Rhizosphere Microbiome of Arid Land Medicinal Plants and Extra Cellular Enzymes Contribute to Their Abundance

Characteristics and functions of volatile organic compounds in the tripartite symbiotic system of Gastrodia elata-Armillaria gallica-Rahnella aceris HPDA25

Tripartite interactions among plants, fungi, and bacteria are critical for maintaining plant growth and fitness, and volatile organic compounds (VOCs) play a significant role in these interactions. However, the functions of VOCs within the niche of mycoheterotrophic plants, which represent unique types of interactions, remain poorly understood. Gastrodia elata, a mycoheterotrophic orchid species, forms a symbiotic relationship with specific Armillaria species, serving as a model system to investigate this intriguing issue. Rahnella aceris HPDA25 is a plant growth-promoting bacteria isolated from G. elata, which has been found to facilitate the establishment of G. elata-Armillaria symbiosis. In this study, using the tripartite symbiotic system of G. elata-Armillaria gallica-R. aceris HPDA25, we investigate the role of VOCs in the interaction among mycoheterotrophic plants, fungi, and bacteria. Our results showed that 33 VOCs of HPDA25-inducible symbiotic G. elata elevated compared to non-symbiotic G. elata, indicating that VOCs indeed play a role in the symbiotic process. Among these, 21 VOCs were accessible, and six active VOCs showed complete growth inhibition activities against A. gallica, while R. aceris HPDA25 had no significant effect. In addition, three key genes of G. elata have been identified that may contribute to the increased concentration of six active VOCs. These results revealed for the first time the VOCs profile of G. elata and demonstrated its regulatory role in the tripartite symbiotic system involving G. elata, Armillaria, and bacteria.

Beyond correlation: Understanding the causal link between microbiome and plant health

Understanding the causal link between the microbiome and plant health is crucial for the future of crop production. Established studies have shown a symbiotic relationship between microbes and plants, reshaping our knowledge of plant microbiomes' role in health and disease. Addressing confounding factors in microbiome study is essential, as standardization enables precise identification of microbiome features that influence outcomes. The microbiome significantly impacts plant development, necessitating holistic investigation for maintaining plant health. Mechanistic studies have deepened our understanding of microbiome structure and function related to plant health, though much research still needs to be carried out. This review, therefore, discusses current challenges and proposes advancing studies from correlation to causation and translation. We explore current knowledge on the microbiome and plant health, emphasizing multi-omics approaches and hypothesis-driven research. Future studies should focus on developing translational research for producing probiotics and prebiotics from biomarkers that regulate the microbiome-plant health connection, promoting sustainable crop production through microbiome applications.

The rhizosphere of a drought-tolerant plant species in Morocco: A refuge of high microbial diversity with no taxon preference

Arid and semi-arid areas are facing increasingly severe water deficits that are being intensified by global climate changes. Microbes associated with plants native to arid regions provide valuable benefits to plants, especially in water-stressed environments. In this study, we used 16S rDNA metabarcoding analysis to examine the bacterial communities in the bulk soil, rhizosphere and root endosphere of the plant Malva sylvestris L. in Morocco, along a gradient of precipitation. We found that the rhizosphere of M. sylvestris did not show significant differences in beta-diversity compared to bulk soil, although, it did display an increased degree of alpha-diversity. The endosphere was largely dominated by the genus Rhizobium and displayed remarkable variation between plants, which could not be attributed to any of the variables observed in this study. Overall, the effects of precipitation level were relatively weak, which may be related to the intense drought in Morocco at the time of sampling. The dominance of Rhizobium in a non-leguminous plant is particularly noteworthy and may permit the utilization of this bacterial taxon to augment drought tolerance; additionally, the absence of any notable selection of the rhizosphere of M. sylvestris suggests that it is not significatively affecting its soil environment.

Silicon: A valuable soil element for improving plant growth and CO2 sequestration

BACKGROUND

Silicon (Si), the second most abundant and quasi-essential soil element, is locked as a recalcitrant silicate mineral in the Earth's crust. The physical abundance of silicates can play an essential role in increasing plant productivity. Plants store Si as biogenic silica (phytoliths), which is mobilized through a chemical weathering process in the soil.

