Bacterial Endophyte Colonization and Distribution within Plants

Insights into the seed microbiome and its ecological significance in plant life

In recent years, the microbiome has attracted much attention because of the multiple roles and functions that microbes play in plants, animals, and human beings. Seed-associated microbes are of particular interest in being the initial microbial inoculum that affects the critical early life stages of a plant. The seed-microbe interactions are also known to improve nutrient acquisition, resilience against pathogens, and resistance against abiotic stresses. Despite these diverse roles, the seed microbiome has received little attention in plant ecology. Thus, we review the current knowledge on seed microbial diversity, community structure, and functions obtained through culture-dependent and culture-independent approaches. Furthermore, we present a comprehensive synthesis of the ecological literature on seed-microbe interactions to better understand the impact of these interactions on plant health and productivity. We suggest that future research should focus on the role of the seed microbiome in the establishment, colonization and spread of plant species in their native and non-native ranges as it may provide new insights into conservation biology and invasion ecology.

Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria

The bacterial colonization dynamics of plants can differ between phylogenetically similar bacterial strains and in the context of complex bacterial communities. Quantitative methods that can resolve closely related bacteria within complex communities can lead to a better understanding of plant-microbe interactions. However, current methods often lack the specificity to differentiate phylogenetically similar bacterial strains. In this study, we describe molecular strategies to study duckweed-associated bacteria. We first systematically optimized a bead-beating protocol to co-isolate nucleic acids simultaneously from duckweed and bacteria. We then developed a generic fingerprinting assay to detect bacteria present in duckweed samples. To detect specific duckweed-bacterium associations, we developed a genomics-based computational pipeline to generate bacterial strain-specific primers. These strain-specific primers differentiated bacterial strains from the same genus and enabled the detection of specific duckweed-bacterium associations present in a community context. Moreover, we used these strain-specific primers to quantify the bacterial colonization of duckweed by normalization to a plant reference gene and revealed differences in colonization levels between strains from the same genus. Lastly, confocal microscopy of inoculated duckweed further supported our PCR results and showed bacterial colonization of the duckweed root-frond interface and root interior. The molecular methods introduced in this work should enable the tracking and quantification of specific plant-microbe associations within plant-microbial communities.

Community Profiling of Seed Endophytes from the Pb-Zn Hyperaccumulator Noccaea caerulescens and Their Plant Growth Promotion Potential

Endophytes within plants are known to be crucial for plant fitness, and while their presence and functions in many compartments have been studied in depth, the research on seed endophytes is still limited. This work aimed to characterize the seed endophytic and rhizospheric bacterial community of two Noccaea caerulescens Pb-Zn hyperaccumulator populations, growing on two heavy-metal-polluted sites in Belgium. Cultured representatives were evaluated for their potential to enhance seed germination and root length of the model species Arabidopsis thaliana. The results indicated that the community structure within the seed is conserved between the two locations, comprising mainly of Proteobacteria (seeds), and Actinobacteria in the bulk soil. Root length of A. thaliana was significantly increased when inoculated with Sphingomonas vulcanisoli. The results of this paper offer insights into the importance of the selection of the core seed endophytic microbiome and highlight the precarious symbiotic relationship they have with the plant and seed.

Reconnoitering the capabilities of nodule endophytic Pantoea dispersa for improved nodulation and grain yield of chickpea (Cicer arietinum L.)

Microorganisms belonging to root and soil provide a wide range of services and benefits to the plant by promoting plant growth and controlling phytopathogens. This study aimed to isolate endophytic bacteria from the root nodules of chickpea (Cicer arietinum L.) and determine their potential in improving plant growth. A total of nineteen different bacterial morphotypes were isolated from root nodules of chickpea and characterized in vitro for plant growth promotion abilities. All bacterial isolates were able to produce indole acetic acid at varying levels, out of which MCA19 was screened as the most efficient indole acetic acid producer (10.25 µg mL^-1). MCA8, MCA9, MCA10, MCA11, MCA16, MCA17 and MCA19 were positive for phosphate solubilization, out of which MCA9 was best phosphate solubilizer (18.8 µg mL^-1). All bacterial strains showed varying ability to grow on nitrogen-free media. Hydrogen cyanide, pectinase, and cellulase production ability were also observed in isolates, in which MCA9, MCA12, MCA17 and MCA19 were found best. Based on in vitro testing, five isolates MCA2, MCA9, MCA11, MCA17 and MCA19 were selected for further studies. Bacterial isolates MCA9, MCA11, MCA17 and MCA19 were identified by 16S rRNA gene sequence analysis as Pantoea dispersa while MCA2 as Rhizobium pusense. This is the first report on the existence of Pantoea dispersa in the root nodules of chickpea. In pot experiment, a maximum increase of 30% was recorded in plant dry weight upon the application of MCA19. Under field conditions, bacterial isolates, MCA2, MCA11 and MCA19 significantly enhanced nodulation and yield parameters of chickpea, compared to control. Pantoea dispersa MCA19 displayed the highest plant growth-promoting potential by increasing 38% grain yield. Our results indicate that Pantoea dispersa MCA19 is a promising biofertilizer for future applications.

Endophytic Penicillium species secretes mycophenolic acid that inhibits the growth of phytopathogenic fungi

The worldwide demand for reduced and restricted use of pesticides in agriculture due to serious environmental effects, health risks and the development of pathogen resistance calls for the discovery of new bioactive compounds. In the medical field, antibiotic-resistant microorganisms have become a major threat to man, increasing mortality. Endophytes are endosymbiotic microorganisms that inhabit plant tissues without causing any visible damage to their host. Many endophytes secrete secondary metabolites with biological activity against a broad range of pathogens, making them potential candidates for novel drugs and alternative pesticides of natural origin. We isolated endophytes from wild plants in Israel, focusing on endophytes that secrete secondary metabolites with biological activity. We isolated 302 different endophytes from 30 different wild plants; 70 of them exhibited biological activity against phytopathogens. One biologically active fungal endophyte from the genus Penicillium, isolated from a squill (Urginea maritima) leaf, was further examined. Chloroform-based extraction of its growth medium was similarly active against phytopathogens. High-performance liquid chromatography separation followed by gas chromatography/mass spectrometry analysis revealed a single compound-mycophenolic acid-as the main contributor to the biological activity of the organic extract.

Characterization of the endophytic bacterial community of Bituminaria bituminosa plant grown in vitro and its interaction with the plant extract

INTRODUCTION

Bituminaria bituminosa is a medicinal plant recognized for its phytochemicals, such as furanocoumarins, pterocarpans, and flavonoids. Since the secondary metabolism is influenced by the plant-endophyte interactions, the endophytic bacterial community of B. bituminosa was explored and the possible interactions with the plant were described.

MATERIALS AND METHODS

Different bacterial strains were isolated from different organs of in vitro plants as shoots, roots, and seeds. The bacterial strains were identified and phenotypically characterized for different traits; strains were also exposed to different concentrations of B. bituminosa plant extract showing different susceptibility, probably determined by different secondary metabolites produced by the plant in the different organs (i.e. aerial parts and roots).

RESULTS AND DISCUSSION

Bacterial strains showed different phenotypic characteristics; the 6 detected haplotypes were dominated by a single species related to Stenotrophomonas rhizophila. Endophytes isolated from the aerial parts produced a higher indole-3-acetic acid (IAA) amount than those of the roots, while all strains were unable to produce biosurfactants and antagonistic activity toward the other strains. The research opens new perspectives for future analysis addressed to test the susceptibility of the endophytic bacterial community of B. bituminosa toward the pure compounds extracted from the plants, and to investigate the role of these compounds on the distribution of endophytes within the different plant tissues.

