Redox Regulation in Diazotrophic Bacteria in Interaction with Plants

Nitrogen fixation in the widely distributed marine γ-proteobacterial diazotroph Candidatus Thalassolituus haligoni

The high diversity and global distribution of heterotrophic bacterial diazotrophs (HBDs) in the ocean has recently become apparent. However, understanding the role these largely uncultured microorganisms play in marine N2 fixation poses a challenge due to their undefined growth requirements and the complex regulation of the nitrogenase enzyme. We isolated and characterized Candidatus Thalassolituus haligoni, a member of a widely distributed clade of HBD belonging to the Oceanospirillales. Analysis of its nifH gene via amplicon sequencing revealed the extensive distribution of Cand. T. haligoni across the Pacific, Atlantic, and Arctic Oceans. Pangenome analysis indicates that the isolate shares >99% identity with an uncultured metagenome-assembled genome called Arc-Gamma-03, recently recovered from the Arctic Ocean. Through combined genomic, proteomic, and physiological approaches, we confirmed that the isolate fixes N2 gas. However, the mechanisms governing nitrogenase regulation in Cand. T. haligoni remain unclear. We propose Cand. T. haligoni as a globally distributed, cultured HBD model species within this understudied clade of Oceanospirillales.

Defense and senescence interplay in legume nodules

Immunity and senescence play a crucial role in the functioning of the legume symbiotic nodules. The miss-regulation of one of these processes compromises the symbiosis leading to death of the endosymbiont and the arrest of the nodule functioning. The relationship between immunity and senescence has been extensively studied in plant organs where a synergistic response can be observed. However, the interplay between immunity and senescence in the symbiotic organ is poorly discussed in the literature and these phenomena are often mixed up. Recent studies revealed that the cooperation between immunity and senescence is not always observed in the nodule, suggesting complex interactions between these two processes within the symbiotic organ. Here, we discuss recent results on the interplay between immunity and senescence in the nodule and the specificities of this relationship during legume-rhizobium symbiosis.

The pleiotropic role of Salinicoccus bacteria in enhancing ROS homeostasis and detoxification metabolism in soybean and oat to cope with pollution of triclosan

Triclosan has been extensively used as a preservative in cosmetics and personal care products. However, its accumulation represents a real environmental threat. Thus, its phytotoxic impact needs more consideration. Our study was conducted to highlight the phytotoxic effect of triclosan on the growth, ROS homeostasis, and detoxification metabolism of two different plant species i.e., legumes (Glycine max) and grass (Avena sativa). Moreover, we investigated the potentiality of plant growth-promoting bacteria (ST-PGPB) in mitigating the phytotoxic effect of triclosan. Triclosan induced biomass (fresh and dry weights) reduction in both plants, but to a higher extent in oats. This decline was associated with a noticeable increment in the oxidative damage (e.g., MDA and H2O2) and detoxification metabolites such as metallothionein (MTC), phytochelatins (PCs), and glutathione-S-transferase (GST). This elevation was associated with a remarkable reduction in both enzymatic and non-enzymatic antioxidants. On the other hand, the bioactive strain of ST-PGPB, Salinicoccus sp. JzA1 significantly alleviated the harmful effect of triclosan on both soybean and oat plants by enhancing their biomass, photosynthesis, as well as levels of minerals (K, Ca, P, Mn, and Zn). In parallel, a striking quenching in oxidative damage and an obvious improvement in non-enzymatic (polyphenols, tocopherols, flavonoids) and enzymatic antioxidants were observed. Furthermore, Salinicoccus sp. JzA1 augmented the detoxification metabolism by enhancing the levels of phytochelatins, metallothionein, and glutathione-S-transferase (GST) activity in a species-specific manner which is more apparent in soybean rather than in oat plants. To this end, stress mitigating impact of Salinicoccus sp. JzA1 provides a basis to improve the resilience of crop species under cosmetics and personal care products toxicity.

