Assessing the role of endophytic bacteria in the halophyte Arthrocnemum macrostachyum salt tolerance

Co-existence of halo-tolerant Pseudomonas fluorescens and Enterococcus hirae with multifunctional growth promoting traits to ameliorate salinity stress in Vigna radiata

Soil salinization has become a prominent obstacle in diverse arid and semi-arid region damaging agricultural productivity globally. From this perspective, present investigation was aimed to compare the potential compatible consortium of bio-inoculants for improving Plant Growth Promoting (PGP) attributes, anti-oxidative enzymes, grain yield and profitability of Vigna radiata in saline soil conditions. A total of 101 rhizobacterium isolated from salt affected regions of Punjab, India were screened for their ability to induce salt tolerance, multifunctional PGP traits and antagonistic activities. The 16S rRNA sequencing identified the strains LSMR-29 and LSMRS-7 as Pseudomonas flourescens and Enterococcus hirae, respectively. In-vitro compatible halo-tolerant dual inoculant (LSMR-29 + LSMRS-7) as bio-inoculants mitigated salt stress in Vigna radiata (spring mungbean) seedling with improved seed germination, biomass and salt tolerance index together with the presence of nifH, acds, pqq and ipdc gene under salinity stress as compared to single inoculants. Further, the potential of single and dual bio-inoculants were also exploited for PGP attributes in pot and field experiments. Results indicated that a significant improvement in chlorophyll content (2.03 fold), nodulation (1.24 fold), nodule biomass (1.23 fold) and leghemoglobin content (1.13 fold) with dual inoculant of LSMR-29 + LSMRS-7 over the LSMR-29 alone. The concentrations of macro & micronutrients, proline, soil enzyme activities i.e. soil dehydrogenase, acid & alkaline phosphatases and antioxidant enzymes such as superoxide dismutase, catalase and peroxidase also found to be high for LSMR-29 + LSMRS-7 as compared to un-inoculated control. The high grain yield thereby leading to Benefit: Cost (B: C) ratio at field scale was indicative of the commercial use bio-inoculants under salt affected Vigna radiata (spring mungbean) to improvement of productivity and soil health. The current finding reveals a co-inoculation of halo-tolerating Pseudomonas fluorescens and Enterococcus hirae containing ACC deaminase could prove to be novel approach for inducing salt tolerance and improving productivity of Vigna radiata (spring mungbean).

Halophilic Plant-Associated Bacteria with Plant-Growth-Promoting Potential

The salinization of soils is a growing agricultural concern worldwide. Irrigation practices, drought, and climate change are leading to elevated salinity levels in many regions, resulting in reduced crop yields. However, there is potential for a solution in the microbiome of halophytes, which are naturally salt-tolerant plants. These plants harbor a salt-tolerant microbiome in their rhizosphere (around roots) and endosphere (within plant tissue). These bacteria may play a significant role in conferring salt tolerance to the host plants. This leads to the possibility of transferring these beneficial bacteria, known as salt-tolerant plant-growth-promoting bacteria (ST-PGPB), to salt-sensitive plants, enabling them to grow in salt-affected areas to improve crop productivity. In this review, the background of salt-tolerant microbiomes is discussed and their potential use as ST-PGPB inocula is explored. We focus on two Gram-negative bacterial genera, Halomonas and Kushneria, which are commonly found in highly saline environments. These genera have been found to be associated with some halophytes, suggesting their potential for facilitating ST-PGPB activity. The study of salt-tolerant microbiomes and their use as PGPB holds promise for addressing the challenges posed by soil salinity in the context of efforts to improve crop growth in salt-affected areas.

Shift in rhizospheric and endophytic microbial communities of dominant plants around Sunit Alkaline Lake

Alkaline lakes are a special type of extreme saline-alkali ecosystem, and the dominant plants store a large number of microbial resources with salinity-tolerant or growth-promoting properties in the littoral zones. In this study, high-throughput sequencing technology and molecular ecological networks were used to analyze the bacteria and fungi from different rhizocompartments of three dominant plants along the salinity gradient in the littoral zones of Sunit Alkali Lake. The study found that fungal communities were more tolerant of environmental abiotic stress, and salinity was not the main environmental factor affecting the composition of microbial communities. Mantel test analysis revealed that SOC (soil organic carbon) was the primary environmental factor affecting the rhizosphere bacterial community as well as the rhizosphere endophyte bacteria and fungi, while CO₃^2- (carbonate ions) had a greater impact on the rhizosphere fungal communities. In addition, keystones identified through the associated molecular network play an important role in helping plants resist saline-alkali environments. There were significant differences in the metabolic pathways of microorganisms from different rhizocompartments predicted by the PICRUSt2 database, which may help to understand how microorganisms resist environmental stress. This study is of great importance for understanding the salt environments around alkaline lakes and excavating potential microbial resources.

Stimulation of PGP Bacteria on the Development of Seeds, Plants and Cuttings of the Obligate Halophyte Arthrocaulon (Arthrocnemum) macrostachyum (Moric.) Piirainen & G. Kadereit

The Earth is undergoing alterations at a high speed, which causes problems such as environmental pollution and difficulty in food production. This is where halophytes are interesting, due to their high potential in different fields, such as remediation of the environment and agriculture. For this reason, it is necessary to deepen the knowledge of the development of halophytes and how plant growth-promoting bacteria (PGP) can play a fundamental role in this process. Therefore, in this work were tested the effects of five PGP bacteria on its rhizosphere and other endophytic bacteria at different concentrations of NaCl on seed germination, plant growth (0 and 171 mM) and cutting growth (0 mM) of Arthrocaulon macrostachyum. The growth promotion in this strict halophyte is highlighted due to the presence of PGP bacteria and the fact that no salt is needed. Thus, without salt, the bacterial strains Kocuria polaris Hv16, Pseudarthrobacter psychrotolerans C58, and Rahnella aceris RTE9 enhanced the biomass production by more than 60% in both stems and roots. Furthermore, germination was encouraged by more than 30% in the presence of both R. aceris RTE9 and K. polaris Hv16 at 171 mM NaCl; the latter also had a biocontrol effect on the fungi that grew on the seeds. Additionally, for the first time in cuttings of this perennial species, the root biomass was improved thanks to the consortium of K. polaris Hv16 and P. psychrotolerans C58. Finally, this study demonstrates the potential of PGPs for optimising the development of halophytes, either for environmental or agronomic purposes.

