Functions, mechanisms and regulation of endophytic and epiphytic microbial communities of plants

Low microbial diversity, yeast prevalence, and nematode-trapping fungal presence in fungal colonization and leaf microbiome of Serjania erecta

Medicinal plant microbiomes undergo selection due to secondary metabolite presence. Resident endophytic/epiphytic microorganisms directly influence plant's bioactive compound synthesis. Hypothesizing low microbial diversity in Serjania erecta leaves, we assessed leaf colonization by epiphytic and endophytic fungi. Given its traditional medicinal importance, we estimated diversity in the endophytic fungal microbiome. Analyses included scanning electron microscopy (SEM), isolation of cultivable species, and metagenomics. Epiphytic fungi interacted with S. erecta leaf tissues, horizontally transmitted via stomata/trichome bases, expressing traits for nematode trapping. Cultivable endophytic fungi, known for phytopathogenic habits, didn't induce dysbiosis symptoms. This study confirms low leaf microbiome diversity in S. erecta, with a tendency towards more fungal species, likely due to antibacterial secondary metabolite selection. The classification of Halicephalobus sp. sequence corroborated the presence of nematode eggs on the epidermal surface of S. erecta by SEM. In addition, we confirmed the presence of methanogenic archaea and a considerable number of methanotrophs of the genus Methylobacterium. The metagenomic study of endophytic fungi highlighted plant growth-promoting yeasts, mainly Malassezia, Leucosporidium, Meyerozyma, and Hannaella. Studying endophytic fungi and S. erecta microbiomes can elucidate their impact on beneficial bioactive compound production, on the other hand, it is possible that the bioactive compounds produced by this plant can recruit specific microorganisms, impacting the biological system.

Kiwifruit resistance to gray mold is enhanced by yeast-induced modulation of the endophytic microbiome

The influence of endophytic microbial community on plant growth and disease resistance is of considerable importance. Prior research indicates that pre-treatment of kiwifruit with the biocontrol yeast Debaryomyces hansenii suppresses gray mold disease induced by Botrytis cinerea. However, the specific underlying mechanisms remain unclear. In this study, Metagenomic sequencing was utilized to analyze the composition of the endophytic microbiome of kiwifruit under three distinct conditions: the healthy state, kiwifruit inoculated with B. cinerea, and kiwifruit treated with D. hansenii prior to inoculation with B. cinerea. Results revealed a dominance of Proteobacteria in all treatment groups, accompanied by a notable increase in the relative abundance of Actinobacteria and Firmicutes. Ascomycota emerged as the major dominant group within the fungal community. Treatment with D. hansenii induced significant alterations in microbial community diversity, specifically enhancing the relative abundance of yeast and exerting an inhibitory effect on B. cinerea. The introduction of D. hansenii also enriched genes associated with energy metabolism and signal transduction, positively influencing the overall structure and function of the microbial community. Our findings highlight the potential of D. hansenii to modulate microbial dynamics, inhibit pathogenic organisms, and positively influence functional attributes of the microbial community.

Metabarcoding analysis reveals an interaction among distinct groups of bacteria associated with three different varietals of grapes used for wine production in Brazil

Grapes are globally popular with wine production being one of the most well-known uses of grapes worldwide. Brazil has a growing wine industry, and the Serra Gaúcha region is a significant contributor to the country's wine production. Nonetheless, other states are increasing their relevance in this segment. Environmental factors and the soil microbiome (bacteria and fungi) heavily influence grape quality, shaping the crucial "terroir" for wines. Here, soil quality was assessed through nutrient analysis and bacteria microbial diversity, which could significantly impact grape health and final wine attributes. Soil samples from São Paulo's vineyards, focusing on Syrah, Malbec, and Cabernet Sauvignon, underwent chemical and microbial analysis via 16S rRNA metabarcoding and highlighted significant differences in soil composition between vineyards. Statistical analyses including PCA and CAP showcased region-based separation and intricate associations between microbiota, region, and grape variety. Correlation analysis pinpointed microbial genera linked to specific soil nutrients. Random Forest analysis identified abundant bacterial genera per grape variety and the Network analysis revealed varied co-occurrence patterns, with Cabernet Sauvignon exhibiting complex microbial interactions. This study unveils complex relationships between soil microbiota, nutrients, and diverse grape varieties in distinct vineyard regions. Understanding how these specific microorganisms are associated with grapes can improve vineyard management, grape quality, and wine production. It can also potentially optimize soil health, bolster grapevine resilience against pests and diseases, and contribute to the unique character of wines known as terroir.

Highly diverse microbial community of regenerated seedlings reveals the high capacity of the bulb in lily, Lilium brownii

Lily bulbs, which have both nutrient storage and reproductive functions, are a representative group of plants for studying the maintenance and transfer of plant-associated microbiomes. In this study, a comparison of the microbial composition of bulbs and their regenerated seedlings cultured under aseptic conditions, as well as subcultured seedlings that succeeded five times, was examined by amplicon sequencing. A total of 62 bacterial taxa and 56 fungal taxa were found to be transferred to the 5th generation in seedlings, which are the core microbiome of lily. After the regeneration of seedlings from bulbs, there was a significant increase in the number of detectable microbial species, and after 1, 3, and 5 successive generations, there was a decrease in the number of detectable species. Interestingly, some "new" microorganisms appeared in each generation of samples; for instance, 167 and 168 bacterial operational taxonomic units (OTUs) in the 3rd and 5th generations of seedlings that were not detected in either bulbs or seedlings of the previous two generations. These results suggest that bulbs can maintain a high diversity of microorganisms, including some with ultra-low abundance, and have a high transfer capacity to tuck shoots through continuous subculture. The diversity and maintenance of the microbiome can provide the necessary microbial reservoir support for regenerating seedlings. This habit of maintaining low abundance and high diversity may be biologically and ecologically critical for maintaining microbiome stability and function due to the sequestration nature of the plant.

Unveiling growth-promoting attributes of peanut root endophyte Micromonospora sp

In this study, 20 endophytic actinobacteria were isolated from different parts of peanut plants growing in cropland with low and high salt in West Bengal, India. The endophytes underwent a rigorous morphological, biochemical, and genetic screening process to evaluate their effectiveness in enhancing plant growth. About 20% of these isolates were identified as potential plant growth-promoting endophytic actinobacteria, which showed high 16S rRNA gene sequence similarity (up to 99-100%) with different species of Micromonospora. Among these isolates, Micromonospora sp. ASENR15 produced the highest levels of indole acetic acid (IAA) and gibberellic acid (GA), while Micromonospora sp. ASENL2, Micromonospora sp. ANENR4, and Micromonospora sp. ASENR12 produced the highest level of siderophore. Among these leaf and root endophytic Micromonospora, strain ANENR4 was tested for its plant growth-promoting attributes. ANENR4 can be transmitted into the roots of a healthy peanut plant, enhances growth, and colonize the roots in abundance, suggesting the potential agricultural significance of the strain. Moreover, the study is the first report of endophytic Micromonospora in peanuts with PGP effects. The outcomes of this study open avenues for further research on harnessing the benefits of this endophytic Micromonospora for optimizing plant growth in agriculture.