AIM OF REVIEW

Although Si is a critical element for plant growth, there is still a considerable need to understand its dissolution, uptake, and translocation in agroecosystems. Here, we show recent progress in understanding the interactome of Si, CO2, the microbiome, and soil chemistry, which can sustainably govern silicate dissolution and cycling in agriculture.

KEY SCIENTIFIC CONCEPTS OF THIS REVIEW

Si cycling is directly related to carbon cycling, and the resulting climate stability can be enhanced by negative feedback between atmospheric CO2 and the silicate uptake process. Improved Si mobilization in the rhizosphere by the presence of reactive elements (for example, Ca, Na, Al, Zn, and Fe) and Si uptake through genetic transporters in plants are crucial to achieving the dual objectives of (i) enhancing crop productivity and (ii) abiotic stress tolerance. Furthermore, the microbiome is a symbiotic partner of plants. Bacterial and fungal microbiomes can solubilize silicate minerals through intriguingly complex bioweathering mechanisms by producing beneficial metabolites and enzymes. However, the interaction of Si with CO2 and the microbiome's function in mobilization have been understudied. This review shows that enhancing our understanding of Si, CO2, the microbiome, and soil chemistry can help in sustainable crop production during climatic stress events.

Microbiome structure variation and soybean's defense responses during flooding stress and elevated CO2

Introduction

With current trends in global climate change, both flooding episodes and higher levels of CO2 have been key factors to impact plant growth and stress tolerance. Very little is known about how both factors can influence the microbiome diversity and function, especially in tolerant soybean cultivars. This work aims to (i) elucidate the impact of flooding stress and increased levels of CO2 on the plant defenses and (ii) understand the microbiome diversity during flooding stress and elevated CO2 (eCO2).

Methods

We used next-generation sequencing and bioinformatic methods to show the impact of natural flooding and eCO2 on the microbiome architecture of soybean plants' below- (soil) and above-ground organs (root and shoot). We used high throughput rhizospheric extra-cellular enzymes and molecular analysis of plant defense-related genes to understand microbial diversity in plant responses during eCO2 and flooding.

Results

Results revealed that bacterial and fungal diversity was substantially higher in combined flooding and eCO2 treatments than in non-flooding control. Microbial diversity was soil>root>shoot in response to flooding and eCO2. We found that sole treatment of eCO2 and flooding had significant abundances of Chitinophaga, Clostridium, and Bacillus. Whereas the combination of flooding and eCO2 conditions showed a significant abundance of Trichoderma and Gibberella. Rhizospheric extra-cellular enzyme activities were significantly higher in eCO2 than flooding or its combination with eCO2. Plant defense responses were significantly regulated by the oxidative stress enzyme activities and gene expression of Elongation factor 1 and Alcohol dehydrogenase 2 in floodings and eCO2 treatments in soybean plant root or shoot parts.

Conclusion

This work suggests that climatic-induced changes in eCO2 and submergence can reshape microbiome structure and host defenses, essential in plant breeding and developing stress-tolerant crops. This work can help in identifying core-microbiome species that are unique to flooding stress environments and increasing eCO2.

Molecular insights and omics-based understanding of plant-microbe interactions under drought stress

The detrimental effects of adverse environmental conditions are always challenging and remain a major concern for plant development and production worldwide. Plants deal with such constraints by physiological, biochemical, and morphological adaptations as well as acquiring mutual support of beneficial microorganisms. As many stress-responsive traits of plants are influenced by microbial activities, plants have developed a sophisticated interaction with microbes to cope with adverse environmental conditions. The production of numerous bioactive metabolites by rhizospheric, endo-, or epiphytic microorganisms can directly or indirectly alter the root system architecture, foliage production, and defense responses. Although plant-microbe interactions have been shown to improve nutrient uptake and stress resilience in plants, the underlying mechanisms are not fully understood. "Multi-omics" application supported by genomics, transcriptomics, and metabolomics has been quite useful to investigate and understand the biochemical, physiological, and molecular aspects of plant-microbe interactions under drought stress conditions. The present review explores various microbe-mediated mechanisms for drought stress resilience in plants. In addition, plant adaptation to drought stress is discussed, and insights into the latest molecular techniques and approaches available to improve drought-stress resilience are provided.