Role of methylglyoxal and redox homeostasis in microbe-mediated stress mitigation in plants

One of the general consequences of stress in plants is the accumulation of reactive oxygen (ROS) and carbonyl species (like methylglyoxal) to levels that are detrimental for plant growth. These reactive species are inherently produced in all organisms and serve different physiological functions but their excessive accumulation results in cellular toxicity. It is, therefore, essential to restore equilibrium between their synthesis and breakdown to ensure normal cellular functioning. Detoxification mechanisms that scavenge these reactive species are considered important for stress mitigation as they maintain redox balance by restricting the levels of ROS, methylglyoxal and other reactive species in the cellular milieu. Stress tolerance imparted to plants by root-associated microbes involves a multitude of mechanisms, including maintenance of redox homeostasis. By improving the overall antioxidant response in plants, microbes can strengthen defense pathways and hence, the adaptive abilities of plants to sustain growth under stress. Hence, through this review we wish to highlight the contribution of root microbiota in modulating the levels of reactive species and thereby, maintaining redox homeostasis in plants as one of the important mechanisms of stress alleviation. Further, we also examine the microbial mechanisms of resistance to oxidative stress and their role in combating plant stress.

The Biosynthesis and Functions of Polyamines in the Interaction of Plant Growth-Promoting Rhizobacteria with Plants

Plant growth-promoting rhizobacteria (PGPR) are members of the plant rhizomicrobiome that enhance plant growth and stress resistance by increasing nutrient availability to the plant, producing phytohormones or other secondary metabolites, stimulating plant defense responses against abiotic stresses and pathogens, or fixing nitrogen. The use of PGPR to increase crop yield with minimal environmental impact is a sustainable and readily applicable replacement for a portion of chemical fertilizer and pesticides required for the growth of high-yielding varieties. Increased plant health and productivity have long been gained by applying PGPR as commercial inoculants to crops, although with uneven results. The establishment of plant-PGPR relationships requires the exchange of chemical signals and nutrients between the partners, and polyamines (PAs) are an important class of compounds that act as physiological effectors and signal molecules in plant-microbe interactions. In this review, we focus on the role of PAs in interactions between PGPR and plants. We describe the basic ecology of PGPR and the production and function of PAs in them and the plants with which they interact. We examine the metabolism and the roles of PAs in PGPR and plants individually and during their interaction with one another. Lastly, we describe some directions for future research.

Comparison of the colonization ability of Burkholderia strain B23 in the citrus rhizoplane and rhizosphere and assessment of the underlying mechanisms using full-length 16S rDNA amplicon and metatranscriptomic analyses

The characterization of bacterial strains with efficient root colonization ability and the mechanisms responsible for their efficient colonization is critical for the identification and application of beneficial bacteria. In this study, we found that Burkholderia strain B23 exhibited a strong niche differentiation between the rhizosphere and rhizoplane (a niche with more abundant easy-to-use nutrients but stronger selective pressures compared with the tightly adjacent rhizosphere) when inoculated into the field-grown citrus trees. Full-length 16S rDNA amplicon analysis demonstrated that the relative abundance of B23 in the rhizoplane microbiome at 3, 5, and 9 days post-inoculation (dpi) was always higher than that at 1 dpi, whereas its relative abundance in the rhizosphere microbiome was decreased continuously, as demonstrated by a 3.18-fold decrease at 9 dpi compared to 1 dpi. Time-series comparative expression profiling of B23 between the rhizoplane and rhizosphere was performed at representative time points (1, 3, and 9 dpi) through metatranscriptomic analysis, and the results demonstrated that multiple genes involved in the uptake and utilization of easy-to-use carbohydrates and amino acids and those involved in metabolism, energy production, replication, and translation were upregulated in the rhizoplane compared with the rhizosphere at 1 dpi and 3 dpi. Several genes involved in resistance to plant- and microbial competitor-derived stresses exhibited higher expression activities in the rhizoplane compared with the rhizosphere. Furthermore, gene loci responsible for the biosynthesis of the key antifungal and antibacterial metabolites occidiofungin and ornibactin were induced, and their expression levels remained relatively stable from 3 dpi to 9 dpi in the rhizoplane but not in the rhizosphere. Collectively, our findings provide novel lights into the mechanisms underlying the root colonization of the inoculated bacterial strains and serve as a basis for the identification of strains with efficient colonization ability, thus contributing to the development of beneficial bacteria applications.