Whole genome analysis for plant growth promotion profiling of Pantoea agglomerans CPHN2, a non-rhizobial nodule endophyte

Reduced agricultural production as well as issues like nutrient-depleted soils, eutrophication, and groundwater contamination have drawn attention to the use of endophyte-based bioformulations to restore soil fertility. Pantoea agglomerans CPHN2, a non-rhizobial nodule endophyte isolated from Cicer arietinum, exhibited a variety of plant growth-promoting traits. In this study, we used NextSeq500 technology to analyze whole-genome sequence information of this plant growth-promoting endophytic bacteria. The genome of P. agglomerans CPHN2 has a length of 4,839,532 bp and a G + C content of 55.2%. The whole genome comprises three different genomic fractions, comprising one circular chromosome and two circular plasmids. A comparative analysis between P. agglomerans CPHN2 and 10 genetically similar strains was performed using a bacterial pan-genome pipeline. All the predicted and annotated gene sequences for plant growth promotions (PGPs), such as phosphate solubilization, siderophore synthesis, nitrogen metabolism, and indole-3-acetic acid (IAA) of P. agglomerans CPHN2, were identified. The whole-genome analysis of P. agglomerans CPHN2 provides an insight into the mechanisms underlying PGP by endophytes and its potential applications as a biofertilizer.

Enzyme Profiling and Identification of Endophytic and Rhizospheric Bacteria Isolated from Arthrocnemum macrostachyum

Endophytic and rhizospheric bacteria isolated from halophytic plants support their host to survive in hyper-saline soil. These bacteria are also known to produce various enzymes with potential industrial applications. In this study, the endophytic and rhizospheric bacteria were isolated from Arthrocnemum macrostachyum collected from Karachi, Pakistan, and their ability to produce various extracellular enzymes was assessed using commercial and natural substrates. In total, 11 bacterial strains were isolated (four endophytic; seven rhizospheric). Bacillus was found to be the most abundant genus (73%), followed by Glutamicibacter (27%). The isolates including Glutamicibacter endophyticus and Bacillus licheniformis are reported for the first time from A. macrostachyum. All of the isolates were capable of producing at least two of the five industrially important hydrolytic enzymes tested, i.e., xylanase, cellulase, amylase, pectinase, and lipase. Lipase production was found to be highest among the isolates, i.e., up to 18 IU mL⁻¹. Although most of the isolates could grow at a wide range of temperatures (4–55 °C), pH (1–11), and salt concentrations (2–12%), under extreme conditions, very little growth was observed and the optimal growth was recorded between 2% and 6% NaCl, 25 and 45 °C, and 7 and 9 pH. Our results suggest that these isolates could be potential producers of enzymes with several biotechnological applications.

Successions and interactions of phyllospheric microbiome in response to NH3 exposure

Phyllosphere and numerous phyllospheric microbiomes present a huge potential for air pollution mitigation. Despite research investigating the microbial compositions in the phyllosphere, the successions and interactions of the phyllospheric microbiome under ammonia gas (NH₃) stress remain poorly understood. Herein, we performed 16S rDNA, the internal transcribed spacer (ITS) profiling and a quantitative microbial element cycling (QMEC) method to reveal successions, co-occurrence, and N-cycling functions changes of phyllospheric bacteria and fungi during NH₃ exposure. The NH₃ input mainly elevated ammonium (NH₄⁺-N) and total nitrogen (TN) levels on the leaf surface. The exposure in the phyllosphere decreased fungal concentration with a homogeneity increase while enhanced bacterial concentration with a noticeable richness drop. Both short-term (2-week) and long-term (6-week) exposure induced significant changes in microbial compositions. Bacterial genera (Nocardioides, Pseudonocardia) and fungal genera (Alternaria, Acremonium) dominated throughout the exposure. Intensive microbial interactions compared to that in the natural phyllosphere were observed via network analysis. Our results showed that N-cycling functional genes were largely stimulated by the exposure and might, in turn contribute to NH₃ pollution buffer and alleviation via microbial metabolism. This study extended the knowledge on microbial responses to NH₃ exposure in the phyllosphere and enlightened phylloremediation on NH₃ through the microbial role.

Maize growth response to different Bacillus strains isolated from a salt-marshland area under salinity stress

Maize (Zea mays) growth performance has been hindered due to the high soil salinity. Salinity is one of the most severe abiotic stresses that has led to growth imbalance and profitability of harvests in arid and semi-arid regions. Plants have taken advantage of salt-tolerant bacteria as plant growth-promoters to enhance growth and reduce the adverse effects of salinity through the regulation of some biochemical, physiological, and molecular features. Preferences for non-chemical, eco-friendly, and economical approaches have caused the inquiry of the Bacillus genus as a joint group of plant growth-promoting rhizobacteria known to alleviate salt-stress impacts. In the present study, halotolerant Bacillus strains were isolated from salt-marshland soil and characterized for their physiological, molecular, and biochemical properties. Twenty-four bacterial isolates collected from high saline fields of salt marshland were analyzed by MALDI-TOF MS proteome analysis, which confirmed the taxonomic affiliation with Bacillus cereus, Bacillus subtilis, Bacillus atrophaeus, and Bacillus thorngiensis. Applying the isolates on maize plants as bio-inoculant bacteria obviously increased the growth parameters (P < 0.01). Pot experiments showed that isolates 74 and 90 were the most prominent strains to minimize the harmful effects of salinity. Its effects are heightening the potassium/sodium ratio and K-Na selectivity in shoots and roots measured by flame atomic absorption photometry (AAS). Accordingly, Bacillus cereus isolate 74 showed a maximum increase in dry weights of the shoot (133.89%), root (237.08%), length of the shoot (125%), and root (119.44%) compared to the control condition. Our findings suggest that bacteria isolated from marshland may be an economical and simple means to increase plant growth and resistance to high salinity soil conditions.

Endophytes and Halophytes to Remediate Industrial Wastewater and Saline Soils: Perspectives from Qatar

Many halophytes are considered to be salt hyperaccumulators, adopting ion extrusion and inclusion mechanisms. Such plants, with high aboveground biomass, may play crucial roles in saline habitats, including soil desalination and phytoremediation of polluted soils and waters. These plants cause significant changes in some of the soil’s physical and chemical properties; and have proven efficient in removing heavy metals and metabolizing organic compounds from oil and gas activities. Halophytes in Qatar, such as Halopeplis perfoliata, Salicornia europaea, Salsola soda, and Tetraena qatarensis, are shown here to play significant roles in the phytoremediation of polluted soils and waters. Microorganisms associated with these halophytes (such as endophytic bacteria) might boost these plants to remediate saline and polluted soils. A significant number of these bacteria, such as Bacillus spp. and Pseudomonas spp., are reported here to play important roles in many sectors of life. We explore the mechanisms adopted by the endophytic bacteria to promote and support these halophytes in the desalination of saline soils and phytoremediation of polluted soils. The possible roles played by endophytes in different parts of native plants are given to elucidate the mechanisms of cooperation between these native plants and the associated microorganisms.