Drought Sensitivity of Spring Wheat Cultivars Shapes Rhizosphere Microbial Community Patterns in Response to Drought

Drought is the most important natural disaster affecting crop growth and development. Crop rhizosphere microorganisms can affect crop growth and development, enhance the effective utilization of nutrients, and resist adversity and hazards. In this paper, six spring wheat varieties were used as research material in the dry farming area of the western foot of the Greater Khingan Mountains, and two kinds of water control treatments were carried out: dry shed rain prevention (DT) and regulated water replenishment (CK). Phenotypic traits, including physiological and biochemical indices, drought resistance gene expression, soil enzyme activity, soil nutrient content, and the responses of potential functional bacteria and fungi under drought stress, were systematically analyzed. The results showed that compared with the control (CK), the leaf wilting, drooping, and yellowing of six spring wheat varieties were enhanced under drought (DT) treatment. The plant height, fresh weight (FW), dry weight (DW), net photosynthetic rate (Pn) and stomatal conductance (Gs), soil total nitrogen (TN), microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), microbial biomass phosphorus (MBP), organic carbon (SOC), and soil alkaline phosphatase (S-ALP) contents were significantly decreased, among which, FW, Gs and MBC decreased by more than 7.84%, 17.43% and 11.31%, respectively. By contrast, the soil total phosphorus (TP), total potassium (TK), and soil catalase (S-CAT) contents were significantly increased (p < 0.05). TaWdreb2 and TaBADHb genes were highly expressed in T.D40, T.L36, and T.L33 and were expressed at low levels in T.N2, T.B12, and T.F5. Among them, the relative expression of the TaWdreb2 gene in T.L36 was significantly increased by 2.683 times compared with CK. Soil TN and TP are the most sensitive to drought stress and can be used as the characteristic values of drought stress. Based on this, a drought-tolerant variety (T.L36) and a drought-sensitive variety (T.B12) were selected to further analyze the changes in rhizosphere microorganisms. Drought treatment and cultivar differences significantly affected the composition of the rhizosphere microbial community. Drought caused a decrease in the complexity of the rhizosphere microbial network, and the structure of bacteria was more complex than that of fungi. The Shannon index and network modular number of bacteria in these varieties (T.L36) increased, with rich small-world network properties. Actinobacteria, Chloroflexi, Firmicutes, Basidiomycota, and Ascomycota were the dominant bacteria under drought treatment. The beneficial bacteria Bacillus, Penicillium, and Blastococcus were enriched in the rhizosphere of T.L36. Brevibacillus and Glycomyce were enriched in the rhizosphere of T.B12. In general, drought can inhibit the growth and development of spring wheat, and spring wheat can resist drought hazards by regulating the expression of drought-related genes, regulating physiological metabolites, and enriching beneficial microorganisms.

The phytomicrobiome: solving plant stress tolerance under climate change

With extraordinary global climate changes, increased episodes of extreme conditions result in continuous but complex interaction of environmental variables with plant life. Exploring natural phytomicrobiome species can provide a crucial resource of beneficial microbes that can improve plant growth and productivity through nutrient uptake, secondary metabolite production, and resistance against pathogenicity and abiotic stresses. The phytomicrobiome composition, diversity, and function strongly depend on the plant's genotype and climatic conditions. Currently, most studies have focused on elucidating microbial community abundance and diversity in the phytomicrobiome, covering bacterial communities. However, least is known about understanding the holistic phytomicrobiome composition and how they interact and function in stress conditions. This review identifies several gaps and essential questions that could enhance understanding of the complex interaction of microbiome, plant, and climate change. Utilizing eco-friendly approaches of naturally occurring synthetic microbial communities that enhance plant stress tolerance and leave fewer carbon-foot prints has been emphasized. However, understanding the mechanisms involved in stress signaling and responses by phytomicrobiome species under spatial and temporal climate changes is extremely important. Furthermore, the bacterial and fungal biome have been studied extensively, but the holistic interactome with archaea, viruses, oomycetes, protozoa, algae, and nematodes has seldom been studied. The inter-kingdom diversity, function, and potential role in improving environmental stress responses of plants are considerably important. In addition, much remains to be understood across organismal and ecosystem-level responses under dynamic and complex climate change conditions.