Isolation and Identification of Endophytic Bacteria Bacillus sp. ME9 That Exhibits Biocontrol Activity against Xanthomonas phaseoli pv. manihotis

In recent years, the bacterial blight of cassava has caused substantial economic losses to the Chinese cassava industry. Chemical control methods have become the primary approach to control this disease; however, their widespread usage and harmful residues have raised concerns about environmental pollution. In order to avoid this, it is urgent to seek a green ecological method to prevent and control it. Biological control through the utilization of microorganisms not only effectively inhibits the disease, but also gives consideration to environmental friendliness. Therefore, investigating an endophytic biological control method for cassava bacterial blight is of great importance. In this study, cassava leaf tissues were used as test specimens in order to isolate endophytic bacteria by using dilution and separation methods. Bacillus ME9, derived from cassava endophytic bacteria, exhibits good antagonism against a diverse range of pathogens, including Xpm11. Its genome consists of a series of genes encoding antibacterial lipopeptides, which may be directly related to its antibacterial capabilities. Furthermore, inoculation resulted in a substantial change in the diversity of the endophytic bacterial community, characterized by improved diversity, and displayed an obvious inhibition of pathogenic bacterial growth, demonstrating successful colonization within plants. The results laid a foundation and provided theoretical support for the development and utilization of cassava endophytic bacterial diversity and endogenous disease control strategies.

Kocuria flava, a Bacterial Endophyte of the Marine Macroalga Bryopsis plumosa, Emits 8-Nonenoic Acid Which Inhibits the Aquaculture Pathogen Saprolegnia parasitica

Secondary metabolites-organic compounds that are often bioactive-produced by endophytes, among others, provide a selective advantage by increasing the organism's survivability. Secondary metabolites mediate the symbiotic relationship between endophytes and their host, potentially providing the host with tolerance to, and protection against biotic and abiotic stressors. Secondary metabolites can be secreted as a dissolved substance or emitted as a volatile. In a previous study, we isolated bioactive endophytes from several macroalgae and tested them in vitro for their ability to inhibit major disease-causing pathogens of aquatic animals in the aquaculture industry. One endophyte (isolate Abp5, K. flava) inhibited and killed, in vitro, the pathogen Saprolegnia parasitica, an oomycete that causes saprolegniasis-a disease affecting a wide range of aquatic animals. Here, using analytical chemistry tools, we found that Abp5 produces the volatile organic compound (VOC) 8-nonenoic acid. Once we confirmed the production of this compound by the endophyte, we tested the compound's ability to treat S. parasitica in in vitro and in vivo bioassays. In the latter, we found that 5 mg/L of the compound improves the survival of larvae challenged with S. parasitica by 54.5%. Our isolation and characterization of the VOC emitted by the endophytic K. flava establish the groundwork for future studies of endophytic biocontrol agents from macroalgae. Use of this compound could enable managing oomycete agricultural pathogens in general, and S. parasitica in particular, a major causal agent in aquaculture diseases.

Microbial interactions and metabolisms in response to bacterial wilt and black shank pathogens in the tobacco rhizosphere

Background

Tobacco bacterial wilt (TBW) and black shank (TBS) are responsible for substantial economic losses worldwide; however, microbial interactions and metabolisms in response to TBW and TBS pathogens in the tobacco rhizosphere remain unclear.

Methods

We explored and compared the response of rhizosphere microbial communities to these two plant diseases with the incidences in moderate and heavy degrees by sequencing of 16S rRNA gene amplicons and bioinformatics analysis.

Results and discussions

We found that the structure of rhizosphere soil bacterial communities was significantly (p < 0.05) changed from the incidences of TBW and TBS, which also led to decreased Shannon diversity and Pielou evenness. Compared with the healthy group (CK), the OTUs with significantly (p < 0.05) decreased relative abundances were mostly affiliated with Actinobacteria (e.g., Streptomyces and Arthrobacter) in the diseased groups, and the OTUs with significantly (p < 0.05) increased relative abundances were mainly identified as Proteobacteria and Acidobacteria. Also, molecular ecological network analysis showed that the nodes (<467) and links (<641) were decreased in the diseased groups compared with the control group (572; 1056), suggesting that both TBW and TBS weakened bacterial interactions. In addition, the predictive functional analysis indicated that the relative abundance of genes related to the biosynthesis of antibiotics (e.g., ansamycins and streptomycin) was significantly (p < 0.05) decreased due to incidences of TBW and TBS, and antimicrobial tests showed that some Actinobacteria strains (e.g., Streptomyces) and their secreted antibiotics (e.g., streptomycin) could effectively inhibit the growth of these two pathogens.

Special Issue “Microbial Endophytes: Functional Biology and Applications”: Editorial

Plants harbour various microbial communities, including bacteria, fungi, actinomycetes, and nematodes, inside or outside their tissues [...]

Ecological linkages between biotechnologically relevant autochthonous microorganisms and phenolic compounds in sugar apple fruit (Annona squamosa L.)

Our study investigated the potential of Annona squamosa (L.) fruit as a reservoir of yeasts and lactic acid bacteria having biotechnological implications, and phenolics capable of modifying the ecology of microbial consortia. Only a single species of lactic acid bacteria (Enterococcus faecalis) was identified, while Annona fruit seemed to be a preferred niche for yeasts (Saccharomyces cerevisiae, Hanseniaspora uvarum), which were differentially distributed in the fruit. In order to identify ecological implications for inherent phenolics, the antimicrobial potential of water- and methanol/water-soluble extracts from peel and pulp was studied. Pulp extracts did not show any antimicrobial activity against the microbial indicators, while some Gram-positive bacteria (Staphylococcus aureus, Staphylococcus saprophyticus, Listeria monocytogenes, Bacillus megaterium) were susceptible to peel extracts. Among lactic acid bacteria used as indicators, only Lactococcus lactis and Weissella cibaria were inhibited. The chemical profiling of methanol/water-soluble phenolics from Annona peel reported a full panel of 41 phenolics, mainly procyanidins and catechin derivatives. The antimicrobial activity was associated to specific compounds (procyanidin dimer type B [isomer 1], rutin [isomer 2], catechin diglucopyranoside), in addition to unidentified catechin derivatives. E. faecalis, which was detected in the epiphytic microbiota, was well adapted to the phenolics from the peel. Peel phenolics had a growth-promoting effect toward the autochthonous yeasts S. cerevisiae and H. uvarum.

Diaporthe atlantica enhances tomato drought tolerance by improving photosynthesis, nutrient uptake and enzymatic antioxidant response

Functional symbiosis with fungal endophytes can help plants adapt to environmental stress. Diaporthe atlantica is one of the most abundant fungal taxa associated with roots of Festuca rubra subsp. pruinosa, a grass growing in sea cliffs. This study aimed to investigate the ability of a strain of this fungus to ameliorate the impact of drought stress on tomato plants. In a greenhouse experiment, tomato plants were inoculated with Diaporthe atlantica strain EB4 and exposed to two alternative water regimes: well-watered and drought stress. Several physiological and biochemical plant parameters were evaluated. Inoculation with Diaporthe promoted plant growth in both water treatments. A significant interactive effect of Diaporthe-inoculation and water-regime showed that symbiotic plants had higher photosynthetic capacity, water-use efficiency, nutrient uptake (N, P, K, Fe and Zn), and proline content under drought stress, but not under well-watered conditions. In addition, Diaporthe improved the enzymatic antioxidant response of plants under drought, through an induced mechanism, in which catalase activity was modulated and conferred protection against reactive oxygen species generation during stress. The results support that Diaporthe atlantica plays a positive role in the modulation of tomato plant responses to drought stress by combining various processes such as improving photosynthetic capacity, nutrient uptake, enzymatic antioxidant response and osmo-protectant accumulation. Thus, drought stress in tomato can be enhanced with symbiotic fungi.

