Colonization pattern of primary tomato roots by Pseudomonas fluorescens A6RI characterized by dilution plating, flow cytometry, fluorescence, confocal and scanning electron microscopy

Microbial assisted alleviation of nickel toxicity in plants: A review

Nickel (Ni) is required in trace amounts (less than 500 µg kg-1) in plants to regulate metabolic processes, the immune system, and to act as an enzymatic catalytic cofactor. Conversely, when nickel is present in high concentration, it is considered as a toxic substance. Excessive human nickel exposure occurs through ingestion, inhalation, and skin contact, ultimately leading to respiratory, cardiovascular, and chronic kidney diseases. Due to anthropogenic activities, the nickel concentrations in various environmental scenarios have progressively risen to levels as high as 26,000 ppm in soil and 0.2 mg L-1 in water; surpassing the established safety threshold limits of 100 ppm for soil and 0.005 ppm for surface water. Nickel is required by various plant species for facilitating biological processes; in the range of 0.01-5 µg g-1 (dry weight). When present in excess, nickel toxicity in plants (10-1000 mg kg-1 dry weight mass) causes many disrupted metabolic processes; leading to lower growth, altered development, hindered seed germination, chlorosis, and necrosis. To tackle any metal-linked pollution issues, various remediation approaches are employed to remove heavy metals (especially nickel) and metalloids including physicochemical, and biological methods. Based on literature, the physicochemical methods are not commonly used due to their costly nature and the potential for producing secondary pollutants. Interestingly, bioremediation is considered by many practitioners as an easy-to-handle, efficient, and cost-effective approach, encompassing techniques such as phytoremediation, bioleaching, bioreactors, green landforming, and bio-augmentation. Operationally, phytoremediation is widely utilized for cleaning up contaminated sites. To support the phytoremediative processes, numerous nickel hyperaccumulating plants have been identified; these species can absorb from their surroundings and store high concentrations of nickel (through various mechanisms) in their biomass, thereby helping to detoxify nickel-contaminated soils via phytoextraction. The microbe-assisted phytoremediation further optimizes the nickel detoxification processes by fostering beneficial interactions between microbes and the nickel-hyperaccumulators; promoting enhanced metal uptake, transformation, and sequestration. Microbe-assisted phytoremediation can be categorized into four subtypes: bacterial-assisted phytoremediation, cyanoremediation, mycorrhizal-assisted remediation, and rhizoremediation. These diverse approaches are likely to offer more effective and sustainable remediative strategy to ecologically restore the nickel-contaminated environments.

Pseudomonas rhodesiae HAI-0804 suppresses Pythium damping off and root rot in cucumber by its efficient root colonization promoted by amendment with glutamate

Plant diseases caused by soil-borne fungi and oomycetes significantly reduce yield and quality of many crops in the agricultural systems and are difficult to control. We herein examine Pseudomonas rhodesiae HAI-0804, a bacterial biological control agent that was originally developed for control of bacterial diseases on the surface of vegetables, and assessed its efficacy at controlling soil-borne diseases caused by oomycetes. Strain HAI-0804 did not exhibit detectable antibiotic activity toward Pythium ultimum, a causal agent of damping-off and root rot; however, it effectively protected against Pythium damping-off and root rot in cucumber. Exogenous glutamate enhanced the efficacy of biocontrol, the production of siderophore pyoverdine, root colonization in cucumber plants, and the ratio of biofilm formation to planktonic cells. The epiphytic fitness of strain HAI-0804 appears to contribute to plant protection efficacy against a broad spectrum of pathogens for both above-ground plant parts and the rhizosphere.

The potential of plant growth-promoting bacteria isolated from arid heavy metal contaminated environments in alleviating salt and water stresses in alfalfa

Co-evolution of plant beneficial microbes in contaminated environments enhances plant growth and mitigates abiotic stress. However, few studies on heavy metal (HM) tolerant plant growth-promoting bacteria (PGPB) promoting crop growth in Morocco's farming areas affected by drought and salinity are available. Plant associated bacteria tolerant to HM and able to produce indole acetic acid and siderophores, display ACC-deaminase activity and solubilize phosphate, were isolated from long-term metal exposed environments. Tolerance to HM and biofilms formation in the absence or presence of HM were assessed. A consortium including two Ensifer meliloti strains (RhOL6 and RhOL8), one Pseudomonas sp. strain (DSP17), and one Proteus sp. strain (DSP1), was used to inoculate alfalfa (Medicago sativa) seedlings under various conditions, namely, salt stress (85 mM) and water stress (30% water holding capacity). Shoot and root dry weights of alfalfa were measured 60 days after sowing. In the presence of HM, DSP17 showed the greatest auxin production, whereas RhOL8 had the highest ACC-deaminase activity and DSP17 formed the densest biofilm. Root dry weight increased 138% and 195% in salt and water stressed plants, respectively, regarding non-inoculated controls. Our results confirm the improvement of alfalfa growth and mitigation of salt and drought stress upon inoculation.

Mobility and growth in confined spaces are important mechanisms for the establishment of Bacillus subtilis in the rhizosphere

The rhizosphere hosts complex and abundant microbiomes whose structure and composition are now well described by metagenomic studies. However, the dynamic mechanisms that enable micro-organisms to establish along a growing plant root are poorly characterized. Here, we studied how a motile bacterium utilizes the microhabitats created by soil pore space to establish in the proximity of plant roots. We have established a model system consisting of Bacillus subtilis and lettuce seedlings co-inoculated in transparent soil microcosms. We carried out live imaging experiments and developed image analysis pipelines to quantify the abundance of the bacterium as a function of time and position in the pore space. Results showed that the establishment of the bacterium in the rhizosphere follows a precise sequence of events where small islands of mobile bacteria were first seen forming near the root tip within the first 12-24 h of inoculation. Biofilm was then seen forming on the root epidermis at distances of about 700-1000 µm from the tip. Bacteria accumulated predominantly in confined pore spaces within 200 µm from the root or the surface of a particle. Using probabilistic models, we could map the complete sequence of events and propose a conceptual model of bacterial establishment in the pore space. This study therefore advances our understanding of the respective role of growth and mobility in the efficient colonization of bacteria in the rhizosphere.