First insights into diversity and potential metabolic pathways of bacterial and fungal communities in the rhizosphere of Argemonemexicana L. (Papaveraceae) from the water-level-fluctuation zone of Wudongde Reservoir of the upper Yangtze river, China

The water-level fluctuation zone (WLFZ) of Wudongde reservoir of the upper Yangtze river is a completely new aquatic-terrestrial transitional zone, and its plant degenerate issue is attracting global concerns. Uncovering the unknown rhizosphere microbiome of dominant plants of this zone is helpful in understanding the plant-microbe interactions and their growth under the largely varying environment. Here, a first exploration of the rhizosphere bacterial and fungal communities of wilted (JB) and unwilted (JA) Argemonemexicana L. individuals from the WLFZ of Wudongde reservoir was carried out using high-throughput sequencing and MetaCyc metabolic pathway analyses. The results showed that rhizosphere of wilted A.mexicana L individuals exhibited a higher microbial richness and diversity than the unwilted ones, irrespective of the bacterial and fungal communities. It was noted that 837 common bacterial amplicon sequence variants (ASV) and 92 common fungal ASV were presented in both JA and JB with 3108 bacteria and 212 fungi unique to JA, and 3569 bacteria and 693 fungi unique to JB. Linear discriminant analysis effect Size (LEfSe) analyses indicated that the taxa that had the most contribution to observed differences between both JA and JB was Proteobacteria, Actinobacteria and Ascomycota for JA, and Bacteroidetes, Firmicutes, Verrucomicrobia, Basidiomycota and Ascomycota for JB. Organic compound conversion pathway (degradation/reduction/oxidation) was consistently highly represented in the rhizosphere microbiomes of both JA and JB. Overall, this study provides insights into the rhizosphere microbiome composition, diversity and metabolic pathways of both wilted and unwilted A.mexicana L. individuals in the WLFZ of Wudongde reservoir, and the results give valuable clues for manipulating microbes to support plant growth in such a recently-formed WLFZ under a dry-hot valley environment.

Bacterial Communities of Lamiacea L. Medicinal Plants: Structural Features and Rhizosphere Effect

Bacterial communities associated with medicinal plants are an essential part of ecosystems. The rhizosphere effect is rather important in the cultivation process. The purpose of the study was to analyze the rhizosphere effect of oregano (Origanum vulgare L.), peppermint (Mentha piperita L.), thyme (Thymus vulgaris L.), creeping thyme (Thymus serpillum L.) and sage (Salvia officinalis L.). To estimate the quantity of 16S bacteria ribosomal genes, qPCR assays were used. To compare bacterial communities' structure of medicinal plants rhizosphere with bulk soil high-throughput sequencing of the 16S rRNA targeting variable regions V3-V4 of bacteria was carried out. The highest bacterial abundance was associated with T. vulgaris L., M. piperita L. and S. officinalis L., and the lowest was associated with the O. vulgare L. rhizosphere. Phylum Actinobacteriota was predominant in all rhizosphere samples. The maximum bacterial α-diversity was found in S. officinalis L. rhizosphere. According to bacterial β-diversity calculated by the Bray-Curtis metric, T. vulgaris L. root zone significantly differed from bulk soil. The rhizosphere effect was positive to the Myxococcota, Bacteroidota, Verrucomicrobiota, Proteobacteria and Gemmatimonadota.