In-depth genome analysis of Bacillus sp. BH32, a salt stress-tolerant endophyte obtained from a halophyte in a semiarid region

Endophytic strains belonging to the Bacillus cereus group were isolated from the halophytes Atriplex halimus L. (Amaranthaceae) and Tamarix aphylla L. (Tamaricaceae) from costal and continental regions in Algeria. Based on their salt tolerance (up to 5%), the strains were tested for their ability to alleviate salt stress in tomato and wheat. Bacillus sp. strain BH32 showed the highest potential to reduce salinity stress (up to + 50% and + 58% of dry weight improvement, in tomato and wheat, respectively, compared to the control). To determine putative mechanisms involved in salt tolerance and plant growth promotion, the whole genome of Bacillus sp. BH32 was sequenced, annotated, and used for comparative genomics against the genomes of closely related strains. The pangenome of Bacillus sp. BH32 and its closest relative was further analyzed. The phylogenomic analyses confirmed its taxonomic position, a member of the Bacillus cereus group, with intergenomic distances (GBDP analysis) pinpointing to a new taxon (digital DNA-DNA hybridization, dDDH < 70%). Genome mining unveiled several genes involved in stress tolerance, production of anti-oxidants and genes involved in plant growth promotion as well as in the production of secondary metabolites. KEY POINTS : • Bacillus sp. BH32 and other bacterial endophytes were isolated from halophytes, to be tested on tomato and wheat and to limit salt stress adverse effects. • The strain with the highest potential was then studied at the genomic level to highlight numerous genes linked to plant growth promotion and stress tolerance. • Pangenome approaches suggest that the strain belongs to a new taxon within the Bacillus cereus group.

Diversity and Plant Growth-Promoting Ability of Endophytic, Halotolerant Bacteria Associated with Tetragonia tetragonioides (Pall.) Kuntze

The diversity of salt-tolerant cultivable endophytic bacteria associated with the halophyte New Zealand spinach (Tetragonia tetragonioides (Pall.) Kuntze) was studied, and their plant beneficial properties were evaluated. The bacteria isolated from leaves and roots belonged to Agrobacterium, Stenotrophomonas, Bacillus, Brevibacterium, Pseudomonas, Streptomyces, Pseudarthrobacter, Raoultella, Curtobacterium, and Pantoea. Isolates exhibited plant growth-promoting traits, including the production of a phytohormone (indole 3-acetic-acid), cell wall degrading enzymes, and hydrogen cyanide production. Furthermore, antifungal activity against the plant pathogenic fungi Fusarium solani, F. oxysporum, and Verticillium dahliae was detected. Ten out of twenty bacterial isolates were able to synthesize ACC deaminase, which plays a vital role in decreasing ethylene levels in plants. Regardless of the origin of isolated bacteria, root or leaf tissue, they stimulated plant root and shoot growth under 200 mM NaCl conditions. Our study suggests that halophytes such as New Zealand spinach are a promising source for isolating halotolerant plant-beneficial bacteria, which can be considered as potentially efficient biofertilizers in the bioremediation of salt-affected soils.

Metabolomics Analyses Reveal Metabolites Affected by Plant Growth-Promoting Endophytic Bacteria in Roots of the Halophyte Mesembryanthemum crystallinum

Mesembryanthemum crystallinum L. (common ice plant) is an edible halophyte. However, if ice plants are used to phytoremediate salinity soil, there are problems of slow initial growth, and a long period before active NaCl uptake occurs under higher salinity conditions. Application of endophytic bacteria may improve the problem, but there remain gaps in our understanding of how endophytic bacteria affect the growth and the biochemical and physiological characteristics of ice plants. The aims of this study were to identify growth-promoting endophytic bacteria from the roots of ice plants and to document the metabolomic response of ice plants after application of selected endophytic bacteria. Two plant growth-promoting endophytic bacteria were selected on the basis of their ability to promote ice plant growth. The two strains putatively identified as Microbacterium spp. and Streptomyces spp. significantly promoted ice plant growth, at 2-times and 2.5-times, respectively, compared with the control and also affected the metabolome of ice plants. The strain of Microbacterium spp. resulted in increased contents of metabolites related to the tricarboxylic acid cycle and photosynthesis. The effects of salt stress were alleviated in ice plants inoculated with the endobacterial strains, compared with uninoculated plants. A deeper understanding of the complex interplay among plant metabolites will be useful for developing microbe-assisted soil phytoremediation strategies, using Mesembryanthemum species.

Potential of Halophilic/Halotolerant Bacteria in Enhancing Plant Growth Under Salt Stress

In the current study, fourteen bacterial strains were obtained in salt contaminated soils. The identification and characterization of the bacterial strains were performed by conventional and molecular techniques. According to the results of 16S rRNA gene sequence analysis, five genera (Bacillus, Staphylococcus, Oceanobacillus, Exiguobacterium, and Halobacillus) were identified with a homology of equal to 99% or higher similarity. Afterward, these fourteen halotolerant/halophilic bacterial strains were investigated for their plant growth promoting (PGP) traits including production of indole-3-acetic acid (IAA) and siderophore, activity of 1-aminocyclopropane-1-carboxylate (ACC) deaminase, fixation of nitrogen, and phosphate solubilization potential. Five of the bacterial strains possessing PGP traits were tested for their effects on the growth of a salt sensitive plant (wheat) in a hydroponic system under salt stress (200 mM). Inoculation of five bacterial strains under salt stress significantly enhanced plant weight (Triticum aestivum) ranged from 71.18 to 89.04%. Salt stress amelioration potential of Oceanobacillus picturae and Staphylococcus succinus on T. aestivum has been shown for the first time in this study. In non-saline soil, the promising effect of plant growth bacteria is clear; however, in saline soil, the use of PGP halophilic and halotolerant bacteria can increase the productivity of salt sensitive plants. Therefore, the novel halophilic and halotolerant bacteria that promote plant growth can be developed for agricultural uses in saline soils.