An Indirect Fluorescence Microscopy Method to Assess Vaginal Lactobacillus Concentrations

Lactobacillus species are the main colonizers of the vaginal microbiota in healthy women. Their absolute quantification by culture-based methods is limited due to their fastidious growth. Flow cytometry can quantify the bacterial concentration of these bacteria but requires the acquisition of expensive equipment. More affordable non-culturable methods, such as fluorescence microscopy, are hampered by the small size of the bacteria. Herein, we developed an indirect fluorescence microscopy method to determine vaginal lactobacilli concentration by determining the correlation between surface area bacterial measurement and initial concentration of an easily cultivable bacterium (Escherichia coli) and applying it to lactobacilli fluorescence microscopy counts. In addition, vaginal lactobacilli were quantified by colony-forming units and flow cytometry in order to compare these results with the indirect method results. The colony-forming-unit values were lower than the results obtained from the other two techniques, while flow cytometry and fluorescence microscopy results agreed. Thus, our developed method was able to accurately quantify vaginal lactobacilli.

An antibiotic produced by Pseudomonas fluorescens CFBP2392 with antifungal activity against Rhizoctonia solani

Pseudomonas fluorescens CFBP2392 has been recognized as a potential biocontrol agent due to its ability to suppress damping-off and root rot disease. This isolate has antibacterial activity in vitro as many other strains from the Pseudomonas fluorescens complex. In this work, the antibacterial and antifungal activity of the strain were explored. Dual culture assays evidenced the antifungal activity of the strain against different phytopathogens: Alternaria sp., Pythium ultimun, Fusarium oxysporum, and Rhizoctonia solani. Purification of an antifungal fraction was performed by preparative HPLC from the chemical extraction of growth media. The fraction showed altered R. solani growth and ultrastructure. Transmission electron microscopy revealed the purified compound induced hypertrophied mitochondria, membranous vesicles, and a higher number of vacuoles in R. salani cytoplasm. In addition, co-cultivation of P. fluorescens CFBP2392 with R. solani resulted in an enlarged and deformed cell wall. To gain genomic insights on this inhibition, the complete genome of P. fluorescens CFBP2392 was obtained with Oxford Nanopore technology. Different biosynthetic gene clusters (BGCs) involved in specialized metabolites production including a lokisin-like and a koreenceine-like cluster were identified. In accordance with the putative BGCs identified, sequence phylogeny analysis of the MacB transporter in the lokisin-like cluster further supports the similarity with other transporters from the amphisin family. Our results give insights into the cellular effects of the purified microbial metabolite in R. solani ultrastructure and provide a genomic background to further explore the specialized metabolite potential.

Counter-attack of biocontrol agents: Environmentally benign Approaches against Root-knot nematodes (Meloidogyne spp.) on Agricultural crops

Root-knot nematodes (Meloidogyne spp.) are obligate sedentary endoparasites, considered severe crop-damaging taxa among all plant-parasitic nematodes globally. Their attacks through parasitic proteins alter the physiology and machinery of the host cells to favour parasitism and reduction in crop yield. Currently, the use of excessive pesticides as a fast remedy to manage this pest is hazardous for both the environment and humans. Keeping this view in mind, there is an urgent need for developing efficient eco-friendly strategies. Bio-control as an eco-friendly is considered the best approach to manage nematodes without disturbing non-target microbes. In bio-control, living agents such as fungi and bacteria are the natural enemies of nematodes and the best substitute for pesticides. Fungi, including nematode-trapping fungi, can sense host signals and produce special trapping devices viz., constricting rings and adhesive knobs/loops, to capture nematodes and kill them. Whereas, endo-parasitic fungi kill nematodes by enzymatic secretions and spore adhesion through their hyphae. Bacteria can also control nematodes by producing antibiotic compounds, competing for nutrients and rhizosphere, production of hydrolytic enzymes viz., chitinases, proteases, lipases, and induction of systemic resistance (ISR) in host plants. Scientists throughout the world are trying to evolve environmentally benign methods that sustain agricultural production and keep nematodes below a threshold level. Whatever methods evolve, in the future the focus should be on important aspects like green approaches for managing nematodes without disturbing human health and the environment.

Paraburkholderia phytofirmans PsJN colonization of rice endosphere triggers an atypical transcriptomic response compared to rice native Burkholderia s.l. endophytes

The plant microbiome has recently emerged as a reservoir for the development of sustainable alternatives to chemical fertilizers and pesticides. However, the response of plants to beneficial microbes emerges as a critical issue to understand the molecular basis of plant-microbiota interactions. In this study, we combined root colonization, phenotypic and transcriptomic analyses to unravel the commonalities and specificities of the response of rice to closely related Burkholderia s.l. endophytes. In general, these results indicate that a rice-non-native Burkholderia s.l. strain, Paraburkholderia phytofirmans PsJN, is able to colonize the root endosphere while eliciting a markedly different response compared to rice-native Burkholderia s.l. strains. This demonstrates the variability of plant response to microbes from different hosts of origin. The most striking finding of the investigation was that a much more conserved response to the three endophytes used in this study is elicited in leaves compared to roots. In addition, transcriptional regulation of genes related to secondary metabolism, immunity, and phytohormones appear to be markers of strain-specific responses. Future studies need to investigate whether these findings can be extrapolated to other plant models and beneficial microbes to further advance the potential of microbiome-based solutions for crop production.