Changes in the Microbial Community in Maize (Zea mays L.) Root Spatial Structure Following Short-Term Nitrogen Application

The beneficial interactions between crop roots and microbiomes play a key role in crop nutrient availability, growth promotion, and disease suppression. Recent research, however, rarely reported the effects of nitrogen (N) application rate on microbial community composition at different spatial structures in the maize root zone. Therefore, one experiment was conducted to examine the influence of three N-application levels (0, 180, and 360 kg N ha^-1) on microbial community composition in three root-associated compartments of maize (bulk soil, rhizoplane, and endosphere). The microbial diversity and community composition differed significantly among the various compartments. The effects of N application on fungal composition decreased in the order bulk soil > rhizosphere > endosphere at different sampling positions. Also, the fungal composition was more sensitive to the N-fertilizer rate in the bulk soil and the rhizosphere than the bacterial community. A total of 14.42, 9.46, and 3.55% of all taxonomic groups were sensitive to N fertilizer, respectively. The keystone species fungal groups were Humicola (bulk soil), Gibberella (rhizosphere soil), and Humicola (endosphere). Together, our results demonstrate that compared with that of the bacterial community, the fungal community composition was more susceptible to different N-application rates. N fertilization affected the distribution of microflora by changing soil physicochemical properties and enzyme activities. There were strong correlations between microbial communities in maize under the N180 treatment. Moreover, the N180 treatment had the maximum fresh yield and biomass at 64.5 and 24.3 kg·ha^-1, respectively.

Uniting the Role of Endophytic Fungi against Plant Pathogens and Their Interaction

Endophytic fungi are used as the most common microbial biological control agents (MBCAs) against phytopathogens and are ubiquitous in all plant parts. Most of the fungal species have roles against a variety of plant pathogens. Fungal endophytes provide different services to be used as pathogen control agents, using an important aspect in the form of enhanced plant growth and induced systemic resistance, produce a variety of antifungal secondary metabolites (lipopeptides, antibiotics and enzymes) through colonization, and compete with other pathogenic microorganisms for growth factors (space and nutrients). The purpose of this review is to highlight the biological control potential of fungal species with antifungal properties against different fungal plant pathogens. We focused on the introduction, biology, isolation, identification of endophytic fungi, and their antifungal activity against fungal plant pathogens. The endosymbionts have developed specific genes that exhibited endophytic behavior and demonstrated defensive responses against pathogens such as antibiosis, parasitism, lytic enzyme and competition, siderophore production, and indirect responses by induced systemic resistance (ISR) in the host plant. Finally, different microscopic detection techniques to study microbial interactions (endophytic and pathogenic fungal interactions) in host plants are briefly discussed.

Antifungal effects and biocontrol potential of lipopeptide-producing Streptomyces against banana Fusarium wilt fungus Fusarium oxysporum f. sp. cubense

Fusarium wilt of banana (FWB), caused by Fusarium oxysporum f. sp. cubense (Foc), especially tropical race 4 (TR4), presents the foremost menace to the global banana production. Extensive efforts have been made to search for efficient biological control agents for disease management. Our previous study showed that Streptomyces sp. XY006 exhibited a strong inhibitory activity against several phytopathogenic fungi, including F. oxysporum. Here, the corresponding antifungal metabolites were purified and determined to be two cyclic lipopeptide homologs, lipopeptin A and lipopeptin B. Combined treatment with lipopeptin complex antagonized Foc TR4 by inhibiting mycelial growth and conidial sporulation, suppressing the synthesis of ergosterol and fatty acids and lowering the production of fusaric acid. Electron microscopy observation showed that lipopeptide treatment induced a severe disruption of the plasma membrane, leading to cell leakage. Lipopeptin A displayed a more pronounced antifungal activity against Foc TR4 than lipopeptin B. In pot experiments, strain XY006 successfully colonized banana plantlets and suppressed the incidence of FWB, with a biocontrol efficacy of up to 87.7%. Additionally, XY006 fermentation culture application improved plant growth parameters and induced peroxidase activity in treated plantlets, suggesting a possible role in induced resistance. Our findings highlight the potential of strain XY006 as a biological agent for FWB, and further research is needed to enhance its efficacy and mode of action in planta.

Endophytic microbiome of Boehmeria nivea and their antagonism against latent fungal pathogens in plants

BACKGROUND

Pathogenic microbes still become obstacles that can reduce the quality of plant growth, including ramie (Boehmeria nivea) plants. The study identified the microbiome and antagonistic interaction of the endophytic community from the B. nivea is necessary to improve the production of the ramie plant, especially ramie stem organs for fiber materials.  RESULTS: Twenty isolates of endophytic microorganisms were obtained from the roots, stems, leaves, and flowers. They were identified using the Internal Transcribed Spacer (ITS) region of ribosomal (rDNA), and its morphotypes obtained 20 isolates, with a composition of 9 species of bacteria and 11 species of fungi. Besides that, the disease observations on ramie stems showed that four species of pathogenic fungi were identified as Fusarium solani isolate 3,248,941, Fusarium solani isolates colpat-359, Fusarium oxysporum isolate N-61-2, Clonostachys rosea strain B3042. The endophytic microorganism of ramie ability was tested to determine their potential to inhibit the growth of the pathogenic fungi based on the in-vivo antagonist test. The isolated bacteria were only able to inhibit the growth of F. solani, with the highest percentage of 54-55%. Three species of endophytic fungi, including Cladosporium tennissimum, Fusarium falciforme, and Penicillium citrinum, showed the best inhibition against the fungal pathogen Fusarium solani with the highest inhibitory presentation of 91-95%. Inhibitory interaction between the endophytic microbes and the ramie pathogens indicated the type of antibiosis, competition, and parasitism.  CONCLUSION: The results of this study succeeded in showing the potential antifungal by endophytic fungi from ramie against the pathogens of the plant itself. P. citrinum isolate MEBP0017 showed the highest inhibition against all the pathogens of the ramie.

Potential Biocontrol Activities of Populus Endophytes against Several Plant Pathogens Using Different Inhibitory Mechanisms

The plant microbiome can be used to bolster plant defense against abiotic and biotic stresses. Some strains of endophytes, the microorganisms within plants, can directly inhibit the growth of plant fungal pathogens. A previously isolated endophyte from wild Populus (poplar), WPB of the species Burkholderia vietnamiensis, had robust in vitro antifungal activity against pathogen strains that are highly virulent and of concern to Pacific Northwest agriculture: Rhizoctonia solani AG-8, Fusarium culmorum 70110023, and Gaemannomyces graminis var. tritici (Ggt) ARS-A1, as well as activity against the oomycete, Pythium ultimum 217. A direct screening method was developed for isolation of additional anti-fungal endophytes from wild poplar extracts. By challenging pathogens directly with dilute extracts, eleven isolates were found to be inhibitory to at least two plant pathogen strains and were therefore chosen for further characterization. Genomic analysis was conducted to determine if these endophyte strains harbored genes known to be involved in antimicrobial activities. The newly isolated Bacillus strains had gene clusters for production of bacillomycin, fengicyn, and bacillibactin, while the gene cluster for the synthesis of sessilin, viscosin and tolaasin were found in the Pseudomonas strains. The biosynthesis gene cluster for occidiofungin (ocf) was present in the Burkholderia vietnamiensis WPB genome, and an ocf deletion mutant lost inhibitory activity against 3 of the 4 pathogens. The new isolates lacked the gene cluster for occidiofungin implying they employ different modes of action. Other symbiotic traits including nitrogen fixation, phosphate solubilization, and the production of auxins and siderophores were investigated. Although it will be necessary to conduct in vivo tests of the candidates with pathogen-infected agricultural crops, the wild poplar tree microbiome may be a rich source of beneficial endophyte strains with potential for biocontrol applications against a variety of pathogens and utilizing varying modes of action.

Effect of Parthenium hysterophorus L. Invasion on Soil Microbial Communities in the Yellow River Delta, China

Parthenium hysterophorus L., as an invasive plant, has negatively impacted the ecosystem functioning and stability of the terrestrial ecosystem in China. However, little information was available for its effects on microorganisms in the Yellow River Delta (YRD), the biggest newly-formed wetland in China. In the present study, high-throughput sequencing technology was used to obtain the bacterial community in soils and roots of different plant species, including P. hysterophorus and some native ones in the YRD. Our results showed that the Proteobacteria, Acidobacteriota, Gemmatimonadota, and Actinobacteriota were dominant in the rhizosphere soils of P. hysterophorus (84.2%) and Setaria viridis (86.47%), and the bulk soils (80.7%). The Proteobacteria and Actinobacteriota were dominant within the root of P. hysterophorus. A total of 2468 bacterial OTUs were obtained from different groups among which 140 were observed in all the groups; 1019 OTUs were shared by P. hysterophorus non-rhizosphere soil bacteria (YNR) P. hysterophorus rhizosphere soil bacteria (YRR) groups. The indexes of the ACE (823.1), Chao1 (823.19), Simpson (0.9971), and Shannon (9.068) were the highest in the YRR groups, showing the greatest bacterial community diversity. Random forest analysis showed that the Methylomirabilota and Dadabacteria (at the phylum level) and the Sphingomonas, and Woeseia (at the genus level) were identified as the main predictors among different groups. The LEfSe results also showed the essential role of the Acidobacteriota in the YRR group. The SourceTracker analysis of the bacterial community of the YRR group was mainly from GBS groups (average 53.14%) and a small part was from YNR groups (average 6.56%), indicating that the P. hysterophorus invasion had a more significant effect on native plants' rhizosphere microorganisms than soil microorganisms. Our observations could provide valuable information for understanding the bacterial diversity and structure of the soil to the invasion of P. hysterophorus.