Roles of Plant Growth-Promoting Rhizobacteria (PGPR) in Stimulating Salinity Stress Defense in Plants: A Review

To date, soil salinity becomes a huge obstacle for food production worldwide since salt stress is one of the major factors limiting agricultural productivity. It is estimated that a significant loss of crops (20-50%) would be due to drought and salinity. To embark upon this harsh situation, numerous strategies such as plant breeding, plant genetic engineering, and a large variety of agricultural practices including the applications of plant growth-promoting rhizobacteria (PGPR) and seed biopriming technique have been developed to improve plant defense system against salt stress, resulting in higher crop yields to meet human's increasing food demand in the future. In the present review, we update and discuss the advantageous roles of beneficial PGPR as green bioinoculants in mitigating the burden of high saline conditions on morphological parameters and on physio-biochemical attributes of plant crops via diverse mechanisms. In addition, the applications of PGPR as a useful tool in seed biopriming technique are also updated and discussed since this approach exhibits promising potentials in improving seed vigor, rapid seed germination, and seedling growth uniformity. Furthermore, the controversial findings regarding the fluctuation of antioxidants and osmolytes in PGPR-treated plants are also pointed out and discussed.

Comparative Analysis of Bacterial Diversity and Community Structure in the Rhizosphere and Root Endosphere of Two Halophytes, Salicornia europaea and Glaux maritima, Collected from Two Brackish Lakes in Japan

Microbial community structures associated with halophytes and their compositions among different habitats, particularly natural saline sites, have not yet been investigated in detail. In the present study, we examined the diversity and composition of the rhizosphere and root endosphere bacteria of two halophytes, Salicornia europaea L. and Glaux maritima L., collected from two adjacent brackish lakes, Lake Notoro and Lake Tofutsu, in Japan. The bacterial species richness and diversity indices of the two halophytes collected from both lakes showed no significant differences in the rhizosphere or root endosphere. In contrast, beta diversity and taxonomic analyses revealed significant differences in the bacterial communities from each halophyte between the two lakes even though the two locations were natural saline sites, indicating that the bacterial communities for S. europaea and G. maritima both fluctuated in a manner that depended on the geographical location. Common and abundant genera associated with each halophyte across the two lakes were then identified to verify the bacterial genera specifically inhabiting each plant species. The results obtained showed that the composition of abundant genera inhabiting each halophyte across two lakes was distinct from that reported previously in other saline soil areas. These results suggest that each halophyte in different geographical sites had an individual complex bacterial community.

Biodiversity and antimicrobial potential of bacterial endophytes from halophyte Salicornia brachiata

Extreme natural habitats like halophytes, marsh land, and marine environment are suitable arena for chemical ecology between plants and microbes having environmental impact. Endophytes are an ecofriendly option for the promotion of plant growth and to serve as sustainable resource of novel bioactive natural products. The present study, focusing on biodiversity of bacterial endophytes from Salicornia brachiata, led to isolation of around 336 bacterial endophytes. Phylogenetic analysis of 63 endophytes revealed 13 genera with 27 different species, belonging to 3 major groups: Firmicutes, Proteobacteria, and Actinobacteria. 30% endophytic isolates belonging to various genera demonstrated broad-spectrum antibacterial and antifungal activities against a panel of human, plant, and aquatic infectious agents. An endophytic isolate Bacillus amyloliquefaciens 5NPA-1, exhibited strong in-vitro antibacterial activity against human pathogen Staphylococcus aureus and phytopathogen Xanthomonas campestris. Investigation through LC-MS/MS-based molecular networking and bioactivity-guided purification led to the identification of three bioactive compounds belonging to lipopeptide class based on ¹H-, ¹³C-NMR and MS analysis. To our knowledge, this is the first report studying bacterial endophytic biodiversity of Salicornia brachiata and the isolation of bioactive compounds from its endophyte. Overall, the present study provides insights into the diversity of endophytes associated with the plants from the extreme environment as a rich source of metabolites with remarkable agricultural applications and therapeutic properties.

Impact of Plant Growth Promoting Bacteria on Salicornia ramosissima Ecophysiology and Heavy Metal Phytoremediation Capacity in Estuarine Soils

Salicornia ramosissima is a C₃ halophyte that grows naturally in South Western Spain salt marshes, under soil salinity and heavy metal pollution (mostly Cu, Zn, As, and Pb) caused by both natural and anthropogenic pressure. However, very few works have reported the phytoremediation potential of S. ramosissima. In this work, we studied a microbe-assisted phytoremediation strategy under greenhouse conditions. We inoculated plant growth promoting (PGP) and heavy metal resistant bacteria in pots with S. ramosissima and natural non-polluted and polluted sediments collected from Spanish estuaries. Then, we analyzed plant ecophysiological and metal phytoaccumulation response. Our data suggested that inoculation in polluted sediments improved S. ramosissima plant growth in terms of relative growth rate (RGR) (32%) and number of new branches (61%). S. ramosissima photosynthetic fitness was affected by heavy metal presence in soil, but bacteria inoculation improved the photochemical apparatus integrity and functionality, as reflected by increments in net photosynthetic rate (21%), functionality of PSII (F_m and F_v/F_m) and electron transport rate, according to OJIP derived parameters. Beneficial effect of bacteria in polluted sediments was also observed by augmentation of intrinsic water use efficiency (28%) and slightly water content (2%) in inoculated S. ramosissima. Finally, our results demonstrated that S. ramosissima was able to accumulate great concentrations of heavy metals, mostly at root level, up to 200 mg Kg^–1 arsenic, 0.50 mg Kg^–1 cadmium, 400 mg Kg^–1 copper, 25 mg Kg^–1 nickel, 300 mg Kg^–1 lead, and 300 mg Kg^–1 zinc. Bioaugmentation incremented S. ramosissima heavy metal phytoremediation potential due to plant biomass increment, which enabled a greater accumulation capacity. Thus, our results suggest the potential use of heavy metal resistant PGPB to ameliorate the capacity of S. ramosissima as candidate for phytoremediation of salty polluted ecosystems.