Plant growth-promoting microorganisms as biocontrol agents of plant diseases: Mechanisms, challenges and future perspectives

Plant diseases and pests are risk factors that threaten global food security. Excessive chemical pesticide applications are commonly used to reduce the effects of plant diseases caused by bacterial and fungal pathogens. A major concern, as we strive toward more sustainable agriculture, is to increase crop yields for the increasing population. Microbial biological control agents (MBCAs) have proved their efficacy to be a green strategy to manage plant diseases, stimulate plant growth and performance, and increase yield. Besides their role in growth enhancement, plant growth-promoting rhizobacteria/fungi (PGPR/PGPF) could suppress plant diseases by producing inhibitory chemicals and inducing immune responses in plants against phytopathogens. As biofertilizers and biopesticides, PGPR and PGPF are considered as feasible, attractive economic approach for sustainable agriculture; thus, resulting in a "win-win" situation. Several PGPR and PGPF strains have been identified as effective BCAs under environmentally controlled conditions. In general, any MBCA must overcome certain challenges before it can be registered or widely utilized to control diseases/pests. Successful MBCAs offer a practical solution to improve greenhouse crop performance with reduced fertilizer inputs and chemical pesticide applications. This current review aims to fill the gap in the current knowledge of plant growth-promoting microorganisms (PGPM), provide attention about the scientific basis for policy development, and recommend further research related to the applications of PGPM used for commercial purposes.

Current Techniques to Study Beneficial Plant-Microbe Interactions

Many different experimental approaches have been applied to elaborate and study the beneficial interactions between soil bacteria and plants. Some of these methods focus on changes to the plant and others are directed towards assessing the physiology and biochemistry of the beneficial plant growth-promoting bacteria (PGPB). Here, we provide an overview of some of the current techniques that have been employed to study the interaction of plants with PGPB. These techniques include the study of plant microbiomes; the use of DNA genome sequencing to understand the genes encoded by PGPB; the use of transcriptomics, proteomics, and metabolomics to study PGPB and plant gene expression; genome editing of PGPB; encapsulation of PGPB inoculants prior to their use to treat plants; imaging of plants and PGPB; PGPB nitrogenase assays; and the use of specialized growth chambers for growing and monitoring bacterially treated plants.

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.

Multiple strategies of plant colonization by beneficial endophytic Enterobacter sp. SA187

Although many endophytic plant growth-promoting rhizobacteria have been identified, relatively little is still known about the mechanisms by which they enter plants and promote plant growth. The beneficial endophyte Enterobacter sp. SA187 was shown to maintain the productivity of crops in extreme agricultural conditions. Here we present that roots of its natural host (Indigofera argentea), alfalfa, tomato, wheat, barley and Arabidopsis are all efficiently colonized by SA187. Detailed analysis of the colonization process in Arabidopsis showed that colonization already starts during seed germination, where seed-coat mucilage supports SA187 proliferation. The meristematic zone of growing roots attracts SA187, allowing epiphytic colonization in the elongation zone. Unlike primary roots, lateral roots are significantly less epiphytically colonized by SA187. Root endophytic colonization was found to occur by passive entry of SA187 at lateral-root bases. However, SA187 also actively penetrates the root epidermis by enzymatic disruption of plant cell wall material. In contrast to roots, endophytic colonization of shoots occurs via stomata, whereby SA187 can actively re-open stomata similarly to pathogenic bacteria. In summary, several entry strategies were identified that allow SA187 to establish itself as a beneficial endophyte in several plant species, supporting its use as a plant growth-promoting bacterium in agriculture systems.

Deciphering bacterial mechanisms of root colonization

Bacterial colonization of the rhizosphere is critical for the establishment of plant-bacteria interactions that represent a key determinant of plant health and productivity. Plants influence bacterial colonization primarily through modulating the composition of their root exudates and mounting an innate immune response. The outcome is a horizontal filtering of bacteria from the surrounding soil, resulting in a gradient of reduced bacterial diversity coupled with a higher degree of bacterial specialization towards the root. Bacteria-bacteria interactions (BBIs) are also prevalent in the rhizosphere, influencing bacterial persistence and root colonization through metabolic exchanges, secretion of antimicrobial compounds and other processes. Traditionally, bacterial colonization has been examined under sterile laboratory conditions that mitigate the influence of BBIs. Using simplified synthetic bacterial communities combined with microfluidic imaging platforms and transposon mutagenesis screening approaches, we are now able to begin unravelling the molecular mechanisms at play during the early stages of root colonization. This review explores the current state of knowledge regarding bacterial root colonization and identifies key tools for future exploration.

CRISPR interference to interrogate genes that control biofilm formation in Pseudomonas fluorescens

Bacterial biofilm formation involves signaling and regulatory pathways that control the transition from motile to sessile lifestyle, production of extracellular polymeric matrix, and maturation of the biofilm 3D structure. Biofilms are extensively studied because of their importance in biomedical, ecological and industrial settings. Gene inactivation is a powerful approach for functional studies but it is often labor intensive, limiting systematic gene surveys to the most tractable bacterial hosts. Here, we adapted the CRISPR interference (CRISPRi) system for use in diverse strain isolates of P. fluorescens, SBW25, WH6 and Pf0-1. We found that CRISPRi is applicable to study complex phenotypes such as cell morphology, motility and biofilm formation over extended periods of time. In SBW25, CRISPRi-mediated silencing of genes encoding the GacA/S two-component system and regulatory proteins associated with the cylic di-GMP signaling messenger produced swarming and biofilm phenotypes similar to those obtained after gene inactivation. Combined with detailed confocal microscopy of biofilms, our study also revealed novel phenotypes associated with extracellular matrix biosynthesis as well as the potent inhibition of SBW25 biofilm formation mediated by the PFLU1114 operon. We conclude that CRISPRi is a reliable and scalable approach to investigate gene networks in the diverse P. fluorescens group.

Monitoring of Rice Transcriptional Responses to Contrasted Colonizing Patterns of Phytobeneficial Burkholderia s.l. Reveals a Temporal Shift in JA Systemic Response

In the context of plant-pathogen and plant-mutualist interactions, the underlying molecular bases associated with host colonization have been extensively studied. However, it is not the case for non-mutualistic beneficial interactions or associative symbiosis with plants. Particularly, little is known about the transcriptional regulations associated with the immune tolerance of plants towards beneficial microbes. In this context, the study of the Burkholderia rice model is very promising to describe the molecular mechanisms involved in associative symbiosis. Indeed, several species of the Burkholderia sensu lato (s.l.) genus can colonize rice tissues and have beneficial effects; particularly, two species have been thoroughly studied: Burkholderia vietnamiensis and Paraburkholderia kururiensis. This study aims to compare the interaction of these species with rice and especially to identify common or specific plant responses. Therefore, we analyzed root colonization of the rice cultivar Nipponbare using DsRed-tagged bacterial strains and produced the transcriptomes of both roots and leaves 7 days after root inoculation. This led us to the identification of a co-expression jasmonic acid (JA)-related network exhibiting opposite regulation in response to the two strains in the leaves of inoculated plants. We then monitored by quantitative polymerase chain reaction (qPCR) the expression of JA-related genes during time course colonization by each strain. Our results reveal a temporal shift in this JA systemic response, which can be related to different colonization strategies of both strains.

