The plant beneficial rhizobacterium Achromobacter sp. 5B1 influences root development through auxin signaling and redistribution

Resistance mechanisms of cereal plants and rhizosphere soil microbial communities to chromium stress

Agricultural soils contaminated with heavy metals poison crops and disturb the normal functioning of rhizosphere microbial communities. Different crops and rhizosphere microbial communities exhibit different heavy metal resistance mechanisms. Here, indoor pot studies were used to assess the mechanisms of grain and soil rhizosphere microbial communities on chromium (Cr) stress. Millet grain variety 'Jingu 21' (Setaria italica) and soil samples were collected prior to control (CK), 6 hours after (Cr_6h), and 6 days following (Cr_6d) Cr stress. Transcriptomic analysis, high-throughput sequencing and quantitative polymerase chain reaction (qPCR) were used for sample determination and data analysis. Cr stress inhibited the expression of genes related to cell division, and photosynthesis in grain plants while stimulating the expression of genes related to DNA replication and repair, in addition to plant defense systems resist Cr stress. In response to chromium stress, rhizosphere soil bacterial and fungal community compositions and diversity changed significantly (p < 0.05). Both bacterial and fungal co-occurrence networks primarily comprised positively correlated edges that would serve to increase community stability. However, bacterial community networks were larger than fungal community networks and were more tightly connected and less modular than fungal networks. The abundances of C/N functional genes exhibited increasing trends with increased Cr exposure. Overall, these results suggest that Cr stress primarily prevented cereal seedlings from completing photosynthesis, cell division, and proliferation while simultaneously triggering plant defense mechanisms to resist the toxic effects of Cr. Soil bacterial and fungal populations exhibited diverse response traits, community-assembly mechanisms, and increased expression of functional genes related to carbon and nitrogen cycling, all of which are likely related to microbial survival during Cr stress. This study provides new insights into resistance mechanisms, microbial community structures, and mechanisms of C/N functional genes responses in cereal plants to heavy metal contaminated agricultural soils. Portions of this text were previously published as part of a preprint (https://www.researchsquare.com/article/rs-2891904/v1).

Sucrose supplements modulate the Pseudomonas chlororaphis-Arabidopsis thaliana interaction via decreasing the production of phenazines and enhancing the root auxin response

Management of the plant microbiome may help support food needs for the human population. Bacteria influence plants through enhancing nutrient uptake, metabolism, photosynthesis, biomass production and/or reinforcing immunity. However, information into how these microbes behave under different growth conditions is missing. In this work, we tested how carbon supplements modulate the interaction of Pseudomonas chlororaphis with Arabidopsis thaliana. P. chlororaphis streaks strongly repressed primary root growth, lateral root formation and ultimately, biomass production. Noteworthy, increasing sucrose availability into the media from 0 to 2.4% restored plant growth and promoted lateral root formation in bacterized seedlings. This effect could not be observed by supplementing sucrose to leaves only, indicating that the interaction was strongly modulated by bacterial access to sugar. Total phenazine content decreased in the bacteria grown in high (2.4%) sucrose medium, and conversely, the expression of phzH and pslA genes were diminished by sugar supply. Pyocyanin antagonized the promoting effects of sucrose in lateral root formation and biomass production in inoculated seedlings, indicating that this virulence factor accounts for growth repression during the plant-bacterial interaction. Defence reporter transgenes PR-1::GUS and LOX2::GUS were induced in leaves, while the expression of the auxin-inducible, synthetic reporter gene DR5::GUS was enhanced in the roots of bacterized seedlings at low and high sucrose treatments, which suggests that growth/defence trade-offs in plants are critically modulated by P. chlororaphis. Collectively, our data suggest that bacterial carbon nutrition controls the outcome of the relation with plants.

Changes in chemical properties and microbial communities' composition of a forest litter-based biofertilizer produced through aerated solid-state culture under different oxygen conditions

Fermented forest litter (FFL) is a bioproduct used as biofertilizer for several decades in Eastern Asia and Latin America. It is locally handcrafted by farmers in anaerobic conditions by fermenting forest litter added with agricultural by-products such as whey, cereal bran, and molasses. The aim of this study was to characterize the FFL process and product through gas and liquid chromatography analyses. It also provides some highlights on the influence of O2 on this solid-state culture. Under anoxic condition, a maximum CO2 production rate (CDPR) of 0.41 mL/h∙g dry matter (dm) was reached after 8 days. The main volatile organic compounds (VOCs) were ethanol and ethyl acetate, with a production rate profile similar to CDPR. After 21 days of culture, no residual sucrose nor lactose was detected. Lactic and acetic acids reached 58.8 mg/g dm and 10.2 mg/g dm, respectively, ensuring the acidification of the matrix to a final pH of 4.72. A metabarcoding analysis revealed that heterolactic acid bacteria (Lentilactobacillus, Leuconostoc), homolactic acid bacteria (Lactococcus), and yeasts (Saccharomyces, Clavispora) were predominant. Predicted genes in the microbiome confirmed the potential link between detected bacteria and acids and VOCs produced. When O2 was fed to the cultures, final pH reached values up to 8.5. No significant amounts of lactic nor acetic acid were found. In addition, a strong shift in microbial communities was observed, with a predominance of Proteobacteria and molds, among which are potential pathogens like Fusarium species. This suggests that particular care must be brought to maintain anoxic conditions throughout the process.