Microbiome analysis revealed distinct microbial communities occupying different sized nodules in field-grown peanut

Legume nodulation is the powerhouse of biological nitrogen fixation (BNF) where host-specific rhizobia dominate the nodule microbiome. However, other rhizobial or non-rhizobial inhabitants can also colonize legume nodules, and it is unclear how these bacteria interact, compete, or combinedly function in the nodule microbiome. Under such context, to test this hypothesis, we conducted 16S-rRNA based nodule microbiome sequencing to characterize microbial communities in two distinct sized nodules from field-grown peanuts inoculated with a commercial inoculum. We found that microbial communities diverged drastically in the two types of peanut nodules (big and small). Core microbial analysis revealed that the big nodules were inhabited by Bradyrhizobium, which dominated composition (>99%) throughout the plant life cycle. Surprisingly, we observed that in addition to Bradyrhizobium, the small nodules harbored a diverse set of bacteria (~31%) that were not present in big nodules. Notably, these initially less dominant bacteria gradually dominated in small nodules during the later plant growth phases, which suggested that native microbial communities competed with the commercial inoculum in the small nodules only. Conversely, negligible or no competition was observed in the big nodules. Based on the prediction of KEGG pathway analysis for N and P cycling genes and the presence of diverse genera in the small nodules, we foresee great potential of future studies of these microbial communities which may be crucial for peanut growth and development and/or protecting host plants from various biotic and abiotic stresses.

Endophytic Beauveria bassiana Induces Oxidative Stress and Enhances the Growth of Fusarium oxysporum-Infected Tomato Plants

Studying the mechanisms through which endophytic fungi confer protection to host plants against parasites will contribute toward elucidating the endophytic fungi−plant−pathogen relationship. In this study, we evaluated the effects of endophytic Beauveria bassiana on the antioxidant activity, oxidative stress, and growth of tomatoes infected with the fusarium wilt pathogen, Fusarium oxysporum f. sp. lycopersici (FOL). Tomato seedlings were inoculated with B. bassiana conidia and then contaminated with FOL experimentally. Four treatments (Control [T1], FOL only [T2], B. bassiana only [T3], and B. bassiana and FOL [T4]) were assessed. The plants from the B. bassiana and FOL treatment (T4) were significantly taller (DF = 3, 56; p < 0.001) and produced more leaves and aerial part biomass than those treated with only FOL (T2). Remarkably, plants in the two treatments with FOL (T2 and T4) had the lowest antioxidant activities; meanwhile, plants from the FOL treatment (T2) had the lowest ROS (superoxide and hydroxyl radicals) contents. Broadly, strong positive correlations between ROS and all the plant growth parameters were recorded in this study. While the current results revealed that the endophytic entomopathogen B. bassiana enhanced antioxidant capacity in plants, it did not improve the antioxidant capacity of F. oxysporum-infected plants. It is possible that the pathogenic FOL employed a hiding strategy to evade the host immune response and the antagonistic actions of endophytic B. bassiana. In conclusion, B. bassiana inoculum enhanced the growth of tomatoes infected with FOL, induced higher oxidative stress in both F. oxysporum-infected and -uninfected tomatoes, and improved antioxidant activities in plants inoculated with B. bassiana only.

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.

Changes in Composition and Diversity of Epiphytic Microorganisms on Field Pea Seeds, Partial Crop Peas, and Whole Crop Peas during Maturation and Ensiling with or without Lactic Acid Bacteria Inoculant

The present study was conducted under the hypothesis that, in field peas, type of plant material, stage of maturity, ensiling, silage additive, and aerobic stress affect the composition and diversity of epiphytic microbial communities. Epiphytic microbial composition and diversity of pea seeds, partial crop peas, and whole crop peas was analyzed at different stages of late maturity, before and after ensiling, and with or without the use of lactic acid bacteria (LAB) as inoculant. Suitable combinations among pea crop variants, maturity stages, and inoculant use for the production of stable silages with sufficient aerobic stability after opening and during feed-out were identified. Genomic DNA was extracted, and 16S and 18S rRNA gene amplicons were sequenced. To assess the quality of the various silages, nutrient concentration, pH value, concentration of lactic acid, short chain fatty acids, and alcohols, and aerobic stability were determined. Pea seeds were barely colonized by epiphytic microorganisms. In partial and whole crop peas, composition and α-diversity (Shannon index) of bacterial communities did not differ between crop variants but differed among maturity stages. Epiphytic eukaryotes were rarely found on partial and whole crop peas. Bacterial composition and α-diversity were affected by ensiling and subsequent aerobic storage. In partial and whole crop peas, plant maturation caused an increase of the relative abundance of naturally occurring LAB (Weissella, Pediococcus, and Lactobacillus spp.). As a possible result, natural LAB support stable ensiling conditions even without the use of inoculants beginning with a maturity of 78 on the BBCH scale. This corresponded with a dry matter (DM) concentration of 341 and 363 g/kg in partial and whole crop peas, respectively. Addition of LAB inoculants, however, reduced ammonia, acetic acid, and butanol concentrations, and supported aerobic stability. Earlier stages of plant maturity (BBCH 76 and 77, 300 g DM/kg or less) were more prone to microbial spoilage. Stable pea seed silages can be produced at a maturity between BBCH 78 (427 g DM/kg) and 79 (549 g DM/kg), but they undoubtedly require LAB inoculation or application of other ensiling agents. IMPORTANCE Field peas are important protein suppliers for human and animal nutrition. They can be grown in many areas of the world, which may reduce imports of protein plants and has beneficial economic and ecological effects. Ensiling is a method of preserving feed that can be implemented easily and cost-effectively at the farm. Peas harvested as seeds, partial crop, or whole crop at different maturities enable a wide range of applications. The study characterized epiphytic microbial communities on peas in terms of composition and diversity depending on the maturity of the plants and feed conservation by ensiling as they play an essential role for the production of silages. Even if this study did not consider year, site, or cultivar effects, the results would show which part of the plant is probably well suited for the production of stable and high-quality silages and at which stage of maturity.

Phytostimulants in sustainable agriculture

The consistent use of synthetic fertilizers and chemicals in traditional agriculture has not only compromised the fragile agroecosystems but has also adversely affected human, aquatic, and terrestrial life. The use of phytostimulants is an alternative eco-friendly approach that eliminates ecosystem disruption while maintaining agricultural productivity. Phytostimulants include living entities and materials, such as microorganisms and nanomaterials, which when applied to plants or to the rhizosphere, stimulate plant growth and induce tolerance to plants against biotic and abiotic stresses. In this review, we focus on plant growth-promoting rhizobacteria (PGPR), beneficial fungi, such as arbuscular mycorrhizal fungi (AMF) and plant growth-promoting fungi (PGPF), actinomycetes, cyanobacteria, azolla, and lichens, and their potential benefits in the crop improvement, and mitigation of abiotic and biotic stresses either alone or in combination. PGPR, AMF, and PGPF are plant beneficial microbes that can release phytohormones, such as indole acetic acid (IAA), gibberellic acid (GA), and cytokinins, promoting plant growth and improving soil health, and in addition, they also produce many secondary metabolites, antibiotics, and antioxidant compounds and help to combat biotic and abiotic stresses. Their ability to act as phytostimulator and a supplement of inorganic fertilizers is considered promising in practicing sustainable agriculture and organic farming. Glomalin is a proteinaceous product, produced by AMF, involved in soil aggregation and elevation of soil water holding capacity under stressed and unstressed conditions. The negative effects of continuous cropping can be mitigated by AMF biofertilization. The synergistic effects of PGPR and PGPF may be more effective. The mechanisms of control exercised by PGPF either direct or indirect to suppress plant diseases viz. by competing for space and nutrients, mycoparasitism, antibiosis, mycovirus-mediated cross-protection, and induced systemic resistance (ISR) have been discussed. The emerging role of cyanobacterial metabolites and the implication of nanofertilizers have been highlighted in sustainable agriculture.