Root colonization and growth promotion of soybean, wheat and Chinese cabbage by Bacillus cereus YL6

Although phosphate-solubilizing bacteria (PSBs) are used in agricultural production, comprehensive research on PSB that colonize the rhizosphere of different plants and promote plant growth is lacking. This study was conducted to examine the growth-promoting effects and colonizing capacity of strain YL6, a PSB. YL6 not only increased the biomass of soybean and wheat in pot experiments but also increased the yield and growth of Chinese cabbage under field conditions. The observed growth promotion was related to the capacity of YL6 to dissolve inorganic and organic phosphorus and to produce indole-3-acetic (IAA) and gibberellin (GA). After applying YL6 to soybean, wheat and Chinese cabbage, the rhizosphere soil available phosphorus (available P) content increased by 120.16%, 62.47% and 7.21%, respectively, and the plant total phosphorus content increased by 198.60%, 6.20% and 78.89%, respectively, compared with plants not treated with YL6. To examine plant colonization, YL6 labeled with green fluorescent protein (YL6-GFP) was inoculated into the plant rhizosphere and found to first colonize the root surface and hairs and then to penetrate into the intercellular spaces and vessels. Collectively, these results demonstrate that YL6 promotes the growth of three different crops and colonizes them in a similar manner. The findings therefore provide a solid foundation for probing the mechanisms by which PSB affect plant growth.

Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation

Rhizosphere-associated Pseudomonas fluorescens are known plant growth promoting (PGP) and mycorrhizal helper bacteria (MHB) of many plants and ectomycorrhizal fungi. We investigated the spatial and temporal dynamics of colonization of mycorrhizal and non-mycorrhizal Aspen seedlings roots by the P. fluorescens strains SBW25, WH6, Pf0-1, and the P. protegens strain Pf-5. Seedlings were grown in laboratory vertical plates systems, inoculated with a fluorescently labeled Pseudomonas strain, and root colonization was monitored over a period of 5 weeks. We observed unexpected diversity of bacterial assemblies on seedling roots that changed over time and were strongly affected by root mycorrhization. P. fluorescens SBW25 and WH6 stains developed highly structured biofilms with internal void spaces forming channels. On mycorrhizal roots bacteria appeared encased in a mucilaginous substance in which they aligned side by side in parallel arrangements. The different phenotypic classes of bacterial assemblies observed for the four Pseudomonas strains were summarized in a single model describing transitions between phenotypic classes. Our findings also reveal that bacterial assembly phenotypes are driven by interactions with mucilaginous materials present at roots.

Isolation and Characterization of a Phosphorus-Solubilizing Bacterium from Rhizosphere Soils and Its Colonization of Chinese Cabbage (Brassica campestris ssp. chinensis)

Phosphate-solubilizing bacteria (PSB) can promote the dissolution of insoluble phosphorus (P) in soil, enhancing the availability of soluble P. Thus, their application can reduce the consumption of fertilizer and aid in sustainable agricultural development. From the rhizosphere of Chinese cabbage plants grown in Yangling, we isolated a strain of PSB (YL6) with a strong ability to dissolve P and showed that this strain promoted the growth of these plants under field conditions. However, systematic research on the colonization of bacteria in the plant rhizosphere remains deficient. Thus, to further study the effects of PSB on plant growth, in this study, green fluorescent protein (GFP) was used to study the colonization of YL6 on Chinese cabbage roots. GFP expression had little effect on the ability of YL6 to grow and solubilize P. In addition, the GFP-expressing strain stably colonized the Chinese cabbage rhizosphere (the number of colonizing bacteria in the rhizosphere soil was 4.9 lg CFU/g). Using fluorescence microscopy, we observed a high abundance of YL6-GFP bacteria at the Chinese cabbage root cap and meristematic zone, as well as in the root hairs and hypocotyl epidermal cells. High quantities of GFP-expressing bacteria were recovered from Chinese cabbage plants during different planting periods for further observation, indicating that YL6-GFP had the ability to endogenously colonize the plants. This study has laid a solid and significant foundation for further research on how PSB affects the physiological processes in Chinese cabbage to promote plant growth.

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

One of the most exciting scientific advances in recent decades has been the realization that the diverse and immensely active microbial communities are not only 'passengers' with plants, but instead play an important role in plant growth, development and resistance to biotic and abiotic stresses. A picture is emerging where plant roots act as 'gatekeepers' to screen soil bacteria from the rhizosphere and rhizoplane. This typically results in root endophytic microbiome dominated by Proteobacteria, Actinobacteria and to a lesser extent Bacteroidetes and Firmicutes, but Acidobacteria and Gemmatimonadetes being almost depleted. A synthesis of available data suggest that motility, plant cell-wall degradation ability and reactive oxygen species scavenging seem to be crucial traits for successful endophytic colonization and establishment of bacteria. Recent studies provide solid evidence that these bacteria serve host functions such as improving of plant nutrients through acquisition of nutrients from soil and nitrogen fixation in leaves. Additionally, some endophytes can engage 'priming' plants which elicit a faster and stronger plant defense once pathogens attack. Due to these plant growth-promoting effects, endophytic bacteria are being widely explored for their use in the improvement of crop performance. Updating the insights into the mechanism of endophytic bacterial colonization and interactions with plants is an important step in potentially manipulating endophytic bacteria/microbiome for viable strategies to improve agricultural production.