Genetic Determinants of Antagonistic Interactions and the Response of New Endophytic Strain Serratia quinivorans KP32 to Fungal Phytopathogens

Fungal phytopathogens are challenging to control due to their penetration into plant tissues. Therefore, plant-colonizing bacteria could serve as an excellent weapon in fighting fungal infections. In this study, we aim to determine the biocontrol potential of the new endophytic strain Serratia quinivorans KP32, isolated from the roots of Petroselinum crispum L.; identify the related mechanisms; and understand the basis of its antagonistic interaction with taxonomically diverse fungi at the molecular level. The KP32 strain presented biological activity against Rhizoctonia solani, Colletotrichum dematium, Fusarium avenaceum, and Sclerotinia sclerotiorum, and its ability to inhibit the growth of the phytopathogens was found to be mediated by a broad spectrum of biocontrol features, such as the production of a number of lytic enzymes (amylases, chitinases, and proteases), siderophores, volatile organic and inorganic compounds, salicylic acid, and N-acyl-homoserine lactones. The higher expression of chitinase (chiA) and genes involved in the biosynthesis of hydrogen cyanide (hcnC), enterobactin (entB), and acetoin (budA) in bacteria exposed to fungal filtrates confirmed that these factors could act in combination, leading to a synergistic inhibitory effect of the strain against phytopathogens. We also confirm the active movement, self-aggregation, exopolysaccharide production, and biofilm formation abilities of the KP32 strain, which are essential for effective plant colonization. Its biological activity and colonization potential indicate that KP32 holds tremendous potential for use as an active biopesticide and plant growth promoter.

Cadmium-resistant Streptomyces stimulates phytoextraction potential of Crotalaria juncea L. in cadmium-polluted soil

This work evaluated the competence of two strains of cadmium (Cd)-resistant Streptomyces, namely Streptomyces rapamycinicus K5PN1, an indole-3-acetic acid (IAA) producer, and Streptomyces cyaneus 11-10SHTh, a siderophore producer on promoting Cd phytoextraction by sunn hemp. The results showed that S. rapamycinicus improved root elongation of sunn hemp seedlings under Cd stress conditions. S. rapamycinicus and S. cyaneus were colonized on the root surface of sunn hemp at concentrations of 2.3 × 10⁴ and 6.4 × 10³ CFU g^-1 root fresh weight, respectively. The results of pot-culture experiments showed that S. rapamycinicus increased the root and shoot lengths, and dry biomass of sunn hemp planted in high Cd-contaminated soil. The Cd concentration in the leaves of sunn hemp inoculated with S. cyaneus (73.82 ± 2.20 mg kg^-1 plant dry wt) was higher than that of plants with S. rapamycinicus inoculation and the uninoculated control. The phytoextraction of Cd by sunn hemp was significantly increased with Cd-resistant Streptomyces inoculation. In conclusion, both strains of Cd-resistant Streptomyces had potential on enhancing Cd phytoextraction efficiency of sunn hemp. Our study suggests the application of Cd-resistant Streptomyces can improve Cd phytoextraction by sunn hemp for restoration of Cd-polluted sites.

Evaluation of inorganic phosphate solubilizing efficiency and multiple plant growth promoting properties of endophytic bacteria isolated from root nodules Erythrina brucei

Background

In soils, phosphorous (P) mostly exists in fixed/insoluble form and unavailable for plants use in soil solution, hence it is in scarcity. P is fixed in the form of aluminium, iron and manganese phosphates in acidic soils and calcium phosphate in alkaline soils. Phosphate solubilizing bacteria, the ecological engineers play a pivotal role in the mobilization of fixed forms of P by using different mechanisms. The objectives of this study were to evaluate inorganic phosphate solubilizing efficiency and other multiple plant growth promoting traits of Erythrina brucei root nodule endophytic bacteria and to investigate effects of the selected endophytic bacteria on the growth of wheat plant under phosphorous deficient sand culture at greenhouse conditions.

Results

Among a total of 304 passenger endophytic bacteria, 119 (39%) exhibited tricalcium phosphate (TCP) solubilization; however, none of them were formed clear halos on solid medium supplemented with aluminum phosphate (Al-P) or iron phosphate (Fe–P). Among 119 isolates, 40% exhibited IAA production. The selected nine potential isolates also exhibited potentials of IAA, HCN, NH₃ and/or hydrolytic enzymes production. All the selected isolates were potential solubilizers of the three inorganic phosphates (Al-P, Fe–P and TCP) included in liquid medium. The highest values of solubilized TCP were recorded by isolates AU4 and RG6 (A. soli), 108.96 mg L⁻¹ and 107.48 mg L⁻¹, respectively at sampling day3 and 120.36 mg L⁻¹ and 112.82 mg L⁻¹, respectively at day 6. The highest values of solubilized Al-P and Fe–P were recorded by isolate RG6, 102.14 mg L⁻¹ and 96.07 mg L⁻¹, respectively at sampling days 3 and 6, respectively. The highest IAA, 313.61 µg mL⁻¹ was recorded by isolate DM17 (Bacillus thuringiensis). Inoculation of wheat with AU4, RG6 and RG5 (Acinetobacter soli) increased shoot length by 11, 17.4 and 14.6%, respectively compared to the negative control. Similarly, 76.9, 69.2 and 53.8% increment in shoot dry weight is recorded by inoculation with RG6, AU4 and RG5, respectively. These nine potential endophytic isolates are identified to Gluconobacter cerinus (4), Acinetobacter soli (3), Achromobacter xylosoxidans (1) and Bacillus thuringiensis (1).

Conclusion

AU4, RG6 and RG5 can be potential bio-inoculants candidates as low cost agricultural inputs in acidic and/or alkaline soils for sustainable crop production.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02688-7.

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

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

Deciphering the role of endophytic microbiome in postharvest diseases management of fruits: Opportunity areas in commercial up-scale production

As endophytes are widely distributed in the plant's internal compartments and despite having enormous potential as a biocontrol agent against postharvest diseases of fruits, the fruit-endophyte-pathogen interactions have not been studied detail. Therefore, this review aims to briefly discuss the colonization patterns of endophytes and pathogens in the host tissue, the diversity and distribution patterns of endophytes in the carposphere of fruits, and host-endophyte-pathogen interactions and the molecular mechanism of the endophytic microbiome in postharvest disease management in fruits. Postharvest loss management is one of the major concerns of the current century. It is considered a critical challenge to food security for the rising global population. However, to manage the postharvest loss, still, a large population relies on chemical fungicides, which affect food quality and are hazardous to health and the surrounding environment. However, the scientific community has searched for alternatives for the last two decades. In this context, endophytic microorganisms have emerged as an economical, sustainable, and viable option to manage postharvest pathogens with integral colonization properties and eliciting a defense response against pathogens. This review extensively summarizes recent developments in endophytic interactions with harvested fruits and pathogens-the multiple biocontrol traits of endophytes and colonization and diversity patterns of endophytes. In addition, the upscale commercial production of endophytes for postharvest disease treatment is discussed.