Endophytic Klebsiella aerogenes HGG15 stimulates mulberry growth in hydro-fluctuation belt and the potential mechanisms as revealed by microbiome and metabolomics

Growth promotion and stress tolerance induced by endophytes have been observed in various plants, but their effects on mulberry regularly suffering flood in the hydro-fluctuation belt are less understood. In the present study, endophytic Klebsiella aerogenes HGG15 was screened out from 28 plant growth promotion (PGP) bacteria as having superior PGP traits in vitro and in planta as well as biosafety for silkworms. K. aerogenes HGG15 could actively colonize into roots of mulberry and subsequently transferred to stems and leaves. The 16S ribosomal RNA (V3–V4 variable regions) amplicon sequencing revealed that exogenous application of K. aerogenes HGG15 altered the bacterial community structures of mulberry roots and stems. Moreover, the genus of Klebsiella was particularly enriched in inoculated mulberry roots and was positively correlated with mulberry development and soil potassium content. Untargeted metabolic profiles uncovered 201 differentially abundant metabolites (DEMs) between inoculated and control mulberry, with lipids and organo-heterocyclic compounds being particularly abundant DEMs. In addition, a high abundance of abiotic stress response factors and promotion growth stimulators such as glycerolipid, sphingolipid, indole, pyridine, and coumarin were observed in inoculated mulberry. Collectively, the knowledge gained from this study sheds light on potential strategies to enhance mulberry growth in hydro-fluctuation belt, and microbiome and metabolite analyses provide new insights into the growth promotion mechanisms used by plant-associated bacteria.

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.

Host genotype interacts with aerial spore communities and influences the needle mycobiome of Norway spruce

The factors shaping the composition of the tree mycobiome are still under investigation. We tested the effects of host genotype, site, host phenotypic traits, and air fungal spore communities on the assembly of the fungi inhabiting Norway spruce needles. We used Norway spruce clones and spore traps within the collection sites and characterized both needle and air mycobiome communities by high‐throughput sequencing of the ITS2 region. The composition of the needle mycobiome differed between Norway spruce clones, and clones with high genetic similarity had a more similar mycobiome. The needle mycobiome also varied across sites and was associated with the composition of the local air mycobiome and climate. Phenotypic traits such as diameter at breast height or crown health influenced the needle mycobiome to a lesser extent than host genotype and air mycobiome. Altogether, our results suggest that the needle mycobiome is mainly driven by the host genotype in combination with the composition of the local air spore communities. Our work highlights the role of host intraspecific variation in shaping the mycobiome of trees and provides new insights on the ecological processes structuring fungal communities inhabiting woody plants.

Endophytic fungus Cladosporium tenuissimum DF11, an efficient inducer of tanshinone biosynthesis in Salvia miltiorrhiza roots

Salvia miltiorrhiza is a traditional medicinal plant mainly used for cardiovascular and cerebrovascular disease treatment. Tanshinones are the main bioactive constituents of S. miltiorrhiza, which mainly accumulate around its root periderm tissue. Endophytic fungi are important bioelicitors or probiotics that can promote the accumulation of secondary metabolites and sustainable cultivation of medicinal plants. Among them, endophytic Cladosporium spp., possessing a variety of biotransformation and metabolic abilities, is an ideal elicitor source. Here, we used a gnotobiotic system to investigate the effects of the endophytic fungus Cladosporium tenuissimum DF11 on tanshinone biosynthesis in S. miltiorrhiza roots. The results showed that C. tenuissimum DF11 mainly colonizes the intercellular space of the root tissues and promotes tanshinone biosynthesis and accumulation in S. miltiorrhiza roots by upregulating the expression of the genes encoding for key enzymes HMGR, DXS, DXR, GGPPS, CPS, KSL and CYP76AH1 of the tanshinone biosynthesis pathway. The expression levels of almost all genes encoding for key enzymes reached the response peak in the first or second week after DF11 colonization. Taken together, the endophytic fungus C. tenuissimum DF11 could promote secondary metabolite accumulation in S. miltiorrhiza roots. These results indicate that DF11 will be a potential biofertilizer fungus to regulate and stabilize the quality of cultivated S. miltiorrhiza medicinal materials.

Endophytic Colletotrichum Species from Aquatic Plants in Southwest China

Colletotrichum species are plant pathogens, saprobes, and endophytes in many economically important hosts. Many studies have investigated the diversity and pathogenicity of Colletotrichum species in common ornamentals, fruits, and vegetables. However, Colletotrichum species occurring in aquatic plants are not well known. During the investigation of the diversity of endophytic fungi in aquatic plants in southwest China, 66 Colletotrichum isolates were obtained from aquatic plants there, and 26 of them were selected for sequencing and analyses of actin (ACT), chitin synthase (CHS-1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), the internal transcribed spacer (ITS) region, and β-tubulin (TUB2) genomic regions. Based on morphological characterization and multi-locus phylogenetic analyses, 13 Colletotrichum species were recognized, namely, C. baiyuense sp. nov., C. casaense sp. nov., C. demersi sp. nov., C. dianense sp. nov., C. fructicola, C. garzense sp. nov., C. jiangxiense, C. karstii, C. philoxeroidis sp. nov., C. spicati sp. nov., C. tengchongense sp. nov., C. vulgaris sp. nov., C. wuxuhaiense sp. nov. Two species complexes, the C. boninense species complex and C. gloeosporioides species complex, were found to be associated with aquatic plants. Pathogenicity tests revealed a broad diversity in pathogenicity and aggressiveness among the eight new Colletotrichum species.

Potentials of Endophytic Fungi in the Biosynthesis of Versatile Secondary Metabolites and Enzymes

World population growth and modernization have engendered multiple environmental problems: the propagation of humans and crop diseases and the development of multi-drug-resistant fungi, bacteria and viruses. Thus, a considerable shift towards eco-friendly products has been seen in medicine, pharmacy, agriculture and several other vital sectors. Nowadays, studies on endophytic fungi and their biotechnological potentials are in high demand due to their substantial, cost-effective and eco-friendly contributions in the discovery of an array of secondary metabolites. For this review, we provide a brief overview of plant–endophytic fungi interactions and we also state the history of the discovery of the untapped potentialities of fungal secondary metabolites. Then, we highlight the huge importance of the discovered metabolites and their versatile applications in several vital fields including medicine, pharmacy, agriculture, industry and bioremediation. We then focus on the challenges and on the possible methods and techniques that can be used to help in the discovery of novel secondary metabolites. The latter range from endophytic selection and culture media optimization to more in-depth strategies such as omics, ribosome engineering and epigenetic remodeling.