Seed biopriming with plant growth promoting rhizobacteria: a review

Beneficial microbes are applied to the soil and plant tissues directly or through seed inoculation, whereas soil application is preferred when there is risk of inhibitors or antagonistic microbes on the plant tissues. Insufficient survival of the microorganisms, hindrance in application of fungicides to the seeds and exposure to heat and sunlight in subsequent seed storage in conventional inoculation methods force to explore appropriate and efficient bacterial application method. Seed priming, where seeds are hydrated to activate metabolism without actual germination followed by drying, increases the germination, stand establishment and stress tolerance in different crops. Seed priming with living bacterial inoculum is termed as biopriming that involves the application of plant growth promoting rhizobacteria. It increases speed and uniformity of germination; also ensures rapid, uniform and high establishment of crops; and hence improves harvest quality and yield. Seed biopriming allows the bacteria to enter/adhere the seeds and also acclimatization of bacteria in the prevalent conditions. This review focuses on methods used for biopriming, and also the role in improving crop productivity and stress tolerance along with prospects of this technology. The comparison of methods being followed is also reviewed proposing biopriming as a promising technique for application of beneficial microbes to the seeds.

Genome Sequence of the Banana Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens PS006

Pseudomonas fluorescens is a well-known plant growth-promoting rhizobacterium (PGPR). We report here the first whole-genome sequence of PGPR P. fluorescens evaluated in Colombian banana plants. The genome sequences contains genes involved in plant growth and defense, including bacteriocins, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, and genes that provide resistance to toxic compounds.

Colonization of lettuce rhizosphere and roots by tagged Streptomyces

Beneficial microorganisms are increasingly used in agriculture, but their efficacy often fails due to limited knowledge of their interactions with plants and other microorganisms present in rhizosphere. We studied spatio-temporal colonization dynamics of lettuce roots and rhizosphere by genetically modified Streptomyces spp. Five Streptomyces strains, strongly inhibiting in vitro the major soil-borne pathogen of horticultural crops, Sclerotinia sclerotiorum, were transformed with pIJ8641 plasmid harboring an enhanced green fluorescent protein marker and resistance to apramycin. The fitness of transformants was compared to the wild-type strains and all of them grew and sporulated at similar rates and retained the production of enzymes and selected secondary metabolites as well as in vitro inhibition of S. sclerotiorum. The tagged ZEA17I strain was selected to study the dynamics of lettuce roots and rhizosphere colonization in non-sterile growth substrate. The transformed strain was able to colonize soil, developing roots, and rhizosphere. When the strain was inoculated directly on the growth substrate, significantly more t-ZEA17I was re-isolated both from the rhizosphere and the roots when compared to the amount obtained after seed coating. The re-isolation from the rhizosphere and the inner tissues of surface-sterilized lettuce roots demonstrated that t-ZEA17I is both rhizospheric and endophytic.

Accounting for soil biotic effects on soil health and crop productivity in the design of crop rotations

There is an urgent need for novel agronomic improvements capable of boosting crop yields while alleviating environmental impacts. One such approach is the use of optimized crop rotations. However, a set of measurements that can serve as guiding principles for the design of crop rotations is lacking. Crop rotations take advantage of niche complementarity, enabling the optimization of nutrient use and the reduction of pests and specialist pathogen loads. However, despite the recognized importance of plant-soil microbial interactions and feedbacks for crop yield and soil health, this is ignored in the selection and management of crops for rotation systems. We review the literature and propose criteria for the design of crop rotations focusing on the roles of soil biota and feedback on crop productivity and soil health. We consider that identifying specific key organisms or consortia capable of influencing plant productivity is more important as a predictor of soil health and crop productivity than assessing the overall soil microbial diversity per se. As such, we propose that setting up soil feedback studies and applying genetic sequencing tools towards the development of soil biotic community databases has a strong potential to enable the establishment of improved soil health indicators for optimized crop rotations.

Plant roots and spectroscopic methods - analyzing species, biomass and vitality

In order to understand plant functioning, plant community composition, and terrestrial biogeochemistry, it is decisive to study standing root biomass, (fine) root dynamics, and interactions belowground. While most plant taxa can be identified by visual criteria aboveground, roots show less distinctive features. Furthermore, root systems of neighboring plants are rarely spatially segregated; thus, most soil horizons and samples hold roots of more than one species necessitating root sorting according to taxa. In the last decades, various approaches, ranging from anatomical and morphological analyses to differences in chemical composition and DNA sequencing were applied to discern species' identity and biomass belowground. Among those methods, a variety of spectroscopic methods was used to detect differences in the chemical composition of roots. In this review, spectroscopic methods used to study root systems of herbaceous and woody species in excised samples or in situ will be discussed. In detail, techniques will be reviewed according to their usability to discern root taxa, to determine root vitality, and to quantify root biomass non-destructively or in soil cores holding mixtures of plant roots. In addition, spectroscopic methods which may be able to play an increasing role in future studies on root biomass and related traits are highlighted.

Colonization of potato rhizosphere by GFP-tagged Bacillus subtilis MB73/2, Pseudomonas sp. P482 and Ochrobactrum sp. A44 shown on large sections of roots using enrichment sample preparation and confocal laser scanning microscopy

The ability to colonize the host plants’ rhizospheres is a crucial feature to study in the case of Plant Growth Promoting Rhizobacteria (PGPRs) with potential agricultural applications. In this work, we have created GFP-tagged derivatives of three candidate PGPRs: Bacillus subtilis MB73/2, Pseudomonas sp. P482 and Ochrobactrum sp. A44. The presence of these strains in the rhizosphere of soil-grown potato (Solanum tuberosum L.) was detected with a classical fluorescence microscope and a confocal laser scanning microscope (CLSM). In this work, we have used a broad-field-of-view CLMS device, dedicated to in vivo analysis of macroscopic objects, equipped with an automated optical zoom system and tunable excitation and detection spectra. We show that features of this type of CLSM microscopes make them particularly well suited to study root colonization by microorganisms. To facilitate the detection of small and scattered bacterial populations, we have developed a fast and user-friendly enrichment method for root sample preparation. The described method, thanks to the in situ formation of mini-colonies, enables visualization of bacterial colonization sites on large root fragments. This approach can be easily modified to study colonization patterns of other fluorescently tagged strains. Additionally, dilution plating of the root extracts was performed to estimate the cell number of MB73/2, P482 and A44 in the rhizosphere of the inoculated plants.