Insights Into Microbially Induced Salt Tolerance and Endurance Mechanisms (STEM) in Plants

Salt stress threatens the achievement of sustainable global food security goals by inducing secondary stresses, such as osmotic, ionic, and oxidative stress, that are detrimental to plant growth and productivity. Various studies have reported the beneficial roles of microbes in ameliorating salt stress in plants. This review emphasizes salt tolerance and endurance mechanisms (STEM) in microbially inoculated (MI) plants that ensure plant growth and survival. Well-established STEM have been documented in MI plants and include conglomeration of osmolytes, antioxidant barricading, recuperating nutritional status, and ionic homeostasis. This is achieved via involvement of P solubilization, siderophore production, nitrogen fixation, selective ion absorption, volatile organic compound production, exopolysaccharide production, modifications to plant physiological processes (photosynthesis, transpiration, and stomatal conductance), and molecular alterations to alter various biochemical and physiological processes. Salt tolerance and endurance mechanism in MI plants ensures plant growth by improving nutrient uptake and maintaining ionic homeostasis, promoting superior water use efficiency and osmoprotection, enhancing photosynthetic efficiency, preserving cell ultrastructure, and reinforcing antioxidant metabolism. Molecular research in MI plants under salt stress conditions has found variations in the expression profiles of genes such as HKT1, NHX, and SOS1 (ion transporters), PIPs and TIPs (aquaporins), RBCS, RBCL (RuBisCo subunits), Lipoxygenase2 [jasmonic acid (JA) signaling], ABA (abscisic acid)-responsive gene, and APX, CAT, and POD (involved in antioxidant defense). Proteomic analysis in arbuscular mycorrhizal fungi-inoculated plants revealed upregulated expression of signal transduction proteins, including Ca²⁺ transporter ATPase, calcium-dependent protein kinase, calmodulin, and energy-related proteins (NADH dehydrogenase, iron-sulfur protein NADH dehydrogenase, cytochrome C oxidase, and ATP synthase). Future research should focus on the role of stress hormones, such as JA, salicylic acid, and brassinosteroids, in salt-stressed MI plants and how MI affects the cell wall, secondary metabolism, and signal transduction in host plants.

When Salt Meddles Between Plant, Soil, and Microorganisms

In extreme environments, the relationships between species are often exclusive and based on complex mechanisms. This review aims to give an overview of the microbial ecology of saline soils, but in particular of what is known about the interaction between plants and their soil microbiome, and the mechanisms linked to higher resistance of some plants to harsh saline soil conditions. Agricultural soils affected by salinity is a matter of concern in many countries. Soil salinization is caused by readily soluble salts containing anions like chloride, sulphate and nitrate, as well as sodium and potassium cations. Salinity harms plants because it affects their photosynthesis, respiration, distribution of assimilates and causes wilting, drying, and death of entire organs. Despite these life-unfavorable conditions, saline soils are unique ecological niches inhabited by extremophilic microorganisms that have specific adaptation strategies. Important traits related to the resistance to salinity are also associated with the rhizosphere-microbiota and the endophytic compartments of plants. For some years now, there have been studies dedicated to the isolation and characterization of species of plants' endophytes living in extreme environments. The metabolic and biotechnological potential of some of these microorganisms is promising. However, the selection of microorganisms capable of living in association with host plants and promoting their survival under stressful conditions is only just beginning. Understanding the mechanisms of these processes and the specificity of such interactions will allow us to focus our efforts on species that can potentially be used as beneficial bioinoculants for crops.

Shift in rhizospheric and endophytic bacterial communities of tomato caused by salinity and grafting

Saline water has to be used as an alternative resource in modern agriculture due to the increasing lack of fresh water. Approaches that promote the growth of crops under saline conditions have, therefore, become crucial. Grafting has been reported to be effective for this; however, the associated bacterial community remains unclear. To obtain a deeper understanding of the underlying microbial mechanisms, both grafted and non-grafted tomatoes were irrigated with three types of water having different electrical conductivity values. The experiment lasted 2.5 months, after which, the soil chemical properties and tomato heights were assessed. The rhizospheric and endophytic bacterial communities of samples from the different treatments were assessed by Illumina sequencing. The results showed that saline water significantly affected leaf-associated endophytic bacterial communities, whereas rhizosphere and root- and stem-associated bacterial communities were not affected. Increasing salinity increased the abundance of Gammaproteobacteria, but decreased the abundance of Actinobacteria, Alphaproteobacteria, Bacilli, and Acidobacteria at the class level of the leaf-associated bacterial community. Moreover, under higher salinity levels, grafting increased the diversity of the leaf-endophytic bacterial community. Overall, this study provides a comprehensive understanding of the rhizosphere and endophytic bacterial communities of tomato under saline conditions. The results highlight the importance of leaf-endophytic bacteria for salt response in plants. This is an important complementary finding to previous studies on the effect of salinity, which mainly focused on plant rhizosphere and root bacterial communities.

Uncovering PGPB Vibrio spartinae inoculation-triggered physiological mechanisms involved in the tolerance of Halimione portulacoides to NaCl excess

Plant growth promoting bacteria' (PGPB) beneficial role on plant tolerance to salinity stress has previously been well recognized. However, bacteria-triggered plant physiological mechanisms involved in this response require investigation, especially in plants with innate salt tolerance. A glasshouse experiment was designed to investigate the effect of the PGPB Vibrio spartinae on Halimione portulacoides growth, physiological performance and ion homeostasis in plants exposed to 0, 171, 510 and 1020 mM NaCl for 100 days. Bacterial inoculation alleviated ~28% of the deleterious impact of salinity excess on the relative growth rate (RGR) in plants grown at 510 mM and led to 30% and 44% enhancements in those exposed to 0 and 171 mM NaCl, respectively. This effect was linked to a reduction in Na tissue concentrations which improved plant ion homeostasis at elevated NaCl concentration, and to the overall protective effects on various steps in the photosynthetic pathway between 0 and 510 mM NaCl. Thus, inoculated plants were able to maintain higher net photosynthesis (A_N) than their non-inoculated counterparts. Hence, A_N differences under saline conditions were ascribed to inoculation amelioration NaCl-induced CO₂ diffusion limitations, as reflected in the greater g_s and C_i values recorded at 171 and 510 mM NaCl, together with an enhancement of photochemical apparatus functionality (in terms of energy absorption, transformation and transport), as indicated by a higher electron transport rate (ETR) and energy fluxes derived from Kautsky curves, compared with their non-inoculated counterparts.

Characteristics and Diversity of Endophytic Bacteria in Endangered Chinese Herb Glehnia littoralis Based on Illumina Sequencing

Glehnia littoralis is an endangered medicinal plant growing in the coastal ecological environment and plays an important role in coastal ecosystems. The endophytes in the plant have a significant role in promoting plant growth and enhancing plant stress resistance. However, the endophytic bacterial structure associated with halophyte G. littoralis is still not revealed. In this project, the construction and diversity of endophytic bacterial consortium associated with different tissues of G. littoralis were illustrated with high throughput sequencing of the V3-V4 region of the bacterial 16S rRNA. The results resolved that the diversity and richness of endophytic bacteria were significantly higher in root than in leaf and stem. The operational taxonomic units (OTU) analysis demonstrated that the Actinobacteria and Proteobacteria were dominant in all the samples at the phylum level, and Pseudomonas, Bacillus, Rhizobium were the dominant genera. Our results unraveled that the bacterial communities differed among different tissues of G. littoralis. Endophytic bacterial communities in leaf and stem shared more similarity than that in the root. Furthermore, the difference of bacteria community and structure among different tissues were also detected by principal coordinate analysis. Taken altogether, we can conclude that the bacterial communities of different tissues are unique, which could facilitate understanding the diversity of endophytic bacteria in G. littoralis.