The plant growth promoting rhizobacterium Achromobacter sp. 5B1, rescues Arabidopsis seedlings from alkaline stress by enhancing root organogenesis and hormonal responses

Soil alkalinity is a critical environmental factor for plant growth and distribution in ecosystems. An alkaline condition (pH > 7) is imposed by the rising concentration of hydroxides and cations, and prevails in semiarid and arid environments, which represent more than 25% of the total arable land of the world. Despite the great pressure exerted by alkalinity for root viability and plant survival, scarce information is available to understand how root microbes contribute to alkaline pH adaptation. Here, we assessed the effects of alkalinity on shoot and root biomass production, chlorophyll content, root growth and branching, lateral root primordia formation, and the expression of CYCB1, TOR kinase, and auxin and cytokinin-inducible trangenes in shoots and roots of Arabidopsis seedlings grown in Petri plates with agar-nutrient medium at pH values of 7.0, 7.5, 8.0, 8.5, and 9.0. The results showed an inverse correlation between the rise of pH and most growth, hormonal and genetic traits analyzed. Noteworthy, root inoculation with Achromobacter sp. 5B1, a beneficial rhizospheric bacterium, with plant growth promoting and salt tolerance features, increased biomass production, restored root growth and branching and enhanced auxin responses in WT seedlings and auxin-related mutants aux1-7 and eir1, indicating that stress adaptation operates independently of canonical auxin transporter proteins. Sequencing of the Achromobacter sp. 5B1 genome unveiled 5244 protein-coding genes, including genes possibly involved in auxin biosynthesis, quorum-sensing regulation and stress adaptation, which may account for its plant growth promotion attributes. These data highlight the critical role of rhizobacteria to increase plant resilience under high soil pH conditions potentially through genes for adaptation to an extreme environment and bacteria-plant communication.

Optimizing concentration and interaction mechanism of Demodesmus sp. and Achromobacter pulmonis sp. consortium to evaluate their potential for dibutyl phthalate removal from synthetic wastewater

A green approach of Desmodesmus sp. to Achromobacter pulmonis (1:1) coculture ratios was optimized to improve the removal efficiency of dibutyl phthalate (DBP) from simulated wastewater. High DBP resistance bacterial strains and microalgae was optimized from plastic contaminated water and acclimation process respectively. The influence of various factors on DBP removal performance was comprehensively investigated. Highest DBP removal 93 % was recorded, when the ratios algae-bacteria 1:1, with sodium acetate, pH-6, shaking speed-120 rpm and lighting periods L:D-12:12. Enough nutrient (TN/TP/TOC) availability and higher protein-108 mg/L and sugar-40 mg/L were observed in presences of 50 mg/L DBP. The degradation and sorption were calculated 81,12; 27,39 & 43,12 % in algae-bacteria, only algae and only bacteria system respectively. The degradation kinetics t1/2 3.74,22.15,12.86 days were evaluated, confirming that algae-bacteria effectively degrade the DBP. This outcome leading to promote a green sustainable approach to remove the emerging contamination from wastewater.

Flavonoids influence key rhizocompetence traits for early root colonization and PCB degradation potential of Paraburkholderia xenovorans LB400

Introduction

Flavonoids are among the main plant root exudation components, and, in addition to their role in symbiosis, they can broadly affect the functionality of plant-associated microbes: in polluted environments, for instance, flavonoids can induce the expression of the enzymatic degradative machinery to clean-up soils from xenobiotics like polychlorinated biphenyls (PCBs). However, their involvement in root community recruitment and assembly involving non-symbiotic beneficial interactions remains understudied and may be crucial to sustain the holobiont fitness under PCB stress.

Methods

By using a set of model pure flavonoid molecules and a natural blend of root exudates (REs) with altered flavonoid composition produced by Arabidopsis mutant lines affected in flavonoid biosynthesis and abundance (null mutant tt4, flavonoid aglycones hyperproducer tt8, and flavonoid conjugates hyperaccumulator ttg), we investigated flavonoid contribution in stimulating rhizocompetence traits and the catabolic potential of the model bacterial strain for PCB degradation Paraburkholderia xenovorans LB400.