Biocontrol of verticillium wilt and colonization of cotton plants by an endophytic bacterial isolate

AIMS

To explore biocontrol potential of 39 DAEB isolates (doubly antagonistic towards both Verticillium dahliae Kleb and Fusarium oxysporum) against verticillium wilt of cotton and to elucidate colonization and category characteristics of an endophytic bacterium with significant biocontrol activity.

METHODS AND RESULTS

Thirty-nine antagonistic endophytic bacteria strains were tested for their ability to control verticillium wilt in cotton plants caused by a defoliating pathotype of V. dahliae 107 in cotton under controlled conditions. The biocontrol trial revealed that an endophytic bacterium, designated HA02, showed a significant biocontrol activity to V. dahliae 107. After cotton seedlings were inoculated with a gfp gene-tagged HA02 (HA02-gfp), HA02-gfp populations were higher in the root than in the stem; in addition, the HA02-gfp was distributed in the maturation zone of cotton root. Furthermore, HA02-gfp also colonized seedlings of maize, rape and soybean after the bacteria inoculation. Phylogenetic trees based on 16S rDNA sequences combined with morphological, physiological and identification showed that the bacterium belongs to the Enterobacter genus.

CONCLUSIONS

Our results showed that only 1 of 39 DAEB isolates demonstrated more efficient biocontrol potential towards V. dahliae 107 in greenhouse and field trials. HA02-gfp mainly colonized cotton in roots. In addition, we quantitatively observed HA02 colonization in other hosts. HA02 belongs to the Enterobacter genus.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study on biocontrol to defoliating pathotype of V. dahliae Kleb by endophytic bacteria. The HA02 showed effective biocontrol to V. dahliae 107 in greenhouse and field trials. Furthermore, we assessed the quantitative and qualitative colonization of HA02 in cotton seedlings. Our study provides basic information to further explore managing strategies to control this critical disease.

Applications of flow cytometry in plant pathology for genome size determination, detection and physiological status

Flow cytometers are probably the most multipurpose laboratory devices available. They can analyse a vast and very diverse range of cell parameters. This technique has left its mark on cancer, human immunodeficiency virus and immunology research, and is indispensable in routine clinical diagnostics. Flow cytometry (FCM) is also a well-known tool for the detection and physiological status assessment of microorganisms in drinking water, marine environments, food and fermentation processes. However, flow cytometers are seldom used in plant pathology, despite FCM's major advantages as both a detection method and a research tool. Potential uses of FCM include the characterization of genome sizes of fungal and oomycete populations, multiplexed pathogen detection and the monitoring of the viability, culturability and gene expression of plant pathogens, and many others. This review provides an overview of the history, advantages and disadvantages of FCM, and focuses on the current applications and future possibilities of FCM in plant pathology.

Root colonization by Pseudomonas sp. DSMZ 13134 and impact on the indigenous rhizosphere bacterial community of barley

Over the last few decades, the ability of rhizosphere bacteria to promote plant growth has been considered to be of scientific, ecological, and economic interest. The properties and mechanisms of interaction of these root-colonizing bacteria have been extensively investigated, and plant protection agents that are based on these bacterial strains have been developed for agricultural applications. In the present study, the root colonization of barley by Pseudomonas sp. DSMZ 13134, that is contained in the commercially available plant protection agent Proradix, was examined using the fluorescence in situ hybridization method with oligonucleotide probes and specific gfp-tagging of the inoculant strain in combination with confocal laser scanning microscopy. In the first phase of root colonization, the inoculant strain competed successfully with seed and soil-borne bacteria (including Pseudomonads) for the colonization of the rhizoplane. Pseudomonas sp. DSMZ 13134 could be detected in all parts of the roots, although it did not belong to the dominant members of the root-associated bacterial community. Gfp-tagged cells were localized particularly in the root hair zone, and high cell densities were apparent on the root hair surface. To investigate the impact of the application of Proradix on the structure of the dominant root-associated bacterial community of barley, T-RFLP analyses were performed. Only a transient community effect was found until 3 weeks post-application.

Combination of fluorescent reporters for simultaneous monitoring of root colonization and antifungal gene expression by a biocontrol pseudomonad on cereals with flow cytometry

Some root-associated pseudomonads sustain plant growth by suppressing root diseases caused by pathogenic fungi. We investigated to which extent select cereal cultivars influence expression of relevant biocontrol traits (i.e., root colonization efficacy and antifungal activity) in Pseudomonas fluorescens CHA0. In this representative plant-beneficial bacterium, the antifungal metabolites 2,4-diacetylphloroglucinol (DAPG), pyrrolnitrin (PRN), pyoluteorin (PLT), and hydrogen cyanide (HCN) are required for biocontrol. To monitor host plant effects on the expression of biosynthetic genes for these compounds on roots, we developed fluorescent dual-color reporters suited for flow cytometric analysis using fluorescence-activated cell sorting (FACS). In the dual-label strains, the constitutively expressed red fluorescent protein mCherry served as a cell tag and marker for root colonization, whereas reporter fusions based on the green fluorescent protein allowed simultaneous recording of antifungal gene expression within the same cell. FACS analysis revealed that expression of DAPG and PRN biosynthetic genes was promoted in a cereal rhizosphere, whereas expression of PLT and HCN biosynthetic genes was markedly less sustained. When analyzing the response of the bacterial reporters on roots of a selection of wheat, spelt, and triticale cultivars, we were able to detect subtle species- and cultivar-dependent differences in colonization and DAPG and HCN gene expression levels. The expression of these biocontrol traits was particularly favored on roots of one spelt cultivar, suggesting that a careful choice of pseudomonad-cereal combinations might be beneficial to biocontrol. Our approach may be useful for selective single-cell level analysis of plant effects in other bacteria-root interactions.

Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities?