Microbiome Variation Across Populations of Desert Halophyte Zygophyllum qatarensis

Microbial symbionts play a significant role in plant health and stress tolerance. However, few studies exist that address rare species of core-microbiome function during abiotic stress. In the current study, we compared the microbiome composition of succulent dwarf shrub halophyte Zygophyllum qatarensis Hadidi across desert populations. The results showed that rhizospheric and endosphere microbiome greatly varied due to soil texture (sandy and gravel). No specific bacterial amplicon sequence variants were observed in the core-microbiome of bulk soil and rhizosphere, however, bacterial genus Alcaligenes and fungal genus Acidea were abundantly distributed across root and shoot endospheres. We also analyzed major nutrients such as silicon (Si), magnesium, and calcium across different soil textures and Z. qatarensis populations. The results showed that the rhizosphere and root parts had significantly higher Si content than the bulk soil and shoot parts. The microbiome variation can be attributed to markedly higher Si - suggesting that selective microbes are contributing to the translocation of soluble Si to root. In conclusion, low core-microbiome species abundance might be due to the harsh growing conditions in the desert - making Z. qatarensis highly selective to associate with microbial communities. Utilizing rare microbial players from plant microbiomes may be vital for increasing crop stress tolerance and productivity during stresses.

Mycorrhizosphere Bacteria, Rahnella sp. HPDA25, Promotes the Growth of Armillaria gallica and Its Parasitic Host Gastrodia elata

Gastrodia elata is an entirely heterotrophic plant, the growth of which is completely reliant on Armillaria gallica, an orchid mycorrhizal fungus. To avoid damaging ecosystems, G. elata cultivation is shifting from woodland to farmland. However, whether the microbial community structure remains stable during this conversation is unknown. Here, we cultivated G. elata in woodland or farmland and found that woodland-cultivated G. elata produced a greater yield and larger tuber size. The relative abundance of Rahnella was 22.84- and 122.25-fold higher in woodland- and farmland-cultivated soil samples, respectively, than that in uncultivated soil samples. To investigate how Rahnella impacts the growth of G. elata and establishes symbiosis with Armillaria gallica, three Rahnella spp. strains (HPDA25, SBD3, and SBD11) were isolated from mycorrhizosphere soil samples. It was found that these strains, especially HPDA25, promoted the growth of A. gallica. Ultra-performance liquid chromatography coupled to a triple quadrupole mass spectrometry analysis detected the indole-3-acetic acid with 16.24 ng/ml in HPDA25 fermentation solution. Co-culturing with the strain HPDA25 or exogenous indole-3-acetic acid increased the branching and fresh weight of rhizomorphs and the growth rate and extracellular laccase activity of A. gallica, compared with A. gallica cultured alone. The results of RNA-seq and quantitative real-time polymerase chain reaction analysis showed that co-culturing A. gallica with HPDA25 increased the expression level of the genes including hydrophobin, SUR7/PalI family, and pectin methylesterase, whereas decreased the expression levels of glycolysis-related genes. Furthermore, co-culturing with the strain HPDA25, A. gallica promotes the growth of G. elata and enhances the tuber size of G. elata. These results provide new insights into an orchid mycorrhizal symbiosis and the cultivation of G. elata.

Nitrogen use efficiency, rhizosphere bacterial community, and root metabolome reprogramming due to maize seed treatment with microbial biostimulants

Seed inoculation with beneficial microorganisms has gained importance as it has been proven to show biostimulant activity in plants, especially in terms of abiotic/biotic stress tolerance and plant growth promotion, representing a sustainable way to ensure yield stability under low input sustainable agriculture. Nevertheless, limited knowledge is available concerning the molecular and physiological processes underlying the root-inoculant symbiosis or plant response at the root system level. Our work aimed to integrate the interrelationship between agronomic traits, rhizosphere microbial population and metabolic processes in roots, following seed treatment with either arbuscular mycorrhizal fungi (AMF) or Plant Growth-Promoting Rhizobacteria (PGPR). To this aim, maize was grown under open field conditions with either optimal or reduced nitrogen availability. Both seed treatments increased nitrogen uptake efficiency under reduced nitrogen supply revealed some microbial community changes among treatments at root microbiome level and limited yield increases, while significant changes could be observed at metabolome level. Amino acid, lipid, flavone, lignan, and phenylpropanoid concentrations were mostly modulated. Integrative analysis of multi-omics datasets (Multiple Co-Inertia Analysis) highlighted a strong correlation between the metagenomics and the untargeted metabolomics datasets, suggesting a coordinate modulation of root physiological traits.