Correlation between Perturbation of Redox Homeostasis and Antibiofilm Capacity of Phytochemicals at Non-Lethal Concentrations

Biofilms are the multicellular lifestyle of microorganisms and are present on potentially every type of biotic or abiotic surface. Detrimental biofilms are generally targeted with antimicrobial compounds. Phytochemicals at sub-lethal concentrations seem to be an exciting alternative strategy to control biofilms, as they are less likely to impose selective pressure leading to resistance. This overview gathers the literature on individual phytocompounds rather than on extracts of which the use is difficult to reproduce. To the best of our knowledge, this is the first review to target only individual phytochemicals below inhibitory concentrations against biofilm formation. We explored whether there is an overall mechanism that can explain the effects of individual phytochemicals at sub-lethal concentrations. Interestingly, in all experiments reported here in which oxidative stress was investigated, a modest increase in intracellular reactive oxygen species was reported in treated cells compared to untreated specimens. At sub-lethal concentrations, polyphenolic substances likely act as pro-oxidants by disturbing the healthy redox cycle and causing an accumulation of reactive oxygen species.

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

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

Establishment and Validation of a New Analysis Strategy for the Study of Plant Endophytic Microorganisms

Amplicon sequencing of bacterial or fungal marker sequences is currently the main method for the study of endophytic microorganisms in plants. However, it cannot obtain all types of microorganisms, including bacteria, fungi, protozoa, etc., in samples, nor compare the relative content between endophytic microorganisms and plants and between different types of endophytes. Therefore, it is necessary to develop a better analysis strategy for endophytic microorganism investigation. In this study, a new analysis strategy was developed to obtain endophytic microbiome information from plant transcriptome data. Results showed that the new strategy can obtain the composition of microbial communities and the relative content between plants and endophytic microorganisms, and between different types of endophytic microorganisms from the plant transcriptome data. Compared with the amplicon sequencing method, more endophytic microorganisms and relative content information can be obtained with the new strategy, which can greatly broaden the research scope and save the experimental cost. Furthermore, the advantages and effectiveness of the new strategy were verified with different analysis of the microbial composition, correlation analysis, inoculant content test, and repeatability test.

Rhodospirillum sp. JY3: An innovative tool to mitigate the phytotoxic impact of galaxolide on wheat (Triticum aestivum) and faba bean (Vicia faba) plants

To date, several studies have considered the phytotoxic impact of cosmetics and personal care products on crop plants. Nonetheless, data are scarce about the toxic impact of galaxolide [hexahydro-hexamethyl cyclopentabenzopyran (HHCB)] on the growth, physiology, and biochemistry of plants from different functional groups. To this end, the impact of HHCB on biomass, photosynthetic efficiency, antioxidant production, and detoxification metabolism of grass (wheat) and legume (faba bean) plants has been investigated. On the other hand, plant growth-promoting bacteria (PGPB) can be effectively applied to reduce HHCB phytotoxicity. HHCB significantly reduced the biomass accumulation and the photosynthetic machinery of both crops, but to more extent for wheat. This growth reduction was concomitant with induced oxidative damage and decreased antioxidant defense system. To mitigate HHCB toxicity, a bioactive strain of diazotrophic plant growth-promoting Rhodospirillum sp. JY3 was isolated from heavy metal-contaminated soil in Jazan, Kingdom of Saudi Arabia, and applied to both crops. Overall, Rhodospirillum mitigated HHCB-induced stress by differently modulating the oxidative burst [malondialdehyde (MDA), hydrogen peroxide (H₂O₂), and protein oxidation] in both wheat and faba beans. This alleviation was coincident with improvement in plant biomass and photosynthetic efficiency, particularly in wheat crops. Considering the antioxidant defense system, JY3 augmented the antioxidants in both wheat and faba beans and the detoxification metabolism under HHCB stress conditions. More interestingly, inoculation with JY3 further enhanced the tolerance level of both wheat and faba beans against contamination with HHCB via quenching the lignin metabolism. Overall, this study advanced our understanding of the physiological and biochemical mechanisms underlying HHCB stress and mitigating its impact using Rhodospirillum sp. JY3, which may strikingly reduce the environmental risks on agriculture sustainability.