Results

Flavonoids influenced the traits involved in bacterial recruitment in the rhizoplane by improving chemotaxis and motility responses, by increasing biofilm formation and by promoting the growth and activation of the PCB-degradative pathway of strain LB400, being thus potentially exploited as carbon sources, stimulating factors and chemoattractant molecules. Indeed, early rhizoplane colonization was favored in plantlets of the tt8 Arabidopsis mutant and reduced in the ttg line. Bacterial growth was promoted by the REs of mutant lines tt4 and tt8 under control conditions and reduced upon PCB-18 stress, showing no significant differences compared with the WT and ttg, indicating that unidentified plant metabolites could be involved. PCB stress presumably altered the Arabidopsis root exudation profile, although a sudden "cry-for-help" response to recruit strain LB400 was excluded and flavonoids appeared not to be the main determinants. In the in vitro plant-microbe interaction assays, plant growth promotion and PCB resistance promoted by strain LB400 seemed to act through flavonoid-independent mechanisms without altering bacterial colonization efficiency and root adhesion pattern.

Discussions

This study further contributes to elucidate the vast array of functions provided by flavonoids in orchestrating the early events of PCB-degrading strain LB400 recruitment in the rhizosphere and to support the holobiont fitness by stimulating the catabolic machinery involved in xenobiotics decomposition and removal.

Differential influence of Bacillus subtilis strains on Arabidopsis root architecture through common and distinct plant hormonal pathways

Plant growth-promoting microbes (PGPM) can enhance crop yield and health, but knowledge of their mode-of-action is limited. We studied the influence of two Bacillus subtilis strains, the natural isolate ALC_02 and the domesticated 168 Gö, on Arabidopsis and hypothesized that they modify the root architecture by modulating hormone transport or signaling. Both bacteria promoted increase of shoot and root surface area in vitro, but through different root anatomical traits. Mutant plants deficient in auxin transport or signaling responded less to the bacterial strains than the wild-type, and application of the auxin transport inhibitor NPA strongly reduced the influence of the strains. Both bacteria produced auxin and enhanced shoot auxin levels in DR5::GUS reporter plants. Accordingly, most of the beneficial effects of the strains were dependent on functional auxin transport and signaling, while only 168 Gö depended on functional ethylene signaling. As expected, only ALC_02 stimulated plant growth in soil, unlike 168 Gö that was previously reported to have reduced biofilms. Collectively, the results highlight that B. subtilis strains can have strikingly different plant growth-promoting properties, dependent on what experimental setup they are tested in, and the importance of choosing the right PGPM for a desired root phenotype.

Pseudomonas aeruginosa LasI-dependent plant growth promotion requires the host nitrate transceptor AtNRT1.1/CHL1 and the nitrate reductases NIA1 and NIA2

MAIN CONCLUSION

In P. aeruginosa, mutation of the gene encoding N-acyl-L-homoserine lactone synthase LasI drives defense and plant growth promotion, and this latter trait requires adequate nitrate nutrition. Cross-kingdom communication with bacteria is crucial for plant growth and productivity. Here, we show a strong induction of genes for nitrate uptake and assimilation in Arabidopsis seedlings co-cultivated with P. aeruginosa WT (PAO1) or ΔlasI mutants defective on the synthesis of the quorum-sensing signaling molecule N-(3-oxododecanoyl)-L-homoserine lactone. Along with differential induction of defense-related genes, the change from plant growth repression to growth promotion upon bacterial QS disruption, correlated with upregulation of the dual-affinity nitrate transceptor CHL1/AtNRT1/NPF6.3 and the nitrate reductases NIA1 and NIA2. CHL1-GUS was induced in Arabidopsis primary root tips after transfer onto P. aeruginosa ΔlasI streaks at low and high N availability, whereas this bacterium required high concentrations of nitrogen to potentiate root and shoot biomass production and to improve root branching. Arabidopsis chl1-5 and chl1-12 mutants and double mutants in NIA1 and NIA2 nitrate reductases showed compromised growth under low nitrogen availability and failed to mount an effective growth promotion and root branching response even at high NH4NO3. WT P. aeruginosa PAO1 and P. aeruginosa ΔlasI mutant promoted the accumulation of nitric oxide (NO) in roots of both the WT and nia1nia2 double mutants, whereas NO donors SNP or SNAP did not improve growth or root branching in nia1nia2 double mutants with or without bacterial cocultivation. Thus, inoculation of Arabidopsis roots with P. aeruginosa drives gene expression for improved nitrogen acquisition and this macronutrient is critical for the plant growth-promoting effects upon disruption of the LasI quorum-sensing system.