Six novel Micromonospora species associated with the phyllosphere and roots of leguminous plants: Micromonospora alfalfae sp. nov., Micromonospora cabrerizensis sp. nov., Micromonospora foliorum sp. nov., Micromonospora hortensis sp. nov., Micromonospora salmantinae sp. nov., and Micromonospora trifolii sp. nov

Six actinobacterial strains isolated from diverse legume tissues collected in various locations in Spain were characterized to determine their taxonomic status. Using 16S rRNA gene sequencing, the strains were primarily identified as members of the genus Micromonospora with more than 99 % similarity. Digital DNA–DNA hybridization values and average nucleotide identities between the six strains and the nearest type strains confirmed that each strain represented a novel species. Genome sequences were analysed to infer their metabolic profiles, their potential to produce secondary metabolites and plant growth promoting features. Chemotaxonomic and physiological studies were carried out to complete the phenotypic characterization and to distinguish the new Micromonospora species. The genomic and phenotypic characterization of the Micromonospora strains strongly support their classification as representatives of new species with the following names: Micromonospora alfalfae sp. nov., Micromonospora cabrerizensis sp. nov., Micromonospora foliorum sp. nov., Micromonospora hortensis sp. nov., Micromonospora salmantinae sp. nov. and Micromonospora trifolii sp. nov., with the type strains MED01T, LAH09T, PSH25T, NIE111T, PSH03T and NIE79T, respectively.

Characterization of diazotrophic root endophytes in Chinese silvergrass (Miscanthus sinensis)

BACKGROUND

Phytoremediation is a potentially cost-effective way to remediate highly contaminated mine tailing sites. However, nutrient limitations, especially the deficiency of nitrogen (N), can hinder the growth of plants and impair the phytoremediation of mine tailings. Nevertheless, pioneer plants can successfully colonize mine tailings and exhibit potential for tailing phytoremediation. Diazotrophs, especially diazotrophic endophytes, can promote the growth of their host plants. This was tested in a mine-tailing habitat by a combination of field sampling, DNA-stable isotope probing (SIP) analysis, and pot experiments.

RESULTS

Bacteria belonging to the genera Herbaspirillum, Rhizobium, Devosia, Pseudomonas, Microbacterium, and Delftia are crucial endophytes for Chinese silvergrass (Miscanthus sinensis) grown in the tailing, the model pioneer plant selected in this study. Further, DNA-SIP using 15N2 identified Pseudomonas, Rhizobium, and Exiguobacterium as putative diazotrophic endophytes of M. sinensis. Metagenomic-binning suggested that these bacteria contained essential genes for nitrogen fixation and plant growth promotion. Finally, two diazotrophic endophytes Rhizobium sp. G-14 and Pseudomonas sp. Y-5 were isolated from M. sinensis. Inoculation of another pioneer plant in mine tailings, Bidens pilosa, with diazotrophic endophytes resulted in successful plant colonization, significantly increased nitrogen fixation activity, and promotion of plant growth.

CONCLUSIONS

This study indicated that diazotrophic endophytes have the potential to promote the growth of pioneer plant B. pilosa in mine tailings. Video Abstract.

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.

Pseudomonas fitomaticsae sp. nov., isolated at Marimurtra Botanical Garden in Blanes, Catalonia, Spain

In the framework of the research project called fitomatics, we have isolated and characterized a bacterial plant-endophyte from the rhizomes of Iris germanica, hereafter referred to as strain FIT81T. The bacterium is Gram negative, rod-shaped with lophotrichous flagella, and catalase- and oxidase-positive. The optimal growth temperature of strain FIT81T is 28 °C, although it can grow within a temperature range of 4–32 °C. The pH growth tolerance ranges between pH 5 and 10, and it tolerates 4% (w/v) NaCl. A 16S rRNA phylogenetic analysis positioned strain FIT81T within the genus Pseudomonas , and multilocus sequence analysis revealed that Pseudomonas gozinkensis IzPS32dT, Pseudomonas glycinae MS586T, Pseudomonas allokribbensis IzPS23T, 'Pseudomonas kribbensis' 46–2 and Pseudomonas koreensis PS9-14T are the top five most closely related species, which were selected for further genome-to-genome comparisons, as well as for physiological and chemotaxonomic characterization. The genome size of strain FIT81T is 6 492 796 base-pairs long, with 60.6 mol% of G+C content. Average nucleotide identity and digital DNA–DNA hybridization analyses yielded values of 93.6 and 56.1%, respectively, when the FIT81T genome was compared to that of the closest type strain P. gozinkensis IzPS32dT. Taken together, the obtained genomic, physiologic and chemotaxonomic data indicate that strain FIT81T is different from its closest relative species, which lead us to suggest that it is a novel species to be included in the list of type strains with the name Pseudomonas fitomaticsae sp. nov. (FIT81T=CECT 30374T=DSM 112699T).

Endophytes and their potential in biotic stress management and crop production

Biotic stress is caused by harmful microbes that prevent plants from growing normally and also having numerous negative effects on agriculture crops globally. Many biotic factors such as bacteria, fungi, virus, weeds, insects, and nematodes are the major constrains of stress that tends to increase the reactive oxygen species that affect the physiological and molecular functioning of plants and also led to the decrease in crop productivity. Bacterial and fungal endophytes are the solution to overcome the tasks faced with conventional farming, and these are environment friendly microbial commodities that colonize in plant tissues without causing any damage. Endophytes play an important role in host fitness, uptake of nutrients, synthesis of phytohormone and diminish the injury triggered by pathogens via antibiosis, production of lytic enzymes, secondary metabolites, and hormone activation. They are also reported to help plants in coping with biotic stress, improving crops and soil health, respectively. Therefore, usage of endophytes as biofertilizers and biocontrol agent have developed an eco-friendly substitute to destructive chemicals for plant development and also in mitigation of biotic stress. Thus, this review highlighted the potential role of endophytes as biofertilizers, biocontrol agent, and in mitigation of biotic stress for maintenance of plant development and soil health for sustainable agriculture.

The Neuroprotective Potential of Endophytic Fungi and Proposed Molecular Mechanism: A Current Update

Millions of people are affected by neuronal disorders that are emerging as a principal cause of death after cancer. Alzheimer's disease, ataxia, Parkinson's disease, multiple system atrophy, and autism comprise the most common ones, being accompanied by loss of cognitive power, impaired balance, and movement. In past decades, natural polyphenols obtained from different sources including bacteria, fungi, and plants have been utilized in the traditional system of medicine for the treatment of several ailments. Endophytes are one such natural producer of secondary metabolites, namely, polyphenols, which exhibit strong abilities to assist in the management of such affections, through modifying multiple therapeutic targets and weaken their complex physiology. Limited research has been conducted in detail on bioactive compounds present in the endophytic fungi and their neuroprotective effects. Therefore, this review aims to provide an update on scientific evidences related to the pharmacological and clinical potential along with proposed molecular mechanism of action of endophytes for neuronal protection.

Exploring the potential of endophytes and their metabolites for bio-control activity

In the current scenario, extensive use of synthetic chemicals in agriculture is creating notable problems such as disease and pest resistance, residues, yield loss, and soil unproductiveness. These harmful chemicals are eventually reaching our food plate through bioaccumulation and biomagnification in a crop. As a result, beneficial microorganisms are regularly being explored as a safer option in the agriculture sector for their ability to produce valuable bioactive secondary metabolites, particularly for crop protection. Such natural (bio) products are harmless to plants, humans, and the environment. In our quest for the search of the sources of bioactive constituents from the microorganisms, endophytes are the front-runner. They mutually reside inside the plant providing support against phytopathogens by releasing an array of bioactive secondary metabolites building climate reliance of the host plant. The purpose of this review is to examine the biocontrol potential of endophytes against bacterial and fungal pathogens in sustainable agriculture. We also attempt to explain the structure and activity of the secondary metabolites produced by bacterial and fungal endophytes in conjunction with their biocontrol function. Additionally, we address potential future research directions for endophytes as biopesticides.