The Root Nodule Microbiome of Cultivated and Wild Halophytic Legumes Showed Similar Diversity but Distinct Community Structure in Yellow River Delta Saline Soils

Symbiotic associations between leguminous plants and their nodule microbiome play a key role in sustainable agriculture by facilitating the fixation of atmospheric nitrogen and enhancing plant stress resistance. This study aimed to decipher the root nodule microbiome of two halophytic legumes, Sesbania cannabina and Glycine soja, which grow in saline soils of the Yellow River Delta, China, using PacBio’s circular consensus sequencing for full-length bacterial 16S rRNA gene to obtain finer taxonomic information. The cultivated legume Glycine max was used for comparison. We identified 18 bacterial genera and 55 species in nodule samples, which mainly classified to Proteobacteria, and rhizobial genus Ensifer was the predominant group. The three legumes showed similarity in operational taxonomic unit (OTU) diversity but distinction in OTU richness, indicating that they harbor similar bacterial species with different relative contents. The results of principal coordinates analysis and ANOSIM tests indicated that G. soja and G. max have similar nodule bacterial communities, and these communities differ from that of S. cannabina. Wild legumes S. cannabina and G. soja both harbored a higher number of rhizobia, while G. max possessed more non-rhizobial bacteria. These differences could be associated with their adaptability to saline–alkali stress and revealed clues on the nodule endophytes with relative importance of culturable rhizobial symbionts.

Bacterial endophyte mediated plant tolerance to salinity: growth responses and mechanisms of action

Salinity stress is one of the key constraints for sustainable crop production. It has gained immense importance in the backdrop of climate change induced imbalanced terrestrial water budgets. The traditional agronomic approaches and breeding salt-tolerant genotypes have often proved insufficient to alleviate salinity stress. Newer approaches like the use of bacterial endophytes associated with agricultural crops have occupied center place recently, owing to their advantageous role in improving crop growth, health and yield. Research evidences have revealed that bacterial endophytes can promote plant growth by accelerating availability of mineral nutrients, helping in production of phytohormones, siderophores, and enzymes, and also by activating systemic resistance against insect pest and pathogens in plants. These research developments have opened an innovative boulevard in agriculture for capitalizing bacterial endophytes, single species or consortium, to enhance plant salt tolerance capabilities, and ultimately lead to translational refinement of crop-production business under salty environments. This article reviews the latest research progress on the identification and functional characterization of salt tolerant endophytic bacteria and illustrates various mechanisms triggered by them for plant growth promotion under saline environment.

Salt-Tolerant Halophyte Rhizosphere Bacteria Stimulate Growth of Alfalfa in Salty Soil

Halophytes are plants that are adapted to grow in saline soils, and have been widely studied for their physiological and molecular characteristics, but little is known about their associated microbiomes. Bacteria were isolated from the rhizosphere and as root endophytes of Salicornia rubra, Sarcocornia utahensis, and Allenrolfea occidentalis, three native Utah halophytes. A total of 41 independent isolates were identified by 16S rRNA gene sequencing analysis. Isolates were tested for maximum salt tolerance, and some were able to grow in the presence of up to 4 M NaCl. Pigmentation, Gram stain characteristics, optimal temperature for growth, and biofilm formation of each isolate aided in species identification. Some variation in the bacterial population was observed in samples collected at different times of the year, while most of the genera were present regardless of the sampling time. Halomonas, Bacillus, and Kushneria species were consistently isolated both from the soil and as endophytes from roots of all three plant species at all collection times. Non-culturable bacterial species were analyzed by Illumina DNA sequencing. The most commonly identified bacteria were from several phyla commonly found in soil or extreme environments: Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Gamma- and Delta-Proteobacteria. Isolates were tested for the ability to stimulate growth of alfalfa under saline conditions. This screening led to the identification of one Halomonas and one Bacillus isolate that, when used to inoculate young alfalfa seedlings, stimulate plant growth in the presence of 1% NaCl, a level that significantly inhibits growth of uninoculated plants. The same bacteria used in the inoculation were recovered from surface sterilized alfalfa roots, indicating the ability of the inoculum to become established as an endophyte. The results with these isolates have exciting promise for enhancing the growth of inoculated alfalfa in salty soil.

Screening of the High-Rhizosphere Competent Limoniastrum monopetalum' Culturable Endophyte Microbiota Allows the Recovery of Multifaceted and Versatile Biocontrol Agents

Halophyte Limoniastrum monopetalum, an evergreen shrub inhabiting the Mediterranean region, has well-documented phytoremediation potential for metal removal from polluted sites. It is also considered to be a medicinal halophyte with potent activity against plant pathogens. Therefore, L. monopetalum may be a suitable candidate for isolating endophytic microbiota members that provide plant growth promotion (PGP) and resistance to abiotic stresses. Selected for biocontrol abilities, these endophytes may represent multifaceted and versatile biocontrol agents, combining pathogen biocontrol in addition to PGP and plant protection against abiotic stresses. In this study 117 root culturable bacterial endophytes, including Gram-positive (Bacillus and Brevibacillus), Gram-negative (Proteus, Providencia, Serratia, Pantoea, Klebsiella, Enterobacter and Pectobacterium) and actinomycete Nocardiopsis genera have been recovered from L. monopetalum. The collection exhibited high levels of biocontrol abilities against bacterial (Agrobacterium tumefaciens MAT2 and Pectobacterium carotovorum MAT3) and fungal (Alternaria alternata XSZJY-1, Rhizoctonia bataticola MAT1 and Fusarium oxysporum f. sp. radicis lycopersici FORL) pathogens. Several bacteria also showed PGP capacity and resistance to antibiotics and metals. A highly promising candidate Bacillus licheniformis LMRE 36 with high PGP, biocontrol, metal and antibiotic, resistance was subsequently tested in planta (potato and olive trees) for biocontrol of a collection of 14 highly damaging Fusarium species. LMRE 36 proved very effective against the collection in both species and against an emerging Fusarium sp. threatening olive trees culture in nurseries. These findings provide a demonstration of our pyramiding strategy. Our strategy was effective in combining desirable traits in biocontrol agents towards broad-spectrum resistance against pathogens and protection of crops from abiotic stresses. Stacking multiple desirable traits into a single biocontrol agent is achieved by first, careful selection of a host for endophytic microbiota recovery; second, stringent in vitro selection of candidates from the collection; and third, application of the selected biocontrol agents in planta experiments. That pyramiding strategy could be successfully used to mitigate effects of diverse biotic and abiotic stresses on plant growth and productivity. It is anticipated that the strategy will provide a new generation of biocontrol agents by targeting the microbiota of plants in hostile environments.