Biostimulants and environmental stress mitigation in crops: A novel and emerging approach for agricultural sustainability under climate change

Pesticide and fertilizer usage is at the center of agricultural production to meet the demands of an ever-increasing global population. However, rising levels of chemicals impose a serious threat to the health of humans, animals, plants, and even the entire biosphere because of their toxic effects. Biostimulants offer the opportunity to reduce the agricultural chemical footprint owing their multilevel, beneficial properties helping to make agriculture more sustainable and resilient. When applied to plants or to the soil an increased absorption and distribution of nutrients, tolerance to environmental stress, and improved quality of plant products explain the mechanisms by which these probiotics are useful. In recent years, the use of plant biostimulants has received widespread attention across the globe as an ecologically acceptable alternative to sustainable agricultural production. As a result, their worldwide market continues to grow, and further research will be conducted to broaden the range of the products now available. Through this review, we present a current understanding of biostimulants, their mode of action and their involvement in modulating abiotic stress responses, including omics research, which may provide a comprehensive assessment of the crop's response by correlating molecular changes to physiological pathways activated under stress conditions aggravated by climate change.

Compounds from rhizosphere microbes that promote plant growth

The rhizosphere is the soil-plant interface colonized by bacterial and fungal species that exert growth-promoting and adaptive benefits. The plant-bacteria relationships rely upon the perception of volatile organic compounds (VOCs), canonical phytohormones such as auxins and cytokinins, and the bacterial quorum sensing-related N-acyl-L-homoserine lactones and cyclodipeptides. On the other hand, plant-beneficial Trichoderma fungi emit highly active VOCs, including 6-pentyl-2H-pyran-2-one (6-PP), and β-caryophyllene, which contribute to plant morphogenesis, but also into how these microbes spread over roots or live as endophytes. Here, we describe recent findings concerning how compounds from beneficial bacteria and fungi affect root architecture and advance into the signaling events that mediate microbial recognition.

Microorganisms Associated with the Ambrosial Beetle Xyleborus affinis with Plant Growth-Promotion Activity in Arabidopsis Seedlings and Antifungal Activity Against Phytopathogenic Fungus Fusarium sp. INECOL_BM-06

Plants interact with a great diversity of microorganisms or insects throughout their life cycle in the environment. Plant and insect interactions are common; besides, a great variety of microorganisms associated with insects can induce pathogenic damage in the host, as mutualist phytopathogenic fungus. However, there are other microorganisms present in the insect-fungal association, whose biological/ecological activities and functions during plant interaction are unknown. In the present work evaluated, the role of microorganisms associated with Xyleborus affinis, an important beetle species within the Xyleborini tribe, is characterized by attacking many plant species, some of which are of agricultural and forestry importance. We isolated six strains of microorganisms associated with X. affinis shown as plant growth-promoting activity and altered the root system architecture independent of auxin-signaling pathway in Arabidopsis seedlings and antifungal activity against the phytopathogenic fungus Fusarium sp. INECOL_BM-06. In addition, evaluating the tripartite interaction plant-microorganism-fungus, interestingly, we found that microorganisms can induce protection against the phytopathogenic fungus Fusarium sp. INECOL_BM-06 involving the jasmonic acid-signaling pathway and independent of salicylic acid-signaling pathway. Our results showed the important role of this microorganisms during the plant- and insect-microorganism interactions, and the biological potential use of these microorganisms as novel agents of biological control in the crops of agricultural and forestry is important.

Plant Disease Resistance-Related Pathways Recruit Beneficial Bacteria by Remodeling Root Exudates upon Bacillus cereus AR156 Treatment

The environmentally friendly biological control strategy that relies on beneficial bacterial inoculants to improve plant disease resistance is a promising strategy. Previously, it has been demonstrated that biocontrol bacteria treatments can change the plant rhizosphere microbiota but whether plant signaling pathways, especially those related to disease resistance, mediate the changes in rhizosphere microbiota has not been explored. Here, we investigated the complex interplay among biocontrol strains, plant disease resistance-related pathways, root exudates, rhizosphere microorganisms, and pathogens to further clarify the biocontrol mechanism of biocontrol bacteria by using plant signaling pathway mutants. Bacillus cereus AR156, which was previously isolated from forest soil by our laboratory, can significantly control tomato bacterial wilt disease in greenhouse and field experiments. Moreover, compared with the control treatment, the B. cereus AR156 treatment had a significant effect on the soil microbiome and recruited 35 genera of bacteria to enrich the rhizosphere of tomato. Among them, the relative rhizosphere abundance of nine genera, including Ammoniphilus, Bacillus, Bosea, Candidimonas, Flexivirga, Brevundimonas, Bordetella, Dyella, and Candidatus_Berkiella, was regulated by plant disease resistance-related signaling pathways and B. cereus AR156. Linear correlation analysis showed that the relative abundances of six genera in the rhizosphere were significantly negatively correlated with pathogen colonization in roots. These rhizosphere bacteria were affected by plant root exudates that are regulated by signaling pathways. IMPORTANCE Our data suggest that B. cereus AR156 can promote the enrichment of beneficial microorganisms in the plant rhizosphere by regulating salicylic acid (SA) and jasmonic acid (JA)/ethylene (ET) signaling pathways in plants, thereby playing a role in controlling bacterial wilt disease. Meanwhile, Spearman correlation analysis showed that the relative abundances of these beneficial bacteria were correlated with the secretion of root exudates. Our study reveals a new mechanism for SA and JA/ET signals to participate in the adjustment of plant resistance whereby the signaling pathways adjust the rhizosphere microecology by changing the root exudates and thus change plant resistance. On the other hand, biocontrol strains can utilize this mechanism to recruit beneficial bacteria by activating disease resistance-related signaling pathways to confine the infection and spread of pathogens. Finally, our data also provide a new idea for the in-depth study of biocontrol mechanisms.