Baseline Data of the Fungal Phytobiome of Three Sorghum (Sorghum bicolor) Cultivars in South Africa using Targeted Environmental Sequencing

Plant-associated fungi, or the mycobiome, inhabit plant surfaces above ground, reside in plant tissues as endophytes, or are rhizosphere in the narrow zone of soil surrounding plant roots. Studies have characterized mycobiomes of various plant species, but little is known about the sorghum mycobiome, especially in Africa, despite sorghum being one of the most important indigenous and commercial cereals in Africa. In this study, the mycobiome associated with above- and below-ground tissues of three commercial sorghum cultivars, as well as from rhizosphere and surrounding bulk soil samples, were sequenced using targeted sequencing with the Illumina MiSeq platform. Relative abundance differences between fungal communities were found between above-ground and below-ground niches, with most differences mostly in the dominant MOTUs, such as Davidiellaceae sp. (Cladosporium), Didymellaceae sp. 1 (Phoma), Fusarium, Cryptococcus and Mucor. Above-ground communities also appeared to be more diverse than below-ground communities, and plants harboured the most diversity. A considerable number of MOTUs were shared between the cultivars although, especially for NS5511, their abundances often differed. Several of the detected fungal groups include species that are plant pathogens of sorghum, such as Fusarium, and, at low levels, Alternaria and the Ustilaginomycetes. Findings from this study illustrate the usefulness of targeted sequencing of the ITS rDNA gene region (ITS2) to survey and monitor sorghum fungal communities and those from associated soils. This knowledge may provide tools for disease management and crop production and improvement.

Plant growth-promoting abilities and community structure of culturable endophytic bacteria from the fruit of an invasive plant Xanthium italicum

Diversity of endophytic bacterial communities of capsular fruit, upper and lower seeds of an invasive plant Xanthium italicum growing in Xinjiang, China, was investigated. All isolates from the seed capsules, the upper seeds, and the lower seeds were identified by 16S rRNA gene sequencing, and sequences were compared to bacterial databases to define operational taxonomic units (OTUs). Finally, we obtained 316 endophytic isolates corresponding to 58 OTUs based on 16S rRNA gene sequences. The most common OTU corresponded most closely to Bacillus zhangzhouensis and comprised 9.49% of all bacterial isolates. The richness and diversity of endophytes in lower seeds were higher than that of the upper seeds; moreover, the Chao estimator and Shannon index of endophytes in the lower seeds were approximate to that in the seed capsules. Bacillus and Staphylococcus were found as the common taxa in three different tissues that were investigated (OTUs belong to these genera constituted > 70% of the total community). The bacterial endophytic communities differed significantly among these three fruit tissues, especially Bacillus strains, which have been reported to contribute to plant growth promotion and stress resilience to their hosts in harsh environment; abundance of Bacillus species was in the following order: capsules (78 OTUs) > lower seeds (55 OTUs) > upper seeds (40 OTUs). The lower seeds harboring more Bacillus species might be responsible for their earlier seed germination compared with the upper seeds.

Farming systems influence the compositional, structural, and functional characteristics of the sugarcane-associated microbiome

Sugarcane (Saccharum spp.) has been produced worldwide as a relevant source of food and sustainable energy. However, the constant need to increase crop yield has led to excessive use of synthetic agrochemical inputs such as inorganic fertilizers, herbicides, and pesticides in plant cultures. It is known that these conventional practices can lead to deleterious effects on health and the environment. Organic farming emerges as a sustainable alternative to conventional systems; however, farm management influences in plant-associated microbiomes remain unclear. Here, the aim is to identify the effects of farming systems on the sugarcane microbiota. To address this issue, we sampled the microbiota from soils and plants under organic and conventional farming from two crop fields in Brazil. Then, we evaluated their compositional, structural, and functional traits through amplification and sequencing of phylogenetic markers of bacteria (16S rRNA gene, V3-V4 region) and fungi (Internal Transcribed Spacer - ITS2). The data processing and analyses by the DADA2 pipeline revealed 12,839 bacterial and 3,222 fungal sequence variants. Moreover, differences between analogous niches were detected considering the contrasting farming systems, with samples from the conventional system showing a slightly greater richness and diversity of microorganisms. The composition is also different between the farming systems, with 389 and 401 differentially abundant taxa for bacteria and fungi, respectively, including taxa capable of promoting plant growth. The microbial co-occurrence networks showed structural changes in microbial communities, where organic networks were more cohesive since they had closer taxa and less modularity by niches. Finally, the functional prediction revealed enriched metabolic pathways, including the increased presence of antimicrobial resistance in the conventional farming system. Taken together, our findings reveal functional, structural, and compositional adaptations of the microbial communities associated with sugarcane plants in the field, according to farming management. With this, we point out the need to unravel the mechanisms driving these adaptations.

Pathogen and drought stress affect cell wall and phytohormone signaling to shape host responses in a sorghum COMT bmr12 mutant

BACKGROUND

As effects of global climate change intensify, the interaction of biotic and abiotic stresses increasingly threatens current agricultural practices. The secondary cell wall is a vanguard of resistance to these stresses. Fusarium thapsinum (Fusarium stalk rot) and Macrophomina phaseolina (charcoal rot) cause internal damage to the stalks of the drought tolerant C4 grass, sorghum (Sorghum bicolor (L.) Moench), resulting in reduced transpiration, reduced photosynthesis, and increased lodging, severely reducing yields. Drought can magnify these losses. Two null alleles in monolignol biosynthesis of sorghum (brown midrib 6-ref, bmr6-ref; cinnamyl alcohol dehydrogenase, CAD; and bmr12-ref; caffeic acid O-methyltransferase, COMT) were used to investigate the interaction of water limitation with F. thapsinum or M. phaseolina infection.

RESULTS

The bmr12 plants inoculated with either of these pathogens had increased levels of salicylic acid (SA) and jasmonic acid (JA) across both watering conditions and significantly reduced lesion sizes under water limitation compared to adequate watering, which suggested that drought may prime induction of pathogen resistance. RNA-Seq analysis revealed coexpressed genes associated with pathogen infection. The defense response included phytohormone signal transduction pathways, primary and secondary cell wall biosynthetic genes, and genes encoding components of the spliceosome and proteasome.

CONCLUSION

Alterations in the composition of the secondary cell wall affect immunity by influencing phenolic composition and phytohormone signaling, leading to the action of defense pathways. Some of these pathways appear to be activated or enhanced by drought. Secondary metabolite biosynthesis and modification in SA and JA signal transduction may be involved in priming a stronger defense response in water-limited bmr12 plants.

Culture-Based and Culture-Independent Assessments of Endophytic Fungal Diversity in Aquatic Plants in Southwest China

Aquatic ecosystems contain tremendous plant and microbial diversity. However, little is known about endophyte diversity in aquatic plants. In this study, we investigated the diversity of endophytic fungi in aquatic plants in southwest China using both culture-based and culture-independent high-throughput sequencing methods. A total of 1,689 fungal isolates belonging to three phyla and 154 genera were obtained from 15,373 plant tissue segments of 30 aquatic plant species. The most abundant endophytic fungi were those in ascomycete genera Aspergillus, Ceratophoma, Fusarium, Penicillium, Phoma and Plectosporium. No difference in fungal isolation rates was observed among tissues from roots, stems, and leaves. Twenty tissue samples from three most common plant species were further subjected to culture-independent meta-barcode sequencing. The sequence-based analyses revealed a total of 1,074 OTUs belonging to six fungal phyla and 194 genera. Among the three plants, Batrachium bungei harbored the highest number of OTUs. Besides, a total of 66 genera were detected by two methods. Both the culture-dependent and independent methods revealed that aquatic plants in southwest China have abundant endophytic fungal diversity. This study significantly expands our knowledge of the fungal community of aquatic plants.