Signaling by reactive molecules and antioxidants in legume nodules

Legume nodules are symbiotic structures formed as a result of the interaction with rhizobia. Nodules fix atmospheric nitrogen into ammonia that is assimilated by the plant and this process requires strict metabolic regulation and signaling. Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are involved as signal molecules at all stages of symbiosis, from rhizobial infection to nodule senescence. Also, reactive sulfur species (RSS) are emerging as important signals for an efficient symbiosis. Homeostasis of reactive molecules is mainly accomplished by antioxidant enzymes and metabolites and is essential to allow redox signaling while preventing oxidative damage. Here, we examine the metabolic pathways of reactive molecules and antioxidants with an emphasis on their functions in signaling and protection of symbiosis. In addition to providing an update of recent findings while paying tribute to original studies, we identify several key questions. These include the need of new methodologies to detect and quantify ROS, RNS, and RSS, avoiding potential artifacts due to their short lifetimes and tissue manipulation; the regulation of redox-active proteins by post-translational modification; the production and exchange of reactive molecules in plastids, peroxisomes, nuclei, and bacteroids; and the unknown but expected crosstalk between ROS, RNS, and RSS in nodules.

The Arabidopsis thaliana–Streptomyces Interaction Is Controlled by the Metabolic Status of the Holobiont

How specific interactions between plant and pathogenic, commensal, or mutualistic microorganisms are mediated and how bacteria are selected by a plant are important questions to address. Here, an Arabidopsis thaliana mutant called chs5 partially deficient in the biogenesis of isoprenoid precursors was shown to extend its metabolic remodeling to phenylpropanoids and lipids in addition to carotenoids, chlorophylls, and terpenoids. Such a metabolic profile was concomitant to increased colonization of the phyllosphere by the pathogenic strain Pseudomonas syringae pv. tomato DC3000. A thorough microbiome analysis by 16S sequencing revealed that Streptomyces had a reduced colonization potential in chs5. This study revealed that the bacteria–Arabidopsis interaction implies molecular processes impaired in the chs5 mutant. Interestingly, our results revealed that the metabolic status of A. thaliana was crucial for the specific recruitment of Streptomyces into the microbiota. More generally, this study highlights specific as well as complex molecular interactions that shape the plant microbiota.

The Impact of Non-Nodulating Diazotrophic Bacteria in Agriculture: Understanding the Molecular Mechanisms That Benefit Crops

Agriculture is facing increasing challenges with regard to achieving sustainable growth in productivity without negatively impacting the environment. The use of bioinoculants is emerging as a sustainable solution for agriculture, especially bioinoculants based on diazotrophic bacteria. Brazil is at the forefront of studies intended to identify beneficial diazotrophic bacteria, as well as in the molecular characterization of this association on both the bacterial and plant sides. Here we highlight the main advances in molecular studies to understand the benefits brought to plants by diazotrophic bacteria. Different molecular pathways in plants are regulated both genetically and epigenetically, providing better plant performance. Among them, we discuss the involvement of genes related to nitrogen metabolism, cell wall formation, antioxidant metabolism, and regulation of phytohormones that can coordinate plant responses to environmental factors. Another important aspect in this regard is how the plant recognizes the microorganism as beneficial. A better understanding of plant–bacteria–environment interactions can assist in the future formulation of more efficient bioinoculants, which could in turn contribute to more sustainable agriculture practices.

Redox-sensitive fluorescent biosensors detect Sinorhizobium meliloti intracellular redox changes under free-living and symbiotic lifestyles

Reactive oxygen species such as hydrogen peroxide (H₂O₂) are key signaling molecules that control the setup and functioning of Rhizobium-legume symbiosis. This interaction results in the formation of a new organ, the root nodule, in which bacteria enter the host cells and differentiate into nitrogen (N₂)-fixing bacteroids. The interaction between Sinorhizobium meliloti and Medicago truncatula is a genetic model to study N₂-fixing symbiosis. In previous work, S. meliloti mutants impaired in the antioxidant defense, showed altered symbiotic properties, emphasizing the importance of redox-based regulation in the bacterial partner. However, direct measurements of S. meliloti intracellular redox state have never been performed. Here, we measured dynamic changes of intracellular H₂O₂ and glutathione redox potential by expressing roGFP2-Orp1 and Grx1-roGFP2 biosensors in S. meliloti. Kinetic analyses of redox changes under free-living conditions showed that these biosensors are suitable to monitor the bacterial redox state in real-time, after H₂O₂ challenge and in different genetic backgrounds. In planta, flow cytometry and confocal imaging experiments allowed the determination of sensor oxidation state in nodule bacteria. These cellular studies establish the existence of an oxidative shift in the redox status of S. meliloti during bacteroid differentiation. Our findings open up new possibilities for in vivo studies of redox dynamics during N₂-fixing symbiosis.