pollen sterility, pollen tube length, growth, flowering, and yield characteristics, the biochemical analysis of the leaves and fruits, as well as other physiological and anatomical parameters. The results showed that T. omanensis provided multiple advantages to tomato grown under drought stress, including improved reproductive characteristics, chlorophyll fluorescence, and some anatomical characteristics such as increased phloem and cortex width and a reduction of pith autolysis that leads to hollow stem. In addition, T. omanensis significantly increased drought-stress related characteristics such as shoot dry weight, root length, the number of flowers, and fruit weight. A significantly higher concentration of gibberellic acid (GA₃) was found in tomato plants treated by T. omanensis, which may enhance their drought tolerance. These results suggest that T. omanensis is a potential biological anti-stress stimulator for important horticultural crops such as tomatoes. This study is the first to report the beneficial effects of T. omanensis in alleviating drought stress in tomatoes.

Anatomical and Biochemical Changes Induced by Gluconacetobacter diazotrophicus Stand Up for Arabidopsis thaliana Seedlings From Ralstonia solanacearum Infection

Nowadays, fertilization and pest control are carried out using chemical compounds that contaminate soil and deteriorate human health. Plant growth promoting bacteria endophytes (PGPBEs), are a well-studied group of bacteria that offers benefits to the host plant, such as phytostimulation, biofertilization, and protection against other microorganisms. The study of Gluconacetobacter diazotrophicus-which belongs to PGPBEs-aids the development of alternative strategies of an integrated approach for crop management practices. Ralstonia solanacearum is responsible for bacterial wilt disease. This phytopathogen is of great interest worldwide due to the enormous economic losses it causes. In this study the action of G. diazotrophicus as a growth promoting bacterium in Arabidopsis thaliana seedlings is analyzed, evaluating the antagonistic mechanisms of this beneficial endophytic bacterium during biotic stress produced by R. solanacearum. Effective colonization of G. diazotrophicus was determined through bacterial counting assays, evaluation of anatomical and growth parameters, and pigments quantification. Biocontrol assays were carried out with Ralstonia pseudosolanacearum GMI1000 model strain and R. solanacearum A21 a recently isolated strain. Inoculation of A. thaliana (Col 0) with G. diazotrophicus Pal 5 triggers a set of biochemical and structural changes in roots, stems, and leaves of seedlings. Discrete callose deposits as papillae were observed at specific sites of root hairs, trichomes, and leaf tissue. Upon R. pseudosolanacearum GMI1000 infection, endophyte-treated plants demonstrated being induced for defense through an augmented callose deposition at root hairs and leaves compared with the non-endophyte-treated controls. The endophytic bacterium appears to be able to prime callose response. Roots and stems cross sections showed that integrity of all tissues was preserved in endophyte-treated plants infected with R. solanacearum A21. The mechanisms of resistance elicited by the plant after inoculation with the endophyte would be greater lignification and sclerosis in tissues and reinforcement of the cell wall through the deposition of callose. As a consequence of this priming in plant defense response, viable phytopathogenic bacteria counting were considerably fewer in endophyte-inoculated plants than in not-inoculated controls. Our results indicate that G. diazotrophicus colonizes A. thaliana plants performing a protective role against the phytopathogenic bacterium R. solanacearum promoting the activation of plant defense system.

Ability of endophytic fungi associated with Withania somnifera L. to control Fusarium Crown and Root Rot and to promote growth in tomato

Fusarium crown and root rot (FCRR), caused by Fusarium oxysporum f. sp. radicis-lycopersici (FORL), is a soilborne tomato disease of increased importance worldwide. In this study, Withania somnifera was used as a potential source of biological control and growth-promoting agents. Seven fungal isolates naturally associated with W. somnifera were able to colonize tomato seedlings. They were applied as conidial suspensions or a cell-free culture filtrate. All isolates enhanced treated tomato growth parameters by 21.5-90.3% over FORL-free control and by 27.6-93.5% over pathogen-inoculated control. All tested isolates significantly decreased by 28.5-86.4% disease severity over FORL-inoculated control. The highest disease suppression, by 86.4-92.8% over control and by 81.3-88.8% over hymexazol-treated control, was achieved by the I6 isolate. FORL radial growth was suppressed by 58.5-82.3% versus control when dual cultured with tested isolates and by 61.8-83.2% using their cell-free culture filtrates. The most active agent was identified as Fusarium sp. I6 (MG835371), which displayed chitinolytic, proteolytic, and amylase activities. This has been the first report on the potential use of fungi naturally associated with W. somnifera for FCRR suppression and for tomato growth promotion. Further investigations are required in regard to mechanisms of action involved in disease suppression and plant growth promotion.