Bacterial volatile organic compounds (VOCs) promote growth and induce metabolic changes in rice

Plant growth-promoting bacteria (PGPB) represent an eco-friendly alternative to reduce the use of chemical products while increasing the productivity of economically important crops. The emission of small gaseous signaling molecules from PGPB named volatile organic compounds (VOCs) has emerged as a promising biotechnological tool to promote biomass accumulation in model plants (especially Arabidopsis thaliana) and a few crops, such as tomato, lettuce, and cucumber. Rice (Oryza sativa) is the most essential food crop for more than half of the world's population. However, the use of VOCs to improve this crop performance has not yet been investigated. Here, we evaluated the composition and effects of bacterial VOCs on the growth and metabolism of rice. First, we selected bacterial isolates (IAT P4F9 and E.1b) that increased rice dry shoot biomass by up to 83% in co-cultivation assays performed with different durations of time (7 and 12 days). Metabolic profiles of the plants co-cultivated with these isolates and controls (without bacteria and non-promoter bacteria-1003-S-C1) were investigated via ¹H nuclear magnetic resonance. The analysis identified metabolites (e.g., amino acids, sugars, and others) with differential abundance between treatments that might play a role in metabolic pathways, such as protein synthesis, signaling, photosynthesis, energy metabolism, and nitrogen assimilation, involved in rice growth promotion. Interestingly, VOCs from IAT P4F9 displayed a more consistent promotion activity and were also able to increase rice dry shoot biomass in vivo. Molecular identification by sequencing the 16S rRNA gene of the isolates IAT P4F9 and E.1b showed a higher identity with Serratia and Achromobacter species, respectively. Lastly, volatilomes of these and two other non-promoter bacteria (1003-S-C1 and Escherichia coli DH5α) were evaluated through headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry. Compounds belonging to different chemical classes, such as benzenoids, ketones, alcohols, sulfide, alkanes, and pyrazines, were identified. One of these VOCs, nonan-2-one, was validated in vitro as a bioactive compound capable of promoting rice growth. Although further analyses are necessary to properly elucidate the molecular mechanisms, our results suggest that these two bacterial isolates are potential candidates as sources for bioproducts, contributing to a more sustainable agriculture.

Polyamine metabolizing rhizobacteria Pseudomonas sp. GBPI_506 modulates hormone signaling to enhance lateral roots and nicotine biosynthesis in Nicotiana benthamiana

Beneficial rhizobacteria in the soil are important drivers of plant health and growth. In this study, we provide the draft genome of a root colonizing and auxin-producing Pseudomonas sp. strain GBPI_506. The bacterium was investigated for its contribution in the growth of Nicotiana benthamiana (Nb) and biosynthesis of nicotine. The bacterium showed chemotaxis towards root exudates potentially mediated by putrescine, a polyamine compound, to colonize the roots of Nb. Application of the bacterium with the roots of Nb, increased plant biomass and total soluble sugars in the leaves, and promoted lateral root (LR) development as compared to the un-inoculated plants. Confocal analysis using transgenic (DR5:GFP) Arabidopsis showed increased auxin trafficking in the LR of inoculated plants. Upregulation of nicotine biosynthesis genes and genes involved in salicylic acid (SA) and jasmonic acid (JA) signaling in the roots of inoculated plants suggested increased nicotine biosynthesis as a result of bacterial application. An increased JA content in roots and nicotine accumulation in leaves provided evidence on JA-mediated upregulation of nicotine biosynthesis in the bacterized plants. The findings suggested that the bacterial root colonization triggered networking between auxin, SA, and JA to facilitate LR development leading to enhanced plant growth and nicotine biosynthesis in Nb.