Induced systemic tolerance mediated by plant-microbe interaction in maize (Zea mays L.) plants under hydrocarbon contamination

The present investigation was committed to examining the effect of soil spiked with diesel contamination (0, 1.5, 2.5, 3.5 g diesel kg^-1 soil) on maize (Zea mays L) varieties (MMRI yellow and Pearl white) with or without bacterial consortium (Pseudomonas aeruginosa BRRI54, Acinetobacter sp. strain BRSI56, Acinetobacter sp. strain ACRH80). Seed and soil bacterial inoculation were done. The studied morphological attributes were fresh and dry weight of shoot and root of both maize varieties. The results documented that bacterial consortium caused 21%, 0.06% and 29%, 34% higher shoot and root fresh/dry weights in "Pearl white" and 14%, 15% and 32%, 22% shoot and root fresh/dry weights respectively in MMRI yellow under control conditions. The biochemical attributes of shoot and root were affected negatively by the 3.5 g diesel kg^-1 soil contamination. Bacterial consortium enhanced enzymatic activity (APX, CAT, POD, SOD, GR) and non-enzymatic (AsA, GSH, Pro, α-Toco) antioxidant and reduction in oxidative stress (H₂O₂, MDA) under hydrocarbon stress as compared to non-inoculated ones in both root and shoot organs. Among both varieties, the highest hydrocarbon removal (75, 64, and 69%) was demonstrated by MMRI yellow with bacterial consortium as compare to Pearl white showed 73, 57, 65% hydrocarbon degradation at 1.5 2.5, 3.5 g diesel kg^-1 soil contamination. Consequently, the microbe mediated biotransformation of hydrocarbons suggested that the use of PGPB would be the most beneficial selection in diesel fuel contaminated soil to overcome the abiotic stress in plants and successfully remediation of hydrocarbon in contaminated soil.

The physicochemical approaches of altering growth and biochemical properties of medicinal plants in saline soils

Medicinal plants are important sources of biochemical compounds affecting human health. However, because large areas of the world are subjected to different stresses including salinity, it is important to find methods, which may control the growth and biochemical properties of medicinal plants in such conditions. Another aspect of cropping medicinal plants in saline soils is the alteration of their biochemical properties by stress. Due to the significance of planting medicinal plants in saline soils, the objective of the present review article is to investigate and analyze the physicochemical approaches including soil leaching, organic fertilization, mineral nutrition, ozonated water, magnetism, superabsorbent polymers, and zeolite, which may control the effects of salinity stress on the growth and biochemical properties (production of secondary metabolites) of medicinal plants. In our just-published review article, we investigated the biological approaches, which may affect the growth and biochemical properties of medicinal properties in saline soils. Although salinity stress may induce the production of biochemical products in medicinal plants, the use of physicochemical approaches is also recommendable for the improved growth and biochemical properties of medicinal plants in saline soils. More has yet to be indicated on the use of the physicochemical approaches, which may affect the growth and biochemical properties of medicinal plants in salt stress conditions. KEY POINTS: • Growth and physiological alteration of medicinal plants in salt stress conditions. • The physicochemical approaches of such alteration have been reviewed. • More has yet to be indicated on the approaches, which may affect such properties.