Assessment of bacterial inoculant formulated with Paraburkholderia tropica to enhance wheat productivity

Paraburkholderia tropica is an endophytic nitrogen-fixing bacterium isolated from the rhizosphere, rhizoplane, and internal tissues of sugarcane and corn plants in different geographical regions. Other plant-growth-promoting abilities, such as phosphate solubilization and antifungal activity, have also been reported for this bacterium. With an aim at investigating the potential use of P. tropica as an inoculant for improving the performance of wheat crop, in this work we evaluated an experimental inoculant formulated with P. tropica MTo-293 with respect to root colonization, the practical aspects of its application, and the effects under field conditions when applied to wheat seeds. Bacterial colonization was monitored by culture dependent techniques and the wheat yield determined by quantifying the total grain production in two different seasons. Rhizoplane and endophytic colonization in wheat roots was achieved efficiently (on average, 8 and 4 log colony-forming units/g fresh weight, respectively) even at relatively low concentrations of viable bacteria in the inoculum under controlled conditions. P. tropica was compatible with a widely used fungicide, maintained viability for 48 h once applied to seeds, and was also able to colonize wheat roots efficiently. Furthermore, we were able to formulate an inoculant that maintained bacterial viability for relatively long time periods. Preliminary field assays were realized, and even though the average yields values for the inoculated treatments remained above the uninoculated ones, no significant effects of inoculation were detected with or without fertilization. The correct physiologic behavior of P. tropica suggests the necessity to continue with field experiments under different conditions.

The plant growth-promoting bacterium Kosakonia radicincitans improves fruit yield and quality of Solanum lycopersicum

BACKGROUND

Production and the quality of tomato fruits have a strong economic relevance. Microorganisms such as the plant growth-promoting bacterium (PGPB) Kosakonia radicincitans (DSM 16656) have been demonstrated to improve shoot and root growth of young tomato plants, but data on yield increase and fruit quality by K. radicincitans are lacking.

RESULTS

This study investigated how K. radicincitans affects tomato fruits. After inoculation of tomato seeds with K. radicincitans or a sodium chloride buffer control solution, stalk length, first flowering and the amount of ripened fruits produced by inoculated and non-inoculated plants were monitored over a period of 21 weeks. Inoculation of tomato seeds with K. radicincitans accelerated flowering and ripening of tomato fruits. Sugars, acidity, amino acids, volatile organic compounds and carotenoids in the fruits were also analyzed.

CONCLUSION

It was found that the PGPB K. radicincitans affected the amino acid, sugar and volatile composition of ripened fruits, contributing to a more pleasant-tasting fruit without forfeiting selected quality indicators. © 2017 Society of Chemical Industry.

An endophytic microbe from an unusual volcanic swamp corn seeks and inhabits root hair cells to extract rock phosphate

In the animal microbiome, localization of microbes to specific cell types is well established, but there are few such examples within the plant microbiome which includes endophytes. Endophytes are non-pathogenic microbes that inhabit plants. Root hairs are single cells, equivalent to the nutrient-absorbing intestinal microvilli of animals, used by plants to increase the root surface area for nutrient extraction from soil including phosphorus (P). There has been significant interest in the microbiome of intestinal microvilli but less is known about the root hair microbiome. Here we describe a bacterial endophyte (3F11) from Zea nicaraguensis, a wild corn discovered in a Nicaraguan swamp above rock-P lava flowing from the San Cristobal volcano. Rock-P is insoluble and a major challenge for plants. Following seed coating and germination on insoluble-P, the endophyte colonized epidermal surfaces, ultimately colonizing root hairs intracellularly. The endophyte promoted root hair growth and secreted acids to solubilize rock-P for uptake by a larger root hair surface. The most interesting observation was that a seed-coated endophyte targeted and colonized a critical cell type, root hair cells, consistent with earlier studies. The endophyte maintained its targeting ability in two evolutionary divergent hosts, suggesting that the host recognition machinery is conserved.