Chromium in plant growth and development: Toxicity, tolerance and hormesis

Research over the last three decades showed that chromium, particularly the oxyanion chromate Cr(VI) behaves as a toxic environmental pollutant that strongly damages plants due to oxidative stress, disruption of nutrient uptake, photosynthesis and metabolism, and ultimately, represses growth and development. However, mild Cr(VI) concentrations promote growth, induce adventitious root formation, reinforce the root cap, and produce twin roots from single root meristems under conditions that compromise cell viability, indicating its important role as a driver for root organogenesis. In recent years, considerable advance has been made towards deciphering the molecular mechanisms for root sensing of chromate, including the identification of regulatory proteins such as SOLITARY ROOT and MEDIATOR 18 that orchestrate the multilevel dynamics of the oxyanion. Cr(VI) decreases the expression of several glutamate receptors, whereas amino acids such as glutamate, cysteine and proline confer protection to plants from hexavalent chromium stress. The crosstalk between plant hormones, including auxin, ethylene, and jasmonic acid enables tissues to balance growth and defense under Cr(VI)-induced oxidative damage, which may be useful to better adapt crops to biotic and abiotic challenges. The highly contrasting responses of plants manifested at the transcriptional and translational levels depend on the concentration of chromate in the media, and fit well with the concept of hormesis, an adaptive mechanism that primes plants for resistance to environmental challenges, toxins or pollutants. Here, we review the contrasting facets of Cr(VI) in plants including the cellular, hormonal and molecular aspects that mechanistically separate its toxic effects from biostimulant outputs.

Micrococcus luteus LS570 promotes root branching in Arabidopsis via decreasing apical dominance of the primary root and an enhanced auxin response

The interaction of plant roots with bacteria is influenced by chemical signaling, where auxins play a critical role. Auxins exert positive or negative influences on the plant traits responsible of root architecture configuration such as root elongation and branching and root hair formation, but how bacteria that modify the plant auxin response promote or repress growth, as well as root structure, remains unknown. Here, we isolated and identified via molecular and electronic microscopy analysis a Micrococcus luteus LS570 strain as a plant growth promoter that halts primary root elongation in Arabidopsis seedlings and strongly triggers root branching and absorptive potential. The root biomass was exacerbated following root contact with bacterial streaks, and this correlated with inducible expression of auxin-related gene markers DR5:GUS and DR5:GFP. Cellular and structural analyses of root growth zones indicated that the bacterium inhibits both cell division and elongation within primary root tips, disrupting apical dominance, and as a consequence differentiation programs at the pericycle and epidermis, respectively, triggers the formation of longer and denser lateral roots and root hairs. Using Arabidopsis mutants defective on auxin signaling elements, our study uncovers a critical role of the auxin response factors ARF7 and ARF19, and canonical auxin receptors in mediating both the primary root and lateral root response to M. luteus LS570. Our report provides very basic information into how actinobacteria interact with plants and direct evidence that the bacterial genus Micrococcus influences the cellular and physiological plant programs ultimately responsible of biomass partitioning.

Motility-Independent Vertical Transmission of Bacteria in Leaf Symbiosis

Hereditary symbioses have the potential to drive transgenerational effects, yet the mechanisms responsible for transmission of heritable plant symbionts are still poorly understood. The leaf symbiosis between Dioscorea sansibarensis and the bacterium Orrella dioscoreae offers an appealing model system to study how heritable bacteria are transmitted to the next generation. Here, we demonstrate that inoculation of apical buds with a bacterial suspension is sufficient to colonize newly formed leaves and propagules, and to ensure transmission to the next plant generation. Flagellar motility is not required for movement inside the plant but is important for the colonization of new hosts. Further, tissue-specific regulation of putative symbiotic functions highlights the presence of two distinct subpopulations of bacteria in the leaf gland and at the shoot meristem. We propose that bacteria in the leaf gland dedicate resources to symbiotic functions, while dividing bacteria in the shoot tip ensure successful colonization of meristematic tissue, glands, and propagules. Compartmentalization of intrahost populations together with tissue-specific regulation may serve as a robust mechanism for the maintenance of mutualism in leaf symbiosis.