Isolation and Characterization of Halotolerant Plant Growth Promoting Rhizobacteria From Durum Wheat (Triticum turgidum subsp. durum) Cultivated in Saline Areas of the Dead Sea Region

Plant growth promoting rhizobacteria (PGPR) are beneficial microorganisms that can be utilized to improve plant responses against biotic and abiotic stresses. In this study, 74 halotolerant bacterial isolates were isolated from rhizosphere and endorhizosphere of durum wheat (Triticum turgidum subsp. durum) plants cultivated in saline environments in the Ghor region near the east of the Dead Sea. 16S rDNA partial sequences and phylogenetic analysis of 62 isolates showed clear clustering of the isolates into three phyla: Firmicutes (61.3%), Proteobacteria (29.0%), and Actinobacteria (9.7%). At the genus level, the majority of them were grouped within the Bacillus, Oceanobacillus, and Halomonas genera. The isolates, which possessed plant growth promoting traits including nitrogen fixation, ACC deaminase activity, auxin production, inorganic phosphate solubilization and siderophore production, were selected. The effect of the inoculation of selected PGPR strains on growth of salt sensitive and salt tolerant durum wheat genotypes under high salt stress conditions was evaluated. Six halotolerant PGPR strains were able to improve survival in inoculated plants under high salinity stress conditions as reflected in higher germination percentages and seedling root growth when compared with non-inoculated plants. Furthermore, three halotolerant PGPR strains were able to improve durum wheat tolerance to water deficit stress. In addition, antagonistic effect in four halotolerant PGPR strains against an aggressive pathogenic isolate of Fusarium culmorum that causes crown rot disease was observed in a dual culture assay. In conclusion, the halotolerant PGPR strains described in this study might have great potential to improve durum wheat productivity under different stress conditions.

Safe Cultivation of Medicago sativa in Metal-Polluted Soils from Semi-Arid Regions Assisted by Heat- and Metallo-Resistant PGPR

Soil contamination with heavy metals is a constraint for plant establishment and development for which phytoremediation may be a solution, since rhizobacteria may alleviate plant stress under these conditions. A greenhouse experiment was conducted to elucidate the effect of toxic metals on growth, the activities of ROS (reactive oxygen species)-scavenging enzymes, and gene expression of Medicago sativa grown under different metal and/or inoculation treatments. The results showed that, besides reducing biomass, heavy metals negatively affected physiological parameters such as chlorophyll fluorescence and gas exchange, while increasing ROS-scavenging enzyme activities. Inoculation of M. sativa with a bacterial consortium of heat- and metallo-resistant bacteria alleviated metal stress, as deduced from the improvement of growth, lower levels of antioxidant enzymes, and increased physiological parameters. The bacteria were able to effectively colonize and form biofilms onto the roots of plants cultivated in the presence of metals, as observed by scanning electron microscopy. Results also evidenced the important role of glutathione reductase (GR), phytochelatin synthase (PCS), and metal transporter NRAMP1 genes as pathways for metal stress management, whereas the gene coding for cytochrome P450 (CP450) seemed to be regulated by the presence of the bacteria. These outcomes showed that the interaction of metal-resistant rhizobacteria/legumes can be used as an instrument to remediate metal-contaminated soils, while cultivation of inoculated legumes on these soils is still safe for animal grazing, since inoculation with bacteria diminished the concentrations of heavy metals accumulated in the aboveground parts of the plants to below toxic levels.

Isolation and identification of a halophilic and alkaliphilic microalgal strain

Halophilic and alkaliphilic microalgal strain SAE1 was isolated from the saline-alkaline soil of Songnen Plain of Northeast China. Morphological observation revealed that SAE1 has a simple cellular structure, single cell, spherical, diameter of four to six μm, cell wall of about 0.22 μm thick, two chloroplasts and one nucleus. Analysis of the phylogenetic tree constructed by 18S sequence homology suggests that SAE1 is highly homologous to Nannochloris sp. BLD-15, with only four base substitutions in the homologous region. SAE1 was initially considered as Nannochloris sp. Analysis of the halophilic and alkaliphilic characteristics of SAE1 indicates that it can grow under one M NaHCO3 and NaCl concentrations, with optimal growth under 400 mM NaHCO3 and 200 mM NaCl. The intracellular ultrastructure of SAE1 significantly changed after NaCl and NaHCO3 treatments. A large number of starch grains accumulated after treatment with 400 mM NaHCO3 in cells, but few were found after treatment with 200 mM NaCl and none in the living condition without treatment. We conjectured that one of the metabolic characteristics of alkaliphilic (NaHCO3) microalga SAE1 is the formation of massive starch grains, which induce glycerol anabolism and increase osmotic pressure, thereby enhancing its ability to resist saline-sodic conditions. This feature of alkaliphilic (NaHCO3) microalga SAE1 contributes to its growth in the carbonate soil of Songnen Plain.

Isolation and Characterization of Halotolerant Plant Growth Promoting Rhizobacteria From Durum Wheat (Triticum turgidum subsp. durum) Cultivated in Saline Areas of the Dead Sea Region

Plant growth promoting rhizobacteria (PGPR) are beneficial microorganisms that can be utilized to improve plant responses against biotic and abiotic stresses. In this study, 74 halotolerant bacterial isolates were isolated from rhizosphere and endorhizosphere of durum wheat (Triticum turgidum subsp. durum) plants cultivated in saline environments in the Ghor region near the east of the Dead Sea. 16S rDNA partial sequences and phylogenetic analysis of 62 isolates showed clear clustering of the isolates into three phyla: Firmicutes (61.3%), Proteobacteria (29.0%), and Actinobacteria (9.7%). At the genus level, the majority of them were grouped within the Bacillus, Oceanobacillus, and Halomonas genera. The isolates, which possessed plant growth promoting traits including nitrogen fixation, ACC deaminase activity, auxin production, inorganic phosphate solubilization and siderophore production, were selected. The effect of the inoculation of selected PGPR strains on growth of salt sensitive and salt tolerant durum wheat genotypes under high salt stress conditions was evaluated. Six halotolerant PGPR strains were able to improve survival in inoculated plants under high salinity stress conditions as reflected in higher germination percentages and seedling root growth when compared with non-inoculated plants. Furthermore, three halotolerant PGPR strains were able to improve durum wheat tolerance to water deficit stress. In addition, antagonistic effect in four halotolerant PGPR strains against an aggressive pathogenic isolate of Fusarium culmorum that causes crown rot disease was observed in a dual culture assay. In conclusion, the halotolerant PGPR strains described in this study might have great potential to improve durum wheat productivity under different stress conditions.