Bioprospecting beneficial endophytic bacterial communities associated with Rosmarinus officinalis for sustaining plant health and productivity

The present study aimed to isolate and identify root endophytic bacteria with multifunctional plant growth promoting (PGP) traits from medicinal plant Rosmarinus officinalis grown in the North-Western Himalayas. A total of 42 strains were isolated, exhibiting variable degrees of PGP traits, including phosphate solubilization (10-375 µg/mL), indole-3-acetic acid (6-66 µg/mL), siderophore (32.37%-301.48% SU) production and antifungal activity in terms of percent growth inhibition (% GI) against Fusarium oxysporum (44.44%-77.77% GI), Fusarium graminearum (48.88%-71.42% GI) and Rhizoctonia solani (44.44%-77.7% GI). The 16S rDNA sequencing results showed lineage of these strains to 15 genera viz., Aneurinibacillus, Bacillus, Beijerinckia, Cedecea, Ensifer, Enterobacter, Kosakonia, Lactobacillus, Lysobacter, Oxynema, Pseudomonas, Pantoea, Paenibacillus, Pseudoxanthomonas and Serratia. Out of 42 strains, 11 potential strains were selected for in vivo growth studies of R. officinalis. The results showed that the inoculation of Bacillus subtilis KU21, Pseudomonas aeruginosa SI12, and Cedecea lapagei KU14 significantly increased the physical growth parameters of plant over uninoculated control viz., number of lateral of branches (43.95%-46.39%), stem height (29.04%-38.57%), root length (32.31%-37.14%), shoot (34.76%-40.91%) and root biomass (62.89%-70.70%). Physiological characteristics such as total chlorophyll (30.41%-30.96%), phenol (14.43%-24.55%) and carotenoids (34.26%-39.87%) content, also showed a relative increase as compared to uninoculated control; furthermore, the macronutrients (NPK) contents of the plant as well as soil also showed an increase. The developed module may be recommended for sustainable production of R. officinalis in the North-Western Himalayan region without hampering the soil health and fertility.

Cure lies in nature: medicinal plants and endophytic fungi in curbing cancer

Success of targeted cancer treatment modalities has generated an ambience of plausible cure for cancer. However, cancer remains to be the major cause of mortality across the globe. The emergence of chemoresistance, relapse after treatment and associated adverse effects has posed challenges to the present therapeutic regimes. Thus, investigating new therapeutic agents of natural origin and delineating the underlying mechanism of action is necessary. Since ages and still in continuum, the phytochemicals have been the prime source of identifying bioactive agents against cancer. They have been exploited for isolating targeted specific compounds to modulate the key regulating signaling pathways of cancer pathogenesis and progression. Capsaicin (alkaloid compound in chilli), catechin, epicatechin, epigallocatechin and epigallocatechin-3-gallate (phytochemicals in green tea), lutein (carotenoid found in yellow fruits), Garcinol (phenolic compound present in kokum tree) and many other naturally available compounds are also very valuable to develop the drugs to treat the cancer. An alternate repository of similar chemical diversity exists in the form of endophytic fungi inhabiting the medicinal plants. There is a high diversity of plant associated endophytic fungi in nature which are potent producers of anti-cancer compounds and offers even stronger hope for the discovery of an efficient anti-cancer drug. These fungi provide various bioactive molecules, such as terpenoids, flavonoids, alkaloids, phenolic compounds, quinines, steroids etc. exhibiting anti-cancerous property. The review discusses the relevance of phytochemicals in chemoprevention and as modulators of miRNA. The perspective advocates the imperative role of anti-cancerous secondary metabolites containing repository of endophytic fungi, as an alternative route of drug discovery.

Stem endophytes increase root development, photosynthesis, and survival of elm plantlets (Ulmus minor Mill.)

Long-lived trees benefit from fungal symbiotic interactions in the adaptation to constantly changing environments. Previous studies revealed a core fungal endobiome in Ulmus minor which has been suggested to play a critical role in plant functioning. Here, we hypothesized that these core endophytes are involved in abiotic stress tolerance. To test this hypothesis, two core endophytes (Cystobasidiales and Chaetothyriales) were inoculated into in vitro U. minor plantlets, which were further subjected to drought. Given that elm genotypes resistant to Dutch elm disease (DED) tend to show higher abiotic stress tolerance than susceptible ones, we tested the endophyte effect on two DED-resistant and two DED-susceptible genotypes. Drought stress was moderate; endophyte presence attenuated stomata closure in response to drought in one genotype but this stress did not affect plant survival. In comparison, long-term in-vitro culture proved stressful to mock-inoculated plants, especially in DED-susceptible genotypes. Interestingly, no endophyte-inoculated plant died during the experiment, as compared to high mortality in mock-inoculated plants. In surviving plants, endophyte presence stimulated root and shoot growth, photosynthetic rates, antioxidant activity and molecular changes involving auxin-signaling. These changes and the observed endophyte stability in elm tissues throughout the experiment suggest endophytes are potential tools to improve survival and stress tolerance of DED-resistant elms in elm restoration programs.

Chemical Interactions at the Interface of Plant Root Hair Cells and Intracellular Bacteria

In this research, we conducted histochemical, inhibitor and other experiments to evaluate the chemical interactions between intracellular bacteria and plant cells. As a result of these experiments, we hypothesize two chemical interactions between bacteria and plant cells. The first chemical interaction between endophyte and plant is initiated by microbe-produced ethylene that triggers plant cells to grow, release nutrients and produce superoxide. The superoxide combines with ethylene to form products hydrogen peroxide and carbon dioxide. In the second interaction between microbe and plant the microbe responds to plant-produced superoxide by secretion of nitric oxide to neutralize superoxide. Nitric oxide and superoxide combine to form peroxynitrite that is catalyzed by carbon dioxide to form nitrate. The two chemical interactions underlie hypothesized nutrient exchanges in which plant cells provide intracellular bacteria with fixed carbon, and bacteria provide plant cells with fixed nitrogen. As a consequence of these two interactions between endophytes and plants, plants grow and acquire nutrients from endophytes, and plants acquire enhanced oxidative stress tolerance, becoming more tolerant to abiotic and biotic stresses.

Endophytic Fungi: Biological Control and Induced Resistance to Phytopathogens and Abiotic Stresses

Plant diseases cause losses of approximately 16% globally. Thus, management measures must be implemented to mitigate losses and guarantee food production. In addition to traditional management measures, induced resistance and biological control have gained ground in agriculture due to their enormous potential. Endophytic fungi internally colonize plant tissues and have the potential to act as control agents, such as biological agents or elicitors in the process of induced resistance and in attenuating abiotic stresses. In this review, we list the mode of action of this group of microorganisms which can act in controlling plant diseases and describe several examples in which endophytes were able to reduce the damage caused by pathogens and adverse conditions. This is due to their arsenal of molecules generated during the interaction by which they form a kind of biological shield in the plant. Furthermore, considering that endophytic fungi can be an important tool in managing for biotic and abiotic stresses due to the large amount of biologically active substances produced, bioprospecting this class of microorganisms is tending to increase and generate valuable products for agriculture.