Plant growth-promoting rhizobacterium Pseudomonas sp. CM11 specifically induces lateral roots

Plant growth-promoting rhizobacteria are involved in altering secondary root (SR) formation, but hitherto there has been no distinction between the different types of SRs upon induction of soil biota, and the genetic pathways involved. By using plate and soil systems, we studied the effects of the Pseudomonas strains CM11 and WCS417 on plant performance with a focus on root development. Through a combination of cellular, molecular and genetic analyses, we investigated the type of SRs induced upon CM11 and WCS417 root inoculation using genetic pathways associated with specific SR types. CM11 was shown to affect the root architecture differently from WCS417. CM11 inoculation leads to primary root arrest, whereas WCS417 reveals a longer primary root. Both CM11 and WCS417 activate the PLETHORA 3,5,7-controlled lateral root pathway, rather than the WUSCHEL-RELATED HOMEOBOX 11,12-controlled adventitious (lateral) root pathway. In addition, CM11 promotes plant growth in model and various crop species. It improves plant fitness traits, such as bigger shoots, faster bolting and higher yield in terms of seeds. Our results indicate that the root system architecture can be promoted by activation of PLETHORA 3,5,7 dependent primed lateral pre-branch sites upon inoculation with CM11, which creates great potential to gain a better understanding of root plasticity.

Screening of Phosphate Solubilization Identifies Six Pseudomonas Species with Contrasting Phytostimulation Properties in Arabidopsis Seedlings

The interaction of plants with bacteria and the long-term success of their adaptation to challenging environments depend upon critical traits that include nutrient solubilization, remodeling of root architecture, and modulation of host hormonal status. To examine whether bacterial promotion of phosphate solubilization, root branching and the host auxin response may account for plant growth, we isolated and characterized ten bacterial strains based on their high capability to solubilize calcium phosphate. All strains could be grouped into six Pseudomonas species, namely P. brassicae, P. baetica, P. laurylsulfatiphila, P. chlororaphis, P. lurida, and P. extremorientalis via 16S rRNA molecular analyses. A Solibacillus isronensis strain was also identified, which remained neutral when interacting with Arabidopsis roots, and thus could be used as inoculation control. The interaction of Arabidopsis seedlings with bacterial streaks from pure cultures in vitro indicated that their phytostimulation properties largely differ, since P. brassicae and P. laurylsulfatiphila strongly increased shoot and root biomass, whereas the other species did not. Most bacterial isolates, except P. chlororaphis promoted lateral root formation, and P. lurida and P. chlororaphis strongly enhanced expression of the auxin-inducible gene construct DR5:GUS in roots, but the most bioactive probiotic bacterium P. brassicae could not enhance the auxin response. Inoculation with P. brassicae and P. lurida improved shoot and root growth in medium supplemented with calcium phosphate as the sole Pi source. Collectively, our data indicate the differential responses of Arabidopsis seedlings to inoculation with several Pseudomonas species and highlight the potential of P. brassicae to manage phosphate nutrition and plant growth in a more eco-friendly manner.

Harnessing rhizobacteria to fulfil inter-linked nutrient dependency on soil and alleviate stresses in plants

Plant rhizo-microbiome comprises of complex microbial communities that colonizes at the interphase of plant roots and soil. Plant-growth-promoting rhizobacteria (PGPR) in the rhizosphere provides important ecosystem services ranging from release of essential nutrients for enhancing soil quality and improving plant health to imparting protection to plants against rising biotic and abiotic stresses. Hence, PGPR serve as restoring agents to rejuvenate soil health and mediate plant fitness in the facet of changing climate. Though, it is evident that nutrients availability in soil are managed through inter-linked mechanisms, how PGPR expediate these processes remain less recognized. Promising results of PGPR inoculation on plant growth are continually reported in controlled environmental conditions, however, their field application often fails due to competition with native microbiota and low colonization efficiency in roots. The development of highly efficient and smart bacterial synthetic communities by integrating bacterial ecological and genetic features provides better opportunities for successful inoculant formulations. This review provides an overview of the inter-play between nutrient availability and disease suppression governed by rhizobacteria in soil followed by the role of synthetic bacterial communities in developing efficient microbial inoculants. Moreover, an outlook on the beneficial activities of rhizobacteria in modifying soil characteristics to sustainably boost agroecosystem functioning is also provided.

Bradyrhizobium japonicum IRAT FA3 Alters Arabidopsis thaliana Root Architecture via Regulation of Auxin Efflux Transporters PIN2, PIN3, PIN7, and ABCB19

Beneficial rhizobacteria can stimulate changes in plant root development. Although root system growth is mediated by multiple factors, the regulated distribution of the phytohormone auxin within root tissues plays a principal role. Auxin transport facilitators help to generate the auxin gradients and maxima that determine root structure. Here, we show that the plant-growth-promoting rhizobacterial strain Bradyrhizobium japonicum IRAT FA3 influences specific auxin efflux transporters to alter Arabidopsis thaliana root morphology. Gene expression profiling of host transcripts in control and B. japonicum-inoculated roots of the wild-type A. thaliana accession Col-0 confirmed upregulation of PIN2, PIN3, PIN7, and ABCB19 with B. japonicum and identified genes potentially contributing to a diverse array of auxin-related responses. Cocultivation of the bacterium with loss-of-function auxin efflux transport mutants revealed that B. japonicum requires PIN3, PIN7, and ABCB19 to increase lateral root development and utilizes PIN2 to reduce primary root length. Accelerated lateral root primordia production due to B. japonicum was not observed in single pin3, pin7, or abcb19 mutants, suggesting independent roles for PIN3, PIN7, and ABCB19 during the plant-microbe interaction. Our work demonstrates B. japonicum's influence over host transcriptional reprogramming during plant interaction with this beneficial microbe and the subsequent alterations to root system architecture.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Innovative Culturomic Approaches and Predictive Functional Metagenomic Analysis: The Isolation of Hydrocarbonoclastic Bacteria with Plant Growth Promoting Capacity