Bacterial Diversity Associated With the Rhizosphere and Endosphere of Two Halophytes: Glaux maritima and Salicornia europaea

Root-associated microbial communities are very important in the adaptation of halophytes to coastal environments. However, little has been reported on microbial community structures related to halophytes, or on comparisons of their compositions among halophytic plant species. Here, we studied the diversity and community structure of both rhizosphere and root endosphere bacteria in two halophytic plants: Glaux maritima and Salicornia europaea. We sampled the rhizosphere, the root endosphere, and bulk control soil samples, and performed bacterial 16S rRNA sequencing using the Illumina MiSeq platform to characterize the bacterial community diversities in the rhizosphere and root endosphere of both halophytes. Among the G. maritima samples, the richness and diversity of bacteria in the rhizosphere were higher than those in the root endosphere but were lower than those of the bulk soil. In contrast for S. europaea, the bulk soil, the rhizosphere, and the root endosphere all had similar bacterial richness and diversity. The number of unique operational taxonomic units within the root endosphere, the rhizosphere, and the bulk soil were 181, 366, and 924 in G. maritima and 126, 416, and 596 in S. europaea, respectively, implying habitat-specific patterns for each halophyte. In total, 35 phyla and 566 genera were identified. The dominant phyla across all samples were Proteobacteria and Bacteroidetes. Actinobacteria was extremely abundant in the root endosphere from G. maritima. Beneficial bacterial genera were enriched in the root endosphere and rhizosphere in both halophytes. Rhizobium, Actinoplanes, and Marinomonas were highly abundant in G. maritima, whereas Sulfurimonas and Coleofasciculus were highly abundant in S. europaea. A principal coordinate analysis demonstrated significant differences in the microbiota composition associated with the plant species and type of sample. These results strongly indicate that there are clear differences in bacterial community structure and diversity between G. maritima and S. europaea. This is the first report to characterize the root microbiome of G. maritima, and to compare the diversity and community structure of rhizosphere and root endosphere bacteria between G. maritima and S. europaea.

Mining Halophytes for Plant Growth-Promoting Halotolerant Bacteria to Enhance the Salinity Tolerance of Non-halophytic Crops

Salinity stress is one of the major abiotic stresses limiting crop production in arid and semi-arid regions. Interest is increasing in the application of PGPRs (plant growth promoting rhizobacteria) to ameliorate stresses such as salinity stress in crop production. The identification of salt-tolerant, or halophilic, PGPRs has the potential to promote saline soil-based agriculture. Halophytes are a useful reservoir of halotolerant bacteria with plant growth-promoting capabilities. Here, we review recent studies on the use of halophilic PGPRs to stimulate plant growth and increase the tolerance of non-halophytic crops to salinity. These studies illustrate that halophilic PGPRs from the rhizosphere of halophytic species can be effective bio-inoculants for promoting the production of non-halophytic species in saline soils. These studies support the viability of bioinoculation with halophilic PGPRs as a strategy for the sustainable enhancement of non-halophytic crop growth. The potential of this strategy is discussed within the context of ensuring sustainable food production for a world with an increasing population and continuing climate change. We also explore future research needs for using halotolerant PGPRs under salinity stress.

Ectomycorrhization of Tricholoma matsutake with Quercus aquifolioides affects the endophytic microbial community of host plant

Tricholoma matsutake (S. Ito et Imai) is an ectomycorrhizal basidiomycete associated with Pinaceae and Fagaceae trees in the Northern Hemisphere. It is still unknown whether the symbiotic relationship with this ectomycorrhiza could affect the host plant's endophytic microbial community. In this study, we used high throughput sequencing to analyze the endophytic microbial communities of different Quercus aquifolioides tissues with or without T. matsutake partner. About 35,000 clean reads were obtained per sample, representing 34 bacterial phyla and 7 fungal phyla. We observed 3980 operational taxonomic units (OTUs) of bacteria and 457 OTUs of fungi at a 97% similarity level. Three bacterial phyla, Proteobacteria, Cyanobacteria, and Bacteroidetes, and the fungal phylum Ascomycota were dominant in all tissues. The relative abundance of these taxa differed significantly between Q. aquifolioides tissues with and without T. matsutake partner (p < 0.05). The bacterial genus Pseudomonas and the fungal genus Cryptosporiopsis were more abundant in mycorrhized roots than in control roots. This study showed that the community structure and dominant species of endophytic microbial communities in Q. aquifolioides tissues might be altered by colonization with T. matsutake. This work provides a new insight into the interactions between ectomycorrhizal fungus and host plant.

Illumina-Based Analysis of Endophytic and Rhizosphere Bacterial Diversity of the Coastal Halophyte Messerschmidia sibirica

Halophytes play important roles in coastal ecosystems. However, few reports have described bacterial communities related to halophytes, and the distribution patterns of these bacteria in different plant tissues have been rarely compared. This paper mainly studied the diversity and community structure of endophytic and rhizosphere (Rh) bacteria related to the halophyte Messerschmidia sibirica, a dominant species in the coastal zone of Shandong Peninsula, China. We collected leaf (Lf), stem (Sm), root (Rt), Rh, and bulk (Bl) control soil samples, and sequenced the V5–V7 region of the bacterial 16S rRNA gene using the Illumina HiSeq platform to identify bacterial communities originating from different plant habitats. We found that the bacterial richness and diversity in Rh were significantly higher than those in the leaves, Sm, and Rt, but lower than those of the Bl control soil. In total, 37 phyla and 438 genera were identified. Microbial-diversity analysis showed that Proteobacteria and Actinobacteria were the dominant phyla and that Pseudomonas, Bacillus, Sphingomonas, Streptomyces, Microbacterium, Rhizobium, and Nocardioides were the dominant genera. However, there were clear differences in community diversity and structure among the samples. Endophytic bacteria community in Lf, Sm, and Rt shared more similarity than those in Rh and Bl control soil. The numbers of operational taxonomic units exclusive to the Lf, stem, Rt, Rh, and Bl control soil samples were 51, 43, 122, 139, and 922, respectively, implying habitat-specific patterns. Principal coordinate analysis demonstrated differences were apparent in the bacterial communities associated with habitats. On the whole, M. sibirica affected bacterial diversity and structured the bacterial community. This study provides insight into the complex microbial compositions of coastal halophytes.