Distribution pattern of endophytic bacteria and fungi in tea plants

Endophytes are critical for plant growth and health. Tea is an economically important crop in China. However, little is known about the distribution pattern and potential functions of endophytic communities in tea trees. In this study, two genotypes (BXZ and MF) cultivated under the same conditions were selected, and endophytic bacteria and fungi were analyzed through 16S rRNA and ITS high-throughput sequencing technologies, respectively. For endophytic bacteria, root tissues harbored the most diverse endophytes, followed by stems and old leaves, and new leaves possessed the lowest diversity. In contrast, old leave tissues harbored more diverse endophytic fungi than did root and stem tissues. Most of the dominant endophytes showed obvious cultivar and tissue preferences. Tissue type played a more important role in shaping community structure than did cultivar. Nevertheless, some endophytic bacterial groups, which mainly affiliated to Chryseobacterium, Sphingomonas, Rhizobium, Morganella, Methylobacterium and Comamonadaceae, could parasitize different tissues, and the average relative abundance of endophytic bacteria was as high as 72.57%. Some endophytic fungal populations, such as Colletotrichum, Uwebraunia, Cladosporium, and Devriesia, could also parasitize tea, and the relative abundance accounted for approximately 25.70–97.26%. The cooperative relationship between endophytic bacteria and fungi in the new leaves was stronger than that in the old leaves, which can better participate in the metabolism of tea material.

Transformation of arsenic species by diverse endophytic bacteria of rice roots

Rice growing in flooded paddy soil often accumulates considerable levels of inorganic and organic arsenic (As) species, which may cause toxicity to plants and/or pose a risk to human health. The bioavailability and toxicity of As in soil depends on its chemical species, which undergo multiple transformations driven primarily by soil microbes. However, the role of endophytes inside rice roots in As species transformation remains largely unknown. We quantified the abundances of microbial functional genes involved in As transformation in the endosphere and rhizosphere of rice roots growing in three paddy soils in a pot experiment. We also isolated 46 different bacterial endophytes and tested their abilities to transform various As species. The absolute abundances of the arsenate reductase gene arsC and the dissimilatory arsenate reductase gene arrA in the endosphere were comparable to those in the rhizosphere, whereas the absolute abundances of the arsenite methylation gene arsM and arsenite oxidation gene aioA in the endosphere were lower. After normalization based on the bacterial 16S rRNA gene, all four As transformation genes showed higher relative abundances in the endosphere than in the rhizosphere. Consistent with the functional gene data, all of the 30 aerobic endophytic isolates were able to reduce arsenate, but only 3 strains could oxidize arsenite. Among the 16 anaerobic endophytic isolates, 4 strains belonging to Desulfovibrio, Terrisporobacter or Clostridium could methylate arsenite and/or methylarsenite. Six strains of aerobic endophytes could demethylate methylarsenite, among which three strains also could reduce and demethylate methylarsenate. None of the isolates could demethylate dimethylarsenate. These results suggest that diverse endophytes living inside rice roots could participate in As species transformation and affect As accumulation and species distribution in rice plants.

Endophytic Fungi and Secondary Metabolites of Rehmannia Glutinosa Based on Traditional Chinese Medicine Fingerprints

Research on the active components of medicinal plants has always been the focus of research, and research on the active components of medicinal plant endophytic fungi and their secondary metabolites has also attracted widespread attention. Endophytic fungi of medicinal plants are widely distributed and are ubiquitous in various biological groups in nature. Rehmannia glutinosa contains a variety of active ingredients, which are regarded as the top grade of Chinese medicinal materials. It is of certain significance to study endophytic fungi and their metabolites of Rehmannia glutinosa. In this paper, endophytic fungi and their secondary metabolites of Rehmannia glutinosa were studied using fingerprint technology, which initially understands the diversity of endophytic fungi in Rehmannia glutinosa. In this paper, the roots and leaves of Rehmannia glutinosa were used as experimental materials. The fungi were cultured in the medium, the fungi were isolated and purified by the tissue block method, the fungal growth of Rehmannia glutinosa in different parts was determined, and the types of endophytic fungi were identified by microscopic identification and fingerprinting. The isolated strains were tested for biological activity using oryza oryzae spores, and highly active strains were screened. Fermentation products of endophytic fungi were separated and purified by chromatography, and the structure of the compounds was identified by nuclear magnetic resonance spectroscopy. Through the above studies, the population structure of endophytic fungi of Rehmannia glutinosa was determined, 3 highly active strains were found, and the structures of 7 endophytic fungi metabolites were identified, of which 3 were newly discovered compounds.

Effects of single- and mixed-bacterial inoculation on the colonization and assembly of endophytic communities in plant roots

The introduction and inoculation of beneficial bacteria in plants have consistently been considered as one of the most important ways to improve plant health and production. However, the effects of bacterial inoculation on the community assembly and composition of the root endophytic microbiome remain largely unknown. In this study, 55 strains were randomly isolated from tomato roots and then inoculated into wheat seeds singly or in combination. Most of the isolated bacterial strains showed an ability to produce lignocellulose-decomposing enzymes and promote plant growth. The results demonstrated that bacterial inoculation had a significant effect on the wheat root endophytic microbiome. The wheat root samples inoculated with single-bacterial species were significantly separated into two groups (A and B) that had different community structures and compositions. Among these, root endophytic communities for most wheat samples inoculated with a single-bacterial strain (Group A) were predominated by one or several bacterial species, mainly belonging to Enterobacterales. In contrast, only a few of the root samples inoculated with a single-bacterial strain (Group B) harbored a rich bacterial flora with relatively high bacterial diversity. However, wheat roots inoculated with a mixed bacterial complex were colonized by a more diverse and abundant bacterial flora, which was mainly composed of Enterobacterales, Actinomycetales, Bacillales, Pseudomonadales, and Rhizobiales. The results demonstrated that inoculation with bacterial complexes could help plants establish more balanced and beneficial endophytic communities. In most cases, bacterial inoculation does not result in successful colonization by the target bacterium in wheat roots. However, bacterial inoculation consistently had a significant effect on the root microbiome in plants. CAP analysis demonstrated that the variation in wheat root endophytic communities was significantly related to the taxonomic status and lignocellulose decomposition ability of the inoculated bacterial strain (p < 0.05). To reveal the role of lignocellulose degradation in shaping the root endophytic microbiome in wheat, four bacterial strains with different colonization abilities were selected for further transcriptome sequencing analysis. The results showed that, compared with that in the dominant bacterial species Ent_181 and Ent_189 of Group A, the expression of lignocellulose-decomposing enzymes was significantly downregulated in Bac_133 and Bac_71 (p < 0.05). In addition, we found that the dominant bacterial species of the tomato endophytic microbiome were more likely to become dominant populations in the wheat root microbiome. In general, our results demonstrated that lignocellulose-decomposing enzymes played a vital role in the formation of endophytes and their successful colonization of root tissues. This finding establishes a theoretical foundation for the development of broad-spectrum probiotics.

Plant-Endophyte Interaction during Biotic Stress Management

Plants interact with diverse microbial communities and share complex relationships with each other. The intimate association between microbes and their host mutually benefit each other and provide stability against various biotic and abiotic stresses to plants. Endophytes are heterogeneous groups of microbes that live inside the host tissue without showing any apparent sign of infection. However, their functional attributes such as nutrient acquisition, phytohormone modulation, synthesis of bioactive compounds, and antioxidant enzymes of endophytes are similar to the other rhizospheric microorganisms. Nevertheless, their higher colonization efficacy and stability against abiotic stress make them superior to other microorganisms. In recent studies, the potential role of endophytes in bioprospecting has been broadly reported. However, the molecular aspect of host–endophyte interactions is still unclear. In this study, we have briefly discussed the endophyte biology, colonization efficacy and diversity pattern of endophytes. In addition, it also summarizes the molecular aspect of plant–endophyte interaction in biotic stress management.

Overview of biofertilizers in crop production and stress management for sustainable agriculture

With the increase in world population, the demography of humans is estimated to be exceeded and it has become a major challenge to provide an adequate amount of food, feed, and agricultural products majorly in developing countries. The use of chemical fertilizers causes the plant to grow efficiently and rapidly to meet the food demand. The drawbacks of using a higher quantity of chemical or synthetic fertilizers are environmental pollution, persistent changes in the soil ecology, physiochemical composition, decreasing agricultural productivity and cause several health hazards. Climatic factors are responsible for enhancing abiotic stress on crops, resulting in reduced agricultural productivity. There are various types of abiotic and biotic stress factors like soil salinity, drought, wind, improper temperature, heavy metals, waterlogging, and different weeds and phytopathogens like bacteria, viruses, fungi, and nematodes which attack plants, reducing crop productivity and quality. There is a shift toward the use of biofertilizers due to all these facts, which provide nutrition through natural processes like zinc, potassium and phosphorus solubilization, nitrogen fixation, production of hormones, siderophore, various hydrolytic enzymes and protect the plant from different plant pathogens and stress conditions. They provide the nutrition in adequate amount that is sufficient for healthy crop development to fulfill the demand of the increasing population worldwide, eco-friendly and economically convenient. This review will focus on biofertilizers and their mechanisms of action, role in crop productivity and in biotic/abiotic stress tolerance.