Bacterial endophytes: Molecular interactions with their hosts

Plant growth promotion has been found associated with plants on the surface (epiphytic), inside (endophytic), or close to the plant roots (rhizospheric). Endophytic bacteria mainly have been researched for their beneficial activities in terms of nutrient availability, plant growth hormones, and control of soil-borne and systemic pathogens. Molecular communications leading to these interactions between plants and endophytic bacteria are now being unrevealed using multidisciplinary approaches with advanced techniques such as metagenomics, metaproteomics, metatranscriptomics, metaproteogenomic, microRNAs, microarray, chips as well as the comparison of complete genome sequences. More than 400 genes in both the genomes of host plant and bacterial endophyte are up- or downregulated for the establishment of endophytism and plant growth-promoting activity. The involvement of more than 20 genes for endophytism, about 50 genes for direct plant growth promotion, about 25 genes for biocontrol activity, and about 10 genes for mitigation of different stresses has been identified in various bacterial endophytes. This review summarizes the progress that has been made in recent years by these modern techniques and approaches.

Quality of Immature and Mature Pepper (Capsicum annuum L.) Seeds in Relation to Bio-Priming with Endophytic Pseudomonas and Bacillus spp

Fruit maturity for seed production can occur at various times because of the continual flowering of pepper plants. Accordingly, seeds with different maturity are acquired as the fruits are collected in a single harvest. Immature seeds obtained in this harvest may lead to a decrease in the quality of seed lots. Therefore, this research aimed to evaluate the influence of four different endophytic bacteria strains (Pseudomonas fluorescens strain L5b, Pseudomonas gessardii strain L13, Bacillus subtilis strain Bs1 and Bacillus mojavensis strain ApBm) on germination and seedling vigor of immature and mature bell pepper seeds. To obtain seeds with different maturity levels, fruits were collected 45–49 days after flowering for immature seeds and 65–69 days for mature seeds. The effectiveness of these bacteria strains was examined by coating seeds with four different endophytic bacteria strains separately. Additionally, to see the activity of endophytic bacteria more clearly, a mock treatment with sterile water was added to the experiment as a control (+) group. Bio-priming (especially strain Bs1 and L13) improved germination and seedling emergence characteristics of both immature and mature seed lots compared to control groups (p < 0.05). The results demonstrate that bio-priming with beneficial endophytic bacteria can be used to stimulate the quality of both immature and mature seeds from the pepper.

Bacterial communities associated with sugarcane under different agricultural management exhibit a diversity of plant growth-promoting traits and evidence of synergistic effect

Plant-associated microbiomes have been a target of interest for the prospection of microorganisms, which may be acting as effectors to increase agricultural productivity. For years, the search for beneficial microorganisms has been carried out from the characterization of functional traits of growth-promotion using tests with a few isolates. However, eventually, the expectations with positive results may not be realized when the evaluation is performed in association with plants. In our study, we accessed the cultivable sugarcane microbiome under two conditions of agronomic management: organic and conventional. From the use of a new customized culture medium, we recovered 944 endophytic and epiphytic bacterial communities derived from plant roots, stalks, leaves, and rhizospheric soil. This could be accomplished by using a large-scale approach, initially performing an in planta (Cynodon dactylon) screening process of inoculation to avoid early incompatibility. The inoculation was performed using the bacterial communities, considering that in this way, they could act synergistically. This process resulted in 38 candidate communities, 17 of which had higher Indole-3-acetic acid (IAA) production and phosphate solubilization activity and, were submitted to a new in planta test using Brachiaria ruziziensis and quantification of functional traits for growth-promotion and physiological tests. Enrichment analysis of selected communities has shown that they derived mainly from epiphytic populations of sugarcane stalks under conventional management. The sequencing of the V3-V4 region of the 16S rRNA gene revealed 34 genera and 24 species distributed among the phylum Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. We also observed a network of genera in these communities where the genus Chryseobacterium stands out with a greater degree of interaction, indicating a possible direct or indirect role as a keystone taxon in communities with plant-growth promotion capacities. From the results achieved, we can conclude that the approach is useful in the recovery of a set of sugarcane bacterial communities and that there is, evidence of synergistic action providing benefits to plants, and that they are compatible with plants of the same family (Poaceae). Thus, we are reporting the beneficial bacterial communities identified as suitable candidates with rated potential to be exploited as bioinoculants for crops.

Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce

The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species Picea abies (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus Cortinarius.

IMPORTANCE A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. Typically, gene expression studies focus on the plant component or, in a limited number of studies, expression in one or more associated organisms. However, metatranscriptomic data are rarely used for taxonomic profiling, which is currently performed using amplicon approaches. We created an assembly-based, reproducible, and hardware-agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data. While we identified some limitations and caveats, we show that functional, taxonomic, and compositional insights can all be obtained from RNA-Seq data. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response, and effect between host plants and their associated microbial communities.

Terroir Is the Main Driver of the Epiphytic Bacterial and Fungal Communities of Mango Carposphere in Reunion Island

The diversity of both bacterial and fungal communities associated with mango surface was explored using a metabarcoding approach targeting fungal ITS2 and bacterial 16S (V3-V4) genomic regions. Fruits were collected in Reunion Island from two different orchards according to a sampling method which allowed the effect of several pre-harvest factors such as geographical location (terroir), cultivars, fruit parts, tree position in the plot, fruit position on the tree (orientation and height), as well as the harvest date to be investigated. A total of 4,266,546 fungal and 2,049,919 bacterial reads were recovered then respectively assigned to 3,153 fungal and 24,087 to bacterial amplicon sequence variants (ASVs). Alpha and beta diversity, as well as differential abundance analyses revealed variations in both bacterial and fungal communities detected on mango surfaces depended upon the studied factor. Results indicated that Burkholderiaceae (58.8%), Enterobacteriaceae (5.2%), Pseudomonadaceae (4.8%), Sphingomonadaceae (4.1%), Beijerinckiaceae (3.5%), and Microbacteriaceae (3.1%) were the dominant bacterial families across all samples. The majority of fungal sequences were assigned to Mycosphaerellaceae (34.5%), Cladosporiaceae (23.21%), Aureobasidiaceae (13.09%), Pleosporaceae (6.92%), Trichosphaeriaceae (5.17%), and Microstromatales_fam_Incertae_sedis (4.67%). For each studied location, mango fruit from each cultivar shared a core microbiome, and fruits of the same cultivar harvested in two different locations shared about 80% fungal and bacterial family taxa. The various factors tested in this study affected bacterial and fungal taxa differently, suggesting that some taxa could act as geographical (terroir) markers and in some cases as cultivar fingerprints. The ranking of the factors investigated in the present study showed that in decreasing order of importance: the plot (terroir), cultivar, fruit parts, harvest date and the position of the fruits are respectively the most impacting factors of the microbial flora, when compared to the orientation and the fruit position (height) on the tree. Overall, these findings provided insights on both bacterial and fungal diversity associated with the mango surface, their patterns from intra-fruit scale to local scale and the potential parameters shaping the mango microbiota.