This review evaluates the importance of root exudates in determining rhizosphere bacterial community structure. We present evidence that indicates that: (1) the direct influence of root exudates on rhizosphere bacterial communities is limited to small spatiotemporal windows related to root apices; (2) upon rapid assimilation by microorganisms, root exudates are modified, independent of plant influences, before rerelease into the rhizosphere by the microorganisms themselves--thus, at short distances from root apices, rhizosphere carbon pools are unlikely to be dominated by root exudates; and (3) many of the major compounds found in root exudates are ubiquitous in the rhizosphere as they are found in other pools of rhizodeposits and in microbial exudates. Following this argument, we suggest that the importance of root exudates in structuring rhizosphere bacterial communities needs to be considered in the context of the wider contribution of other rhizosphere carbon pools. Finally, we discuss the implications of rhizosphere bacterial distribution trends for the development of effective strategies to manage beneficial plant-microorganism interactions.

A novel method for sampling bacteria on plant root and soil surfaces at the microhabitat scale

This study reports the first method for sampling bacteria at a spatial scale approximating a microhabitat. At the core of this method is the use of tungsten rods with laser-cut tips of known surface area (0.013 mm(2)). Exposed plant root or soil surfaces were viewed with a dissecting microscope and micro-sampling rods were guided to sample sites using a micro-manipulator. Bacteria that adhered to the sampling tips were then recovered for microbiological analyses. The efficiency of this method for removing bacteria from root surfaces was similar to that with which bacteria are recovered from dissected root segments using the conventional technique of washing. However, as the surface area of the micro-sampling tips was known, the new method has the advantage of eliminating inaccuracy in estimates of bacterial densities due to inaccurate estimation of the root or soil surface sampled. When used to investigate spatial distributions of rhizoplane bacteria, the new technique revealed trends that were consistent with those reported with existing methods, while providing access to additional information about community structure at a much smaller spatial scale. The spatial scale of this new method is ca. 1000-times smaller than other sampling methods involving swabbing. This novel technique represents an important methodological step facilitating microbial ecological investigations at a microhabitat scale.

Endophytic colonization of Vitis vinifera L. by Burkholderia phytofirmans strain PsJN: from the rhizosphere to inflorescence tissues

The colonization pattern of Vitis vinifera L. by Burkholderia phytofirmans strain PsJN was determined using grapevine fruiting cuttings with emphasis on putative inflorescence colonization under nonsterile conditions. Two-week-old rooted plants harbouring flower bud initials, grown in nonsterile soil, were inoculated with PsJN:gfp2x. Plant colonization was subsequently monitored at various times after inoculation with plate counts and epifluorescence and/or confocal microscopy. Strain PsJN was chronologically detected on the root surfaces, in the endorhiza, inside grape inflorescence stalks, not inside preflower buds and flowers but rather as an endophyte inside young berries. Data demonstrated low endophytic populations of strain PsJN in inflorescence organs, i.e. grape stalks and immature berries with inconsistency among plants for bacterial colonization of inflorescences. Nevertheless, endophytic colonization of inflorescences by strain PsJN was substantial for some plants. Microscopic analysis revealed PsJN as a thriving endophyte in inflorescence organs after the colonization process. Strain PsJN was visualized colonizing the root surface, entering the endorhiza and spreading to grape inflorescence stalks, pedicels and then to immature berries through xylem vessels. In parallel to these observations, a natural microbial communities was also detected on and inside plants, demonstrating the colonization of grapevine by strain PsJN in the presence of other microorganisms.

Detection of plant-modulated alterations in antifungal gene expression in Pseudomonas fluorescens CHA0 on roots by flow cytometry

The biocontrol activity of the root-colonizing Pseudomonas fluorescens strain CHA0 is largely determined by the production of antifungal metabolites, especially 2,4-diacetylphloroglucinol. The expression of these metabolites depends on abiotic and biotic environmental factors, in particular, elements present in the rhizosphere. In this study, we have developed a new method for the in situ analysis of antifungal gene expression using flow cytometry combined with green fluorescent protein (GFP)-based reporter fusions to the phlA and prnA genes essential for the production of the antifungal compounds 2,4-diacetylphloroglucinol and pyrrolnitrin, respectively, in strain CHA0. Expression of phlA-gfp and prnA-gfp in CHA0 cells harvested from the rhizosphere of a set of plant species as well as from the roots of healthy, leaf pathogen-attacked, and physically stressed plants were analyzed using a FACSCalibur. After subtraction of background fluorescence emitted by plant-derived particles and CHA0 cells not carrying the gfp reporters, the average gene expression per bacterial cell could be calculated. Levels of phlA and prnA expression varied significantly in the rhizospheres of different plant species. Physical stress and leaf pathogen infection lowered phlA expression levels in the rhizosphere of cucumber. Our results demonstrate that the newly developed approach is suitable to monitor differences in levels of antifungal gene expression in response to various plant-derived factors. An advantage of the method is that it allows quantification of bacterial gene expression in rhizosphere populations at a single-cell level. To our best knowledge, this is the first study using flow cytometry for the in situ analysis of biocontrol gene expression in a plant-beneficial bacterium in the rhizosphere.

Quantitative isolation of biocontrol agents Trichoderma spp., Gliocladium spp. and actinomycetes from soil with culture media

Soil biodiversity plays a key role in the sustainability of agriculture systems and indicates the level of health of soil, especially when considering the richness of microorganisms that are involved in biological control of soilborne diseases. Cultural practices may produce changes in soil microflora, which can be quantified through the isolation of target microorganisms. Rhizosphere soil samples were taken from an assay with different crop rotations and tillage systems, and populations of Trichoderma spp., Gliocladium spp. and actinomycetes were quantified in order to select the general and selective culture media that better reflect the changes of these microbial populations in soil. The most efficient medium for the isolation of Trichoderma spp. and Gliocladium spp. was potato dextrose agar modified by the addition of chloramphenicol, streptomycin and rose bengal, and for actinomycetes was Küster medium, with cycloheximide and sodium propionate.