Cannabis Seedlings Inherit Seed-Borne Bioactive and Anti-Fungal Endophytic Bacilli

Throughout the hundreds of millions of years of co-evolution, plants and microorganisms have established intricate symbiotic and pathogenic relationships. Microbial communities associated with plants are in constant flux and can ultimately determine whether a plant will successfully reproduce or be destroyed by their environment. Inheritance of beneficial microorganisms is an adaptation plants can use to protect germinating seeds against biotic and abiotic stresses as seedlings develop. The interest in Cannabis as a modern crop requires research into effective biocontrol of common fungal pathogens, an area that has seen little research. This study examines the seed-borne endophytes present across 15 accessions of Cannabis grown to seed across Western Canada. Both hemp and marijuana seedlings inherited a closely related group of bioactive endophytic Bacilli. All Cannabis accessions possessed seed-inherited Paenibacillus mobilis with the capacity to solubilize mineral phosphate. Additionally, seeds were found to carry genera of fungal isolates known to be Cannabis pathogens and post-harvest molds: Alternaria, Penicillium, Cladosporium, Chaetomium, Aspergillus, Rhizopus, and Fusarium. Thirteen seed-borne endophytes showed antibiotic activity against Alternaria, Aspergillus, Penicillium, and Fusarium. This study suggests both fungal pathogens and bacterial endophytes that antagonize them are vectored across generations in Cannabis as they compete over this shared niche.

Endophytic Bacillus subtilis SR22 Triggers Defense Responses in Tomato against Rhizoctonia Root Rot

Rhizoctonia root rot is one of the most destructive diseases of tomato and other crops. The biocontrol of plant diseases using endophytic bacteria has gained significant attention due to their distinct advantages compared with the free-living ones, as well as their new unexplored and unique properties. Endophytic Bacillus subtilis SR22 represents a promising and more effective biocontrol and growth-promoting agent for tomato plants than the free-living agents, being an ecofriendly and sustainable tool in modern agriculture. In this study, the direct antagonistic activity of B. subtilis SR22 was investigated against Rhizoctonia solani in vitro. The biocontrol activity of B. subtilis SR22 against Rhizoctonia root rot of tomato was also investigated. Effects on the level of the transcriptional expression of defense-related genes, biochemical responses, and the vegetative growth of tomato plants were also studied. The dual culture test showed 51% inhibition in the mycelial growth of R. solani due to B. subtilis SR22, indicating its potent antagonistic behavior. Using a GC-MS analysis, twenty bioactive compounds were detected to be produced by B. subtilis SR22, including chlorogenic acid, pyrrolo [1,2-a]pyrazine-1,4-dione, hexahydro, propyl thioglycolic acid, phthalic acid, and 2,3-butanediol. Under greenhouse conditions, the application of B. subtilis SR22 led to a reduction (up to 51%) in Rhizoctonia root rot of tomato. Furthermore, an upregulation in the expression of the responsive factor JERF3 (10.9-fold) and the defense-related genes POD (9.1-fold) and PR1 (4.5-fold) in tomato plants was recorded due to the application of B. subtilis SR22. In addition, this treatment enhanced the total phenolic content (76.8%) and activity of the antioxidant enzymes POD (56%) and PPO (29.2%) in tomato roots, indicating its resistance-inducing effect on tomato plants. Moreover, this treatment enhanced most of the evaluated growth parameters in tomato plants (up to 35%). We can conclude that B. subtilis SR22 is a promising biocontrol agent and growth promoter in tomato plants against Rhizoctonia root rot. An evaluation of the formulation and field application of this bio-agent is necessary in future studies.

Bioactive potentiality of secondary metabolites from endophytic bacteria against SARS-COV-2: An in-silico approach

Five endophytic bacterial isolates were studied to identify morphologically and biochemically, according to established protocols and further confirmed by 16S rDNA Sanger sequencing, as Priestia megaterium, Staphylococcus caprae, Neobacillus drentensis, Micrococcus yunnanensis, and Sphingomonas paucimobiliz, which were then tested for phytohormone, ammonia, and hydrolytic enzyme production. Antioxidant compounds total phenolic content (TPC), and total flavonoid content (TFC) were assessed by using bacterial crude extracts obtained from 24-hour shake-flask culture. Phylogenetic tree analysis of those identified isolates shared sequence similarities with the members of Bacillus, Micrococcus, Staphylococcus, and Pseudomonas species, and after GenBank submission, accession numbers for the nucleotide sequences were found to be MW494406, MW494408, MW494401, MW494402, and MZ021340, respectively. In silico analysis was performed to identify their bioactive genes and compounds in the context of bioactive secondary metabolite production with medicinal value, where nine significant bioactive compounds according to six different types of bioactive secondary metabolites were identified, and their structures, gene associations, and protein-protein networks were analyzed by different computational tools and servers, which were reported earlier with their antimicrobial, anti-infective, antioxidant, and anti-cancer capabilities. These compounds were then docked to the 3-chymotrypsin-like protease (3CLpro) of the novel SARS-COV-2. Docking scores were then compared with 3CLpro reference inhibitor (lopinavir), and docked compounds were further subjected to ADMET and drug-likeness analyses. Ligand-protein interactions showed that two compounds (microansamycin and aureusimine) interacted favorably with coronavirus 3CLpro. Besides, in silico analysis, we also performed NMR for metabolite detection whereas three metabolites (microansamycin, aureusimine, and stenothricin) were confirmed from the 1H NMR profiles. As a consequence, the metabolites found from NMR data aligned with our in-silico analysis that carries a significant outcome of this research. Finally, Endophytic bacteria collected from medicinal plants can provide new leading bioactive compounds against target proteins of SARS-COV-2, which could be an effective approach to accelerate drug innovation and development.

Microbial Metabolites Beneficial to Plant Hosts Across Ecosystems

Plants are intimately connected with their associated microorganisms. Chemical interactions via natural products between plants and their microbial symbionts form an important aspect in host health and development, both in aquatic and terrestrial ecosystems. These interactions range from negative to beneficial for microbial symbionts as well as their hosts. Symbiotic microbes synchronize their metabolism with their hosts, thus suggesting a possible coevolution among them. Metabolites, synthesized from plants and microbes due to their association and coaction, supplement the already present metabolites, thus promoting plant growth, maintaining physiological status, and countering various biotic and abiotic stress factors. However, environmental changes, such as pollution and temperature variations, as well as anthropogenic-induced monoculture settings, have a significant influence on plant-associated microbial community and its interaction with the host. In this review, we put the prominent microbial metabolites participating in plant-microbe interactions in the natural terrestrial and aquatic ecosystems in a single perspective and have discussed commonalities and differences in these interactions for adaptation to surrounding environment and how environmental changes can alter the same. We also present the status and further possibilities of employing chemical interactions for environment remediation. Our review thus underlines the importance of ecosystem-driven functional adaptations of plant-microbe interactions in natural and anthropogenically influenced ecosystems and their possible applications.