Innovative culturomic approaches were adopted to isolate hydrocarbonoclastic bacteria capable of degrading diesel oil, bitumen and a selection of polycyclic aromatic hydrocarbons (PAH), e.g., pyrene, anthracene, and dibenzothiophene, from a soil historically contaminated by total petroleum hydrocarbons (TPH) (10,347 ± 98 mg TPH/kg). The culturomic approach focussed on the isolation of saprophytic microorganisms and specialist bacteria utilising the contaminants as sole carbon sources. Bacterial isolates belonging to Pseudomonas, Arthrobacter, Achromobacter, Bacillus, Lysinibacillus, Microbacterium sps. were isolated for their capacity to utilise diesel oil, bitumen, pyrene, anthracene, dibenzothiphene, and their mixture as sole carbon sources. Pseudomonas, Arthrobacter, Achromobacter and Microbacterium sps. showed plant growth promoting activity, producing indole-3-acetic acid and expressing 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity. In parallel to the culturomic approach, in the microbial community of interest, bacterial community metabarcoding and predictive functional metagenomic analysis were adopted to confirm the potentiality of the isolates in terms of their functional representativeness. The combination of isolation and molecular approaches for the characterisation of a TPH contaminated soil microbial community is proposed as an instrument for the construction of an artificial hydrocarbonoclastic microbiota for environmental restoration.

Multiple plant hormone catabolism activities: an adaptation to a plant-associated lifestyle by Achromobacter spp

Elaborating the plant hormone catabolic activities of bacteria is important for developing a detailed understanding of plant-microbe interactions. In this work, the plant hormone catabolic and plant growth promotion activities of Achromobacter xylosoxidans SOLR10 and A. insolitus AB2 are described. The genome sequences of these strains were obtained and analysed in detail, revealing the genetic mechanisms behind its multiple plant hormone catabolism abilities. Achromobacter strains catabolized indoleacetic acid (IAA) and phenylacetic acid (PAA) (auxins); salicylic acid (SA) and its precursor, benzoic acid (BA); and the ethylene precursor 1-aminocyclopropane-1-carboxylate (ACC). The inoculation of cucumber plants resulted in increased plant growth and development, indicating the beneficial properties of SOLR10 and AB2 strains. Genomic analysis demonstrated the presence of IAA, PAA and BA degradation gene clusters, as well as the nag gene cluster (SA catabolism) and the acdS gene (ACC deaminase), in the genomes of strains SOLR10 and AB2. Additionally, detailed analysis revealed that plant hormone catabolism genes were commonly detected in the Achromobacter genus but were mostly absent in the Bordetella genus, consistent with the notion that Achromobacter evolved in soils in close association with its plant hosts.

Abscisic Acid Regulates the Root Growth Trajectory by Reducing Auxin Transporter PIN2 Protein Levels in Arabidopsis thaliana

The root is in direct contact with soil. Modulation of root growth in response to alterations in soil conditions is pivotal for plant adaptation. Extensive research has been conducted concerning the adjustment of root elongation and architecture in response to environmental factors. However, little is known about the modulation of the root growth trajectory, as well as its hormonal mechanism. Here we report that abscisic acid (ABA) participated in controlling root growth trajectory. The roots upon ABA treatment or from ABA-accumulation double mutant cyp707a1,3 exhibit agravitropism-like growth pattern (wavy growth trajectory). The agravitropism-like phenotype is mainly ascribed to the compromised shootward transportation of auxin since we detected a reduced fluorescence intensity of auxin reporter DR5:VENUS in the root epidermis upon exogenous ABA application or in the endogenous ABA-accumulation double mutant cyp707a1,3. We then tried to decipher the mechanism by which ABA suppressed shootward auxin transport. The membrane abundance of PIN2, a facilitator of shootward auxin transport, was significantly reduced following ABA treatment and in cyp707a1,3. Finally, we revealed that ABA reduced the membrane PIN2 intensity through suppressing the PIN2 expression rather than accelerating PIN2 degradation. Ultimately, our results suggest a pivotal role for ABA in the root growth trajectory and the hormonal interactions orchestrating this process.