Survival of gfp-tagged antagonistic bacteria in the rhizosphere of tomato plants and their effects on the indigenous bacterial community

The survival and colonization patterns of Pseudomonas putida PRD16 and Enterobacter cowanii PRF116 in the rhizosphere of greenhouse-grown tomato plants and the effects of their inoculation on the indigenous bacterial community were followed by selective plating, molecular fingerprinting, and confocal laser scanning microscopy (CLSM) over 3 weeks. Both strains, which showed in vitro antagonistic activity against Ralstonia solanacearum, were previously tagged with gfp. Seed and root inoculation were compared. Although plate counts decreased for both gfp-tagged antagonists, PRD16 showed a better survival in the rhizosphere of tomato roots independent of the inoculation method. Analysis of 16S rRNA gene fragments amplified from total community DNA by denaturing gradient gel electrophoresis and CLSM confirmed the decrease in the relative abundance of the inoculant strains. Pronounced differences in the Pseudomonas community patterns for plants inoculated with PRD16 compared to the control were detected 3 weeks after root inoculation, indicating a longer-lasting effect. Analysis by CLSM showed rather heterogeneous colonization patterns for both inoculant strains. In comparison with seed inoculation, root inoculation led to a much better colonization as evidenced by all three methods. The colonization patterns observed by CLSM provide important information on the sampling strategy required for monitoring inoculant strains in the rhizosphere.

Root cap influences root colonisation by Pseudomonas fluorescens SBW25 on maize

We investigated the influence of root border cells on the colonisation of seedling Zea mays roots by Pseudomonas fluorescens SBW25 in sandy loam soil packed at two dry bulk densities. Numbers of colony forming units (CFU) were counted on sequential sections of root for intact and decapped inoculated roots grown in loose (1.0 mg m(-3)) and compacted (1.3 mg m(-3)) soil. After two days of root growth, the numbers of P. fluorescens (CFU cm(-1)) were highest on the section of root just below the seed with progressively fewer bacteria near the tip, irrespective of density. The decapped roots had significantly more colonies of P. fluorescens at the tip compared with the intact roots: approximately 100-fold more in the loose and 30-fold more in the compact soil. In addition, confocal images of the root tips grown in agar showed that P. fluorescens could only be detected on the tips of the decapped roots. These results indicated that border cells, and their associated mucilage, prevented complete colonization of the root tip by the biocontrol agent P. fluorescens, possibly by acting as a disposable surface or sheath around the cap.

Colonization of tomato root seedling by Pseudomonas fluorescens 92 rkG5: spatio-temporal dynamics, localization, organization, viability, and culturability

The localization, viability, and culturability of Pseudomonas fluorescens 92 rkG5 were analyzed on three morphological root zones (root tip + elongation, root hair, and collar) of 3-, 5-, and 7-day-old tomato plants. Qualitative information about the localization and viability was collected by confocal laser scanning microscopy. Quantitative data concerning the distribution, viability, and culturability were obtained through combined dilution plating and flow cytometry. Colonization by P. fluorescens affected root development in a complex way, causing a general increase in the length of the collar and early stimulation of the primary root growth (3rd day), followed by a reduction in length (7th day). The three root zones showed different distribution, organization, and viability of the bacterial cells, but the distribution pattern within each zone did not change with time. Root tips were always devoid of bacteria, whereas with increasing distance from the apex, microcolonies or strings of cells became more and more prominent. Viability was high in the elongation zone, but it declined in the older parts of the roots. The so-called viable but not culturable cells were observed on the root, and their proportion in the distal (root tip + elongation) zone dramatically increased with time. These results suggest the existence of a specific temporal and spatial pattern of root colonization, related to cell viability and culturability, expressed by the plant-beneficial strain P. fluorescens 92 rkG5.

Microbial co-operation in the rhizosphere

Soil microbial populations are immersed in a framework of interactions known to affect plant fitness and soil quality. They are involved in fundamental activities that ensure the stability and productivity of both agricultural systems and natural ecosystems. Strategic and applied research has demonstrated that certain co-operative microbial activities can be exploited, as a low-input biotechnology, to help sustainable, environmentally-friendly, agro-technological practices. Much research is addressed at improving understanding of the diversity, dynamics, and significance of rhizosphere microbial populations and their co-operative activities. An analysis of the co-operative microbial activities known to affect plant development is the general aim of this review. In particular, this article summarizes and discusses significant aspects of this general topic, including (i) the analysis of the key activities carried out by the diverse trophic and functional groups of micro-organisms involved in co-operative rhizosphere interactions; (ii) a critical discussion of the direct microbe-microbe interactions which results in processes benefiting sustainable agro-ecosystem development; and (iii) beneficial microbial interactions involving arbuscular mycorrhiza, the omnipresent fungus-plant beneficial symbiosis. The trends of this thematic area will be outlined, from molecular biology and ecophysiological issues to the biotechnological developments for integrated management, to indicate where research is needed in the future.

Biological control of soil-borne pathogens by fluorescent pseudomonads

Particular bacterial strains in certain natural environments prevent infectious diseases of plant roots. How these bacteria achieve this protection from pathogenic fungi has been analysed in detail in biocontrol strains of fluorescent pseudomonads. During root colonization, these bacteria produce antifungal antibiotics, elicit induced systemic resistance in the host plant or interfere specifically with fungal pathogenicity factors. Before engaging in these activities, biocontrol bacteria go through several regulatory processes at the transcriptional and post-transcriptional levels.

Colonisation of Pinus halepensis roots by Pseudomonas fluorescens and interaction with the ectomycorrhizal fungus Suillus granulatus

Colonisation of Pinus halepensis roots by GFP-tagged Pseudomonas fluorescens Aur6 was monitored by epifluorescence microscopy and dilution plating. Aur6-GFP was able to colonise and proliferate on P. halepensis roots. Co-inoculation with the ectomycorrhizal fungus Suillus granulatus did not affect the bacterial colonisation pattern whereas it had an effect on bacterial density. Bacterial counts increased during the first 20 days of seedling growth, irrespective of seedlings being mycorrhizal or not. After 40 days, bacterial density significantly decreased and bacteria concentrated on the upper two-thirds of the pine root. The presence of S. granulatus significantly stimulated survival of bacteria in the root elongation zone where fungal colonisation was higher. The number of mycorrhizas formed by S. granulatus was not affected by co-inoculation with Aur6-GFP. Neither Aur6-GFP nor S. granulatus stimulated P. halepensis development when inoculated alone, but a synergistic effect was observed on seedling growth when bacteria and fungus were co-inoculated.