Current Techniques to Study Beneficial Plant-Microbe Interactions

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

Exploration of plant growth-promoting endophytic bacteria from Pisum sativum and Cicer arietinum from South-West Haryana

In the present study, nonrhizobial endophytes were isolated from Pisum sativum and Cicer arietinum from Haryana, India. A total of 355 bacterial endophytes were screened for plant growth promoting traits. Out of all, 96 bacterial endophytes were selected based on morphological characters and multi-PGP traits, and their diversity analyzed by amplified ribosomal DNA restriction analysis. Based on their ARDRA profile, the 25 representative isolates (12 from P. sativum and 13 from C. arietinum), were selected and identified by 16S ribosomal DNA sequencing. Genetic relatedness based on BLAST analysis revealed the similarity of these isolates with members of three prominent phyla, that is, Proteobacteria, Firmicutes, and Actinobacteria. The dominant cluster, Firmicutes, constituted 60% of the isolates, assigned to four different genera, Bacillus, Staphylococcus, Ornithinibacillus, and Lysinibacillus. Phylum α-proteobacteria included two genera, namely Paenochrobactrum and Ochrobactrum and three genera in phylum γ-proteobacteria, namely Pseudomonas, Pantoea and Proteus. The phylum Actinobacteria was constituted of two genera, Microbacterium and Arthrobacter. Bacillus zhangzhouensis, Bacillus safensis, Arthrobacter enclensis from P. sativum and Bacillus haynesii, Paenochrobactrum sp. from C. arietinum are documented as plant growth promoting endophytic bacteria for the first time in the present study. The in vitro and in vivo assessment based on bonitur score revealed that the endophytic isolates Bacillus mojavensis PRN2, Pseudomonas chlororaphis PHN9, B. safensis PRER2, Pseudomonas sp. RCP1, Pseudomonas lini PRN1 and B. haynensii RCP3 from P. sativum and C. arietinum significantly enhanced the plant growth parameters. Therefore, these potential isolates can be further harnessed for preparation of bioformulations to enhance sustainable agriculture.

Analysis of Microbial Community, Volatile Flavor Compounds, and Flavor of Cigar Tobacco Leaves From Different Regions

Despite the booming international trade in cigar tobacco leaves (CTLs), the main characteristics of tobacco leaves from different producing areas are rarely reported. This study aimed to characterize the microbial community, volatile flavor compounds (VFCs), and flavor of CTLs from four famous cigar-producing areas, including Dominica, Brazil, Indonesia, and China. High-throughput sequencing results showed that the dominant genera in CTLs were Staphylococcus, Pseudomonas, Aspergillus, Sampaiozyma, and Alternaria. Sensory analysis revealed that Indonesian and Chinese CTLs were characterized by leathery, peppery, and baked aroma. Brazilian CTLs were dominated by caramel and herb aroma. Dominican CTLs had aromas of milk, fruity, sour, cream, flower, nutty, and honey. Supplemented with the determination of volatile flavor compounds (VFCs), the flavor of CTLs could be scientifically quantified. Most of these VFCs were aldehydes and ketones, and 20 VFCs showed significant differences in CTLs from different regions. The microbial community, VFCs, and flavor of CTLs vary widely due to geographic differences. Network analysis revealed the microbial community was closely related to most VFCs, but the relationships between the fungal community and VFCs were less than the bacterial community, and most of them were negative. Furthermore, it also found that the bacterial community had a greater contribution to the flavor of CTLs than the fungal community. This study obtained essential information on CTLs, which laid a foundation for deeply excavating the relationship between microbes and VFCs and flavor, and establishing a tobacco information database.

Authentication of putative competitive bacterial endophytes of rice by re-isolation and DNA fingerprinting assay

AIM

The plant-growth-promoting putative competitive endophytes offer significant benefits to sustainable agriculture. The unworthy opportunistic and passenger endophytes are inevitable during the isolation of putative competitive endophytes. This study aimed to discriminate the putative competitive endophytes undoubtedly from the opportunistic and passenger endophytes.

METHODS AND RESULTS

The newly-isolated endophytes from field-grown rice were inoculated to 5-days old rice seedlings under gnotobiotic conditions. Re-isolation of the inoculated strains from the root surface, inner tissues of the whole plant, root, and shoot was performed after 5-days. All the re-isolated colonies were compared with native isolate for the homology by BOX-A1R-based repetitive extragenic palindromic-PCR (BOX-PCR) and enterobacterial repetitive intergenic consensus (ERIC-PCR) DNA fingerprints. The results revealed that the putative competitive endophyte (RE25 and RE10) showed positive for re-isolation and BOX and ERIC fingerprints for the whole plant, root, and shoot. The opportunistic (RE27 and RE8) and passenger endophytes (RE44 and RE18) failed in re-isolation either from root or shoot. The epiphytes (ZSB15 and Az204) showed negative for endophytic re-isolation and positive for surface colonization.

CONCLUSION

This modified procedure can discriminate the putative competitive endophytes from others.

SIGNIFICANCE AND IMPACT OF THE STUDY

Eliminating the opportunistic and passenger endophytes and epiphytes early by this method would help develop endophytic inoculants to enhance rice productivity.

Plant growth-promoting characteristics of halotolerant endophytic bacteria isolated from Sporobolus specatus (Vahr) Kunth and Cyperus laevigatus L. of Ethiopian rift valley lakes

Understanding plant microbes' intimate relationship and search for beneficial microbes is a sustainable alternative to improve plant growth and yield under a wide range of biotic and abiotic stress conditions. More than 20% of the total global agricultural land is affected by salinity. High salinity challenges crop plants by affecting several metabolic pathways and decreasing plant growth and yield. Unlike chemical fertilizers and pesticides, endophytic microbes offer an eco-friendly approach to increasing crop yield via various metabolites during salinity stress. The objective of this study was to isolate and characterize endophytic halotolerant bacterial isolates from haloalkaliphytes, investigate their plant growth-promoting (PGP) properties and tolerance for various stress conditions. Sporobolus specatus (Vahr) Kunth and Cyperus laevigatus L. grass samples were collected from the shores of two Ethiopian soda lakes (Lakes Abijata, and Chitu, respectively). A total of 167 halotolerant endophytic bacterial isolates, that clustered into 21 ARDRA (Amplified ribosomal DNA restriction analysis) groups, affiliated to members of 11 bacterial genera, namely Halomonas, Agrobacterium, Exiguobacterium, Jonesia, Stenotrophomonas, Pseudomonas, Alishewanella, Kosakonia, Bacillus, Paracoccus and Pannonibacter, were identified based on 16S rRNA sequencing. Most of the strains were able to produce IAA (indole-3-acetic acid) and hydrogen cyanide, grow on a nitrogen-free medium and solubilize phosphate. In vitro tolerance tests reveal that isolates were tolerant to: 5.0-15% NaCl, up to 40% PEG 6000, temperatures up to 50 °C, and pH 5-11. These characteristics of the isolates indicate their potential PGP application under various plant stress conditions.

Unraveling Nitrogen Fixing Potential of Endophytic Diazotrophs of Different Saccharum Species for Sustainable Sugarcane Growth

Sugarcane (Saccharum officinarum L.) is one of the world’s highly significant commercial crops. The amounts of synthetic nitrogen (N₂) fertilizer required to grow the sugarcane plant at its initial growth stages are higher, which increases the production costs and adverse environmental consequences globally. To combat this issue, sustainable environmental and economic concerns among researchers are necessary. The endophytic diazotrophs can offer significant amounts of nitrogen to crops through the biological nitrogen fixation mediated nif gene. The nifH gene is the most extensively utilized molecular marker in nature for studying N₂ fixing microbiomes. The present research intended to determine the existence of novel endophytic diazotrophs through culturable and unculturable bacterial communities (EDBCs). The EDBCs of different tissues (root, stem, and leaf) of five sugarcane cultivars (Saccharum officinarum L. cv. Badila, S. barberi Jesw.cv Pansahi, S. robustum, S. spontaneum, and S. sinense Roxb.cv Uba) were isolated and molecularly characterized to evaluate N₂ fixation ability. The diversity of EDBCs was observed based on nifH gene Illumina MiSeq sequencing and a culturable approach. In this study, 319766 operational taxonomic units (OTUs) were identified from 15 samples. The minimum number of OTUs was recorded in leaf tissues of S. robustum and maximum reads in root tissues of S. spontaneum. These data were assessed to ascertain the structure, diversity, abundance, and relationship between the microbial community. A total of 40 bacterial families with 58 genera were detected in different sugarcane species. Bacterial communities exhibited substantially different alpha and beta diversity. In total, 16 out of 20 genera showed potent N₂-fixation in sugarcane and other crops. According to principal component analysis (PCA) and hierarchical clustering (Bray–Curtis dis) evaluation of OTUs, bacterial microbiomes associated with root tissues differed significantly from stem and leaf tissues of sugarcane. Significant differences often were observed in EDBCs among the sugarcane tissues. We tracked and validated the plethora of individual phylum strains and assessed their nitrogenase activity with a culture-dependent technique. The current work illustrated the significant and novel results of many uncharted endophytic microbial communities in different tissues of sugarcane species, which provides an experimental system to evaluate the biological nitrogen fixation (BNF) mechanism in sugarcane. The novel endophytic microbial communities with N₂-fixation ability play a remarkable and promising role in sustainable agriculture production.