Mangrove's rhizospheric engineering with bacterial inoculation improve degradation of diesel contamination

Mangroves (Avicennia marina) growing in intertidal areas are often exposed to diesel spills, adversely damaging the ecosystem. Herein, we showed for the first time that mangrove seedlings' associations with bacteria could reprogram host-growth, physiology, and ability to degrade diesel. We found four bacterial strains [Sphingomonas sp.-LK11, Rhodococcus corynebacterioides-NZ1, Bacillus subtilis-EP1 Bacillus safensis-SH10] exhibiting significant growth during diesel degradation (2% and 5%, v/v) and higher expression of alkane monooxygenase compared to control. This is in synergy with reduced long-chain n-alkanes (C24-C30) during microbe-diesel interactions in the bioreactor. Among individual strains, SH10 exhibited significantly higher potential to improve mangrove seedling's morphology, anatomy and growth during diesel treatment in rhizosphere compared to control. This was also evidenced by reduced activities and gene expression of antioxidant enzymes (catalases, peroxidases, ascorbic peroxidases, superoxide dismutases and polyphenol peroxidases) and lipid peroxidation during microbe-diesel interactions. Interestingly, we noticed significantly higher soil-enzyme activities (phosphatases and glucosidases) and essential metabolites in seedling's rhizosphere after bacteria and diesel treatments. Degradation of longer n-alkane chains in the rhizosphere also revealed a potential pathway that benefits mangroves by bacterial strains during diesel contaminations. Current results support microbes' application to rhizoengineer plant growth, responses, and phytoextraction abilities in environments contaminated with diesel spills. AVAILABILITY OF DATA AND MATERIALS: The datasets generated during the current study are available in the NCBI GenBank ((https://www.ncbi.nlm.nih.gov).

Selection of ACC deaminase positive, thermohalotolerant and drought tolerance enhancing plant growth-promoting bacteria from rhizospheres of Cyamopsis tetragonoloba grown in arid regions

Plant growth-promoting bacteria (PGPB) expressing 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity are widely acknowledged to have a role in mitigation of abiotic stress caused by extreme environmental conditions. Consequently, several studies have focused on the isolation of ACC deaminase positive PGPBs. However, the application of such strains in drought-prone arid regions has remained grossly under-exploited. In order to be used in arid agroecosystems, PGPBs need to have the dual capability: to express ACC deaminase and to have the ability to tolerate increased temperature and salt concentration. Conspicuously, to date, very few studies have reported about isolation and characterization of PGPBs with this kind of dual capability. Here we report the isolation of bacterial strains from rhizosphere(s) of Cyamopsis tetragonoloba, a commercial crop from arid regions of Rajasthan, India, and their characterization for ACC deaminase activity and thermohalotolerance. Isolates found positive for desired traits were subsequently assessed for plant growth promotion under simulated drought conditions. Our finding showed that although the bacterial diversity within the rhizosphere of C. tetragonoloba grown in the arid region is quite poor, multiple isolates are ACC deaminase positive. Four isolates were found to be ACC deaminase positive, thermohalotolerant, and successfully enhanced drought tolerance. These isolates were identified as strains belonging to genera Pseudomonas, Enterobacter, and Stenotrophomonas based on 16S rRNA sequence homology.

The biological approaches of altering the growth and biochemical properties of medicinal plants under salinity stress

Due to their interesting properties for human health, medicinal plants are of worldwide interest, including Iran. More has yet to be investigated and analyzed on the use of methods affecting medicinal plant growth and biochemical properties under stress. The important question about medicinal plants is the purpose of their plantation, determining their growth conditions. The present review article is about the effects of salinity stress on the growth and production of secondary metabolites (SM) in medicinal plants. In stressful conditions including salinity, while the growth of medicinal plants decreases, the production of secondary metabolites (SM) may increase significantly affecting plant medicinal properties. SMs are self-protective substances that medicinal plants quickly accumulate to resist changes in the external environment. Although previous research has indicated the effects of salt stress on the growth and yield of medicinal plants, more has yet to be indicated on how the use of biological methods including plant growth regulators (PGR) and soil microbes (mycorrhizal fungi and plant growth-promoting rhizobacteria, PGPR) may affect the physiology of medicinal plants and the subsequent production of SM in salt stress conditions. The use of modern omics has become significantly important for the identification and characterization of new SM, transcriptomics, genomics, and proteomics of medicinal plants, as well as for the high production of plant-derived medicines. Accordingly, the possible biological mechanisms, which may affect such properties, have been presented. Future research perspectives for the production of medicinal plants in saline fields, using biological methods, have been suggested. KEY POINTS: • The important question about medicinal plants is the purpose of their plantation. • Secondary metabolites (SM) may significantly increase under salinity stress. • Biological methods, affecting the production of SM by stressed medicinal plants.