The persistence and performance of phosphate-solubilizing Gluconacetobacter liquefaciens qzr14 in a cucumber soil

The persistence and performance of plant growth-promoting microorganisms (PGPMs) in soil are considered critical features for effectiveness, yet they are poorly understood. Here, we investigated the colonization and activity of a new PGPM, phosphate-solubilizing Gluconacetobacter liquefaciens qzr14, in a pot culture experiment using cucumber as test crop for 20 days. The number of G. liquefaciens and bacterial diversity in the rhizosphere and bulk soil were monitored by real-time PCR and DGGE, respectively. Soil phosphorus and cucumber biomass were also examined. G. liquefaciens qzr14 effectively colonized the rhizosphere soil (bacterial density ranging from 2.70 × 10⁸ to 1.18 × 10⁹ copies per gram dry soil). G. liquefaciens qzr14 inoculation had significantly positive effects on bacterial diversity (BD) of the rhizosphere and bulk soil and the ratio of soluble phosphorus to total phosphorus (SP/TP). The number of G. liquefaciens in the rhizosphere soil was significantly related to SP/TP and the BD of the rhizosphere and bulk soil. BD in rhizosphere soil was significantly related to SP/TP and BD in bulk soil. Based on the results of correlation analysis, we inferred that the introduced G. liquefaciens qzr14 effectively colonized the rhizosphere of cucumber, and then expanded its bacterial community by solubilizing soil phosphorus. The expanded bacterial communities might promote cucumber growth by some new functions.

Improving Crop Yield and Nutrient Use Efficiency via Biofertilization-A Global Meta-analysis

The application of microbial inoculants (biofertilizers) is a promising technology for future sustainable farming systems in view of rapidly decreasing phosphorus stocks and the need to more efficiently use available nitrogen (N). Various microbial taxa are currently used as biofertilizers, based on their capacity to access nutrients from fertilizers and soil stocks, to fix atmospheric nitrogen, to improve water uptake or to act as biocontrol agents. Despite the existence of a considerable knowledge on effects of specific taxa of biofertilizers, a comprehensive quantitative assessment of the performance of biofertilizers with different traits such as phosphorus solubilization and N fixation applied to various crops at a global scale is missing. We conducted a meta-analysis to quantify benefits of biofertilizers in terms of yield increase, nitrogen and phosphorus use efficiency, based on 171 peer reviewed publications that met eligibility criteria. Major findings are: (i) the superiority of biofertilizer performance in dry climates over other climatic regions (yield response: dry climate +20.0 ± 1.7%, tropical climate +14.9 ± 1.2%, oceanic climate +10.0 ± 3.7%, continental climate +8.5 ± 2.4%); (ii) meta-regression analyses revealed that yield response due to biofertilizer application was generally small at low soil P levels; efficacy increased along higher soil P levels in the order arbuscular mycorrhizal fungi (AMF), P solubilizers, and N fixers; (iii) meta-regressions showed that the success of inoculation with AMF was greater at low organic matter content and at neutral pH. Our comprehensive analysis provides a basis and guidance for proper choice and application of biofertilizers.

The chequered history of the development and use of simultaneous equations for the accurate determination of chlorophylls a and b

Over the last half century, the most frequently used assay for chlorophylls in higher plants and green algae, the Arnon assay [Arnon DI (1949) Plant Physiol 24: 1-15], employed simultaneous equations for determining the concentrations of chlorophylls a and b in aqueous 80% acetone extracts of chlorophyllous plant and algal materials. These equations, however, were developed using extinction coefficients for chlorophylls a and b derived from early inaccurate spectrophotometric data. Thus, Arnon's equations give inaccurate chlorophyll a and b determinations and, therefore, inaccurate chlorophyll a/b ratios, which are always low. This paper describes how the ratios are increasingly and alarmingly low as the proportion of chlorophyll a increases. Accurate extinction coefficients for chlorophylls a and b, and the more reliable simultaneous equations derived from them, have been published subsequently by many research groups; these new post-Arnon equations, however, have been ignored by many researchers. This Minireview records the history of the development of accurate simultaneous equations and some difficulties and anomalies arising from the retention of Arnon's seriously flawed equations.