Endophytism: A Multidimensional Approach to Plant-Prokaryotic Microbe Interaction

Plant growth and development are positively regulated by the endophytic microbiome via both direct and indirect perspectives. Endophytes use phytohormone production to promote plant health along with other added benefits such as nutrient acquisition, nitrogen fixation, and survival under abiotic and biotic stress conditions. The ability of endophytes to penetrate the plant tissues, reside and interact with the host in multiple ways makes them unique. The common assumption that these endophytes interact with plants in a similar manner as the rhizospheric bacteria is a deterring factor to go deeper into their study, and more focus was on symbiotic associations and plant–pathogen reactions. The current focus has shifted on the complexity of relationships between host plants and their endophytic counterparts. It would be gripping to inspect how endophytes influence host gene expression and can be utilized to climb the ladder of “Sustainable agriculture.” Advancements in various molecular techniques have provided an impetus to elucidate the complexity of endophytic microbiome. The present review is focused on canvassing different aspects concerned with the multidimensional interaction of endophytes with plants along with their application.

Antiobesity, Antihyperglycemic, and Antidepressive Potentiality of Rice Fermented Food Through Modulation of Intestinal Microbiota

The present study has been aimed at evaluating the antiobesity, antihyperglycemic, and antidepressive potentials of Asparagus racemosus starter-based rice fermented foods. High-throughput NGS technology has revealed a number of bacterial genera in the prepared fermented rice, such as Lactobacillus (29.44%), Brevundimonas (16.21%), Stenotrophomonas (6.18%), Pseudomonas (3.11%), Bacillus (2.88%), and others (<2%). Eight-week administration of rice fermented food has increased food intake, whole-body weight, organ weight, different fat masses, serum lipid profiles, and histology of liver and adipose tissues in HFD-induced obese mice. In addition, upregulation of fatty acid oxidation and downregulation of adipocytogenesis- and lypogenesis-related genes along with the expression of their regulatory nuclear factors such as PPARα, PPARγ, PPARδ, and SREBP-1c have also been noted. Moreover, fermented food decreases fasting blood glucose level and improves glucose and insulin tolerance as well as the expression of GLUT4 receptor. Antiobesity and antihyperglycemic effects are also supported by the changes in insulin, leptin, and adiponectin hormone levels. The real-time polymerase chain reaction (RT-PCR) and denaturing gradient gel electrophoresis (DGGE) analyses have clearly demonstrated the intense colonization of Bacteroides, Lactobacillus, and Bifidobacterium, as well as the suppressed growth rate of γ- and δ-Proteobacteria and Firmicutes in the gut after fermented food intake. In the intestine, the latter group of microorganisms possibly modulate short-chain fatty acid (SCFA) levels such as acetate, butyrate, and propionate more than twofold. The impairment of memory-learning and anxiety-like obesity-associated cognitive phenotypes is mitigated significantly (p < 0.01) by fermented food as well. Thus, the formulated fermented food could be used as a natural therapeutic to alleviate obesity and its associated psychological and pathophysiological ailments.

The Biodiversity of Grapevine Bacterial Endophytes of Vitis amurensis Rupr

In this paper, the composition profiles of bacterial endophytes in wild-growing Amur grape Vitis amurensis Rupr. grown in the south of the Russian Far East were analyzed using both a cultivation-dependent (sowing bacteria) and a cultivation-independent (next generation sequencing, NGS) approach. Both methods revealed the prevalent endophytes in V. amurensis were represented by Gammaproteobacteria—40.3–75.8%, Alphaproteobacteria—8.6–18.7%, Actinobacteria—9.2–15.4%, and Bacilli—6.1–6.6%. NGS also showed a large proportion of Bacteroidia (12.2%) and a small proportion of other classes (less than 5.7%). In general, NGS revealed a greater variety of classes and genera in the endophytic bacterial community due to a high number of reads (574,207) in comparison with the number of colonies (933) obtained after the cultivation-dependent method. A comparative analysis performed in this study showed that both wild grape V. amurensis from Russia and domesticated cultivars of V. vinifera from Germany and California (USA) exhibit the same basic composition of endophytic bacteria, while the percentages of major taxa and minor taxa showed some differences depending on the plant organ, grape individuals, environmental conditions, and sampling time. Furthermore, the obtained data revealed that lower temperatures and increased precipitation favored the number and diversity of endophytic bacteria in the wild Amur grape. Thus, this study firstly described and analyzed the biodiversity of endophytic bacteria in wild grapevine V. amurensis.

Engineered plant control of associative nitrogen fixation

Inoculation of cereals with diazotrophic (N₂-fixing) bacteria offers a sustainable alternative to the application of nitrogen fertilizers in agriculture. While natural diazotrophs have evolved multilayered regulatory mechanisms that couple N₂ fixation with assimilation of the product NH₃ and prevent release to plants, genetic modifications can permit excess production and excretion of NH₃. However, a lack of stringent host-specificity for root colonization by the bacteria would allow growth promotion of target and nontarget plants species alike. Here, we exploit synthetic transkingdom signaling to establish plant host-specific control of the N₂-fixation catalyst nitrogenase in Azorhizobium caulinodans occupying barley roots. This work demonstrates how partner-specific interactions can be established to avoid potential growth promotion of nontarget plants.

Engineering N₂-fixing symbioses between cereals and diazotrophic bacteria represents a promising strategy to sustainably deliver biologically fixed nitrogen (N) in agriculture. We previously developed novel transkingdom signaling between plants and bacteria, through plant production of the bacterial signal rhizopine, allowing control of bacterial gene expression in association with the plant. Here, we have developed both a homozygous rhizopine producing (RhiP) barley line and a hybrid rhizopine uptake system that conveys upon our model bacterium Azorhizobium caulinodans ORS571 (Ac) 10³-fold improved sensitivity for rhizopine perception. Using this improved genetic circuitry, we established tight rhizopine-dependent transcriptional control of the nitrogenase master regulator nifA and the N metabolism σ-factor rpoN, which drove nitrogenase expression and activity in vitro and in situ by bacteria colonizing RhiP barley roots. Although in situ nitrogenase activity was suboptimally effective relative to the wild-type strain, activation was specific to RhiP barley and was not observed on the roots of wild-type plants. This work represents a key milestone toward the development of a synthetic plant-controlled symbiosis in which the bacteria fix N₂ only when in contact with the desired host plant and are prevented from interaction with nontarget plant species.

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.

Improved Growth Performance of Elaeis guineensis Jacq. Through the Applications of Arbuscular Mycorrhizal (AM) Fungi and Endophytic Bacteria

Agrochemical application in the oil palm industry has been estimated to be the largest component amounting to almost 30% of the operational costing. Therefore, there is a huge pressure in the oil palm cultivation to exercise sustainable practices, preferably using cheaper alternatives such as biofertilizers and organic substrates. This study investigates the effect of arbuscular mycorrhizal (AM) fungi and endophytic bacteria applied independently and in combination on oil palm growth and nutrient uptake. Greenhouse and field studies were conducted with plant responses assessed through growth parameters. Greenhouse plants were significantly stimulated by AM fungi, Rhizophagus intraradices UT126 (M1), through single microbe application. An increase of 36% in leaf area was noted in M1 plants while the calcium (Ca) uptake in leaves increased by 11%. There was no significant improvement in overall nitrogen, phosphate, and potassium (NPK) uptake but a significant improvement of Ca measurement in greenhouse and field was observed in the leaves. The predicted synergism between mixed inocula of M1 and R. clarus BR152B (M2) on vegetative growth was not observed, suggesting the probability of interspecies incompatibility that requires further investigation. Growth readings in plants treated with the combination of M1-M2 and Pseudomonas aeruginosa UPMP3 in the field were highest without a significant difference as compared to single application of M1. The difference in readings for field and greenhouse may have been influenced by other external factors such as soil type, rhizospheric microbial community, and climate, and therefore requires further elucidation. These findings suggest R. intraradices UT126 as a promising biostimulant candidate in sustainable agronomic practices especially in the nursery practices.