Climatic Zone and Soil Properties Determine the Biodiversity of the Soil Bacterial Communities Associated to Native Plants from Desert Areas of North-Central Algeria

Algeria is the largest country in Africa characterized by semi-arid and arid sites, located in the North, and hypersaline zones in the center and South of the country. Several autochthonous plants are well known as medicinal plants, having in common tolerance to aridity, drought and salinity. In their natural environment, they live with a great amount of microbial species that altogether are indicated as plant microbiota, while the plants are now viewed as a “holobiont”. In this work, the microbiota of the soil associated to the roots of fourteen economically relevant autochthonous plants from Algeria have been characterized by an innovative metagenomic approach with a dual purpose: (i) to deepen the knowledge of the arid and semi-arid environment and (ii) to characterize the composition of bacterial communities associated with indigenous plants with a strong economic/commercial interest, in order to make possible the improvement of their cultivation. The results presented in this work highlighted specific signatures which are mainly determined by climatic zone and soil properties more than by the plant species.

Rhizomicrobiomics of Caesalpinia bonducella, a wonder plant for PCOS treatment

Plant and rhizobacterial interactions contribute partly to a plant's medicinal properties and are well studied through metagenomics. In this study, 16S rDNA, 18S rDNA, and ITS meta-sequencing were performed using the genomic DNA obtained from the rhizosphere of Caesalpinia bonducella-a medicinal shrub widely used to treat polycystic ovary syndrome (PCOS). Of the 665 Operational Taxonomic Units (OTUs) obtained from 16S rDNA sequencing, 23.9% comprised of microbes that increase the therapeutic value of plants (Bacillus, Paenibacillus), 6.4% belonged to stress and drought tolerant microbes (Pseudomonas, Rhizobium, Serratia), 8% belonged to plant-growth promoting rhizobacteria-predominantly Proteobacteria, and Firmicutes and the remaining were the microbes performing various other functions. Alpha diversity indexing by GAIA-metagenomics tool revealed the presence of a highly diverse group of microbes in the rhizosphere of C. bonducella; Chao.1 index (665), Shannon Weiner index (3.53), Simpson index (0.83) and Fisher index (106.13). The highly diverse microbes lingering around the roots of C. bonducella could possibly be due to a strong symbiotic association with the plant; root exudates nourish the microbes and the microbes in turn enrich the medicinal value of the plant.

Understanding Phytomicrobiome: A Potential Reservoir for Better Crop Management

Recent crop production studies have aimed at an increase in the biotic and abiotic tolerance of plant communities, along with increased nutrient availability and crop yields. This can be achieved in various ways, but one of the emerging approaches is to understand the phytomicrobiome structure and associated chemical communications. The phytomicrobiome was characterized with the advent of high-throughput techniques. Its composition and chemical signaling phenomena have been revealed, leading the way for “rhizosphere engineering”. In addition to the above, phytomicrobiome studies have paved the way to best tackling soil contamination with various anthropogenic activities. Agricultural lands have been found to be unbalanced for crop production. Due to the intense application of agricultural chemicals such as herbicides, fungicides, insecticides, fertilizers, etc., which can only be rejuvenated efficiently through detailed studies on the phytomicrobiome component, the phytomicrobiome has recently emerged as a primary plant trait that affects crop production. The phytomicrobiome also acts as an essential modifying factor in plant root exudation and vice versa, resulting in better plant health and crop yield both in terms of quantity and quality. Not only supporting better plant growth, phytomicrobiome members are involved in the degradation of toxic materials, alleviating the stress conditions that adversely affect plant development. Thus, the present review compiles the progress in understanding phytomicrobiome relationships and their application in achieving the goal of sustainable agriculture.