Biocontrol Potential of Grapevine Endophytic and Rhizospheric Fungi Against Trunk Pathogens

Grapevine Trunk Diseases (GTDs) are a major challenge to the grape industry worldwide. GTDs are responsible for considerable loss of quality, production, and vineyard longevity. Seventy-five percent of Chilean vineyards are estimated to be affected by GTDs. GTDs are complex diseases caused by several fungi species, including members of the Botryosphaeriaceae family and Phaeomoniella chlamydospora, considered some of the most important causal agents for these diseases in Chile. In this study, we isolated 169 endophytic and 209 rhizospheric fungi from grapevines grown under organic and conventional farming in Chile. Multiple isolates of Chaetomium sp., Cladosporium sp., Clonostachys rosea, Epicoccum nigrum, Purpureocillium lilacinum, and Trichoderma sp. were evaluated for their potential of biocontrol activity against Diplodia seriata, Neofusicoccum parvum, and Pa. chlamydospora. Tests of antagonism were carried out using two dual-culture-plate methods with multiple media types, including agar containing grapevine wood extract to simulate in planta nutrient conditions. Significant pathogen growth inhibition was observed by all isolates tested. Clonostachys rosea showed 98.2% inhibition of all pathogens in the presence of grapevine wood extract. We observed 100% pathogen growth inhibition when autoclaved lignified grapevine shoots were pre-inoculated with either C. rosea strains or Trichoderma sp. Overall, these results show that C. rosea strains isolated from grapevines are promising biocontrol agents against GTDs.

Influence of vintage, geographic location and cultivar on the structure of microbial communities associated with the grapevine rhizosphere in vineyards of San Juan Province, Argentina

Soil microbiomes, as a primary reservoir for plant colonizing fungi and bacteria, play a major role in determining plant productivity and preventing invasion by pathogenic microorganisms. The use of 16S rRNA and ITS high-throughput amplicon sequencing for analysis of complex microbial communities have increased dramatically in recent years, establishing links between wine specificity and, environmental and viticultural factors, which are framed into the elusive terroir concept. Given the diverse and complex role these factors play on microbial soil structuring of agricultural crops, the main aim of this study is to evaluate how external factors, such as vintage, vineyard location, cultivar and soil characteristics, may affect the diversity of the microbial communities present. Additionally, we aim to compare the influence these factors have on the structuring of bacterial and fungal populations associated with Malbec grapevine rhizosphere with that of the more widespread Cabernet Sauvignon grapevine cultivar. Samples were taken from Malbec and Cabernet Sauvignon cultivars from two different vineyards in the San Juan Province of Argentina. Total DNA extracts from the rhizosphere soil samples were sequenced using Illumina’s Miseq technology, targeting the V3-V4 hypervariable 16S rRNA region in prokaryotes and the ITS1 region in yeasts. The major bacterial taxa identified were Proteobacteria, Bacteroidetes and Firmicutes, while the major fungal taxa were Ascomycetes, Basidiomycetes, Mortierellomycetes and a low percentage of Glomeromycetes. Significant differences in microbial community composition were found between vintages and vineyard locations, whose soils showed variances in pH, organic matter, and content of carbon, nitrogen, and absorbable phosphorus.

Cooperation, Competition, and Specialized Metabolism in a Simplified Root Nodule Microbiome

Microbiomes associated with various plant structures often contain members with the potential to make specialized metabolites, e.g., molecules with antibacterial, antifungal, or siderophore activities. However, when and where microbes associated with plants produce specialized metabolites, and the potential role of these molecules in mediating intramicrobiome interactions, is not well understood. Root nodules of legume plants are organs devoted to hosting symbiotic bacteria that fix atmospheric nitrogen and have recently been shown to harbor a relatively simple accessory microbiome containing members with the ability to produce specialized metabolites in vitro On the basis of these observations, we sought to develop a model nodule microbiome system for evaluating specialized microbial metabolism in planta Starting with an inoculum derived from field-grown Medicago sativa nodules, serial passaging through gnotobiotic nodules yielded a simplified accessory community composed of four members: Brevibacillus brevis, Paenibacillus sp., Pantoea agglomerans, and Pseudomonas sp. Some members of this community exhibited clear cooperation in planta, while others were antagonistic and capable of disrupting cooperation between other partners. Using matrix-assisted laser desorption ionization-imaging mass spectrometry, we found that metabolites associated with individual taxa had unique distributions, indicating that some members of the nodule community were spatially segregated. Finally, we identified two families of molecules produced by B. brevisin planta as the antibacterial tyrocidines and a novel set of gramicidin-type molecules, which we term the britacidins. Collectively, these results indicate that in addition to nitrogen fixation, legume root nodules are likely also sites of active antimicrobial production.

Patents on Endophytic Fungi for Agriculture and Bio- and Phytoremediation Applications

Plant endophytic fungi spend all or part of their lives inside host tissues without causing disease symptoms. They can colonize the plant to protect against predators, pathogens and abiotic stresses generated by drought, salinity, high concentrations of heavy metals, UV radiation and temperature fluctuations. They can also promote plant growth through the biosynthesis of phytohormones and nutrient acquisition. In recent years, the study of endophytic fungi for biological control of plant diseases and pests has been intensified to try to reduce the ecological and public health impacts due the use of chemicals and the emergence of fungicide resistance. In this review, we examine 185 patents related to endophytic fungi (from January 1988 to December 2019) and discuss their applicability for abiotic stress tolerance and growth promotion of plants, as agents for biocontrol of herbivores and plant pathogens and bio- and phytoremediation applications.

Plant endophytes promote growth and alleviate salt stress in Arabidopsis thaliana

Plant growth promoting rhizobacteria (PGPR) are a functionally diverse group of microbes having immense potential as biostimulants and stress alleviators. Their exploitation in agro-ecosystems as an eco-friendly and cost-effective alternative to traditional chemical inputs may positively affect agricultural productivity and environmental sustainability. The present study describes selected rhizobacteria, from a range of origins, having plant growth promoting potential under controlled conditions. A total of 98 isolates (ectophytic or endophytic) from various crop and uncultivated plants were screened, out of which four endophytes (n, L, K and Y) from Phalaris arundinacea, Solanum dulcamara, Scorzoneroides autumnalis, and Glycine max, respectively, were selected in vitro for their vegetative growth stimulating effects on Arabidopsis thaliana Col-0 seedlings with regard to leaf surface area and shoot fresh weight. A 16S rRNA gene sequencing analysis of the strains indicated that these isolates belong to the genera Pseudomonas, Bacillus, Mucilaginibacter and Rhizobium. Strains were then further tested for their effects on abiotic stress alleviation under both Petri-plate and pot conditions. Results from Petri-dish assay indicated strains L, K and Y alleviated salt stress in Arabidopsis seedlings, while strains K and Y conferred increases in fresh weight and leaf area under osmotic stress. Results from subsequent in vivo trials indicated all the isolates, especially strains L, K and Y, distinctly increased A. thaliana growth under both normal and high salinity conditions, as compared to control plants. The activity of antioxidant enzymes (ascorbate peroxidase, catalase and peroxidase), proline content and total antioxidative capacity also differed in the inoculated A. thaliana plants. Furthermore, a study on spatial distribution of the four strains, using either conventional Petri-plate counts or GFP-tagged bacteria, indicated that all four strains were able to colonize the endosphere of A. thaliana root tissue. Thus, the study revealed that the four selected rhizobacteria are good candidates to be explored as plant growth stimulators, which also possess salt stress mitigating property, partially by regulating osmolytes and antioxidant enzymes. Moreover, the study is the first report of Scorzoneroides autumnalis (fall dandelion) and Solanum dulcamara (bittersweet) associated endophytes with PGP effects.

Role of Microorganisms in the Remediation of Wastewater in Floating Treatment Wetlands: A Review

This article provides useful information for understanding the specific role of microbes in the pollutant removal process in floating treatment wetlands (FTWs). The current literature is collected and organized to provide an insight into the specific role of microbes toward plants and pollutants. Several aspects are discussed, such as important components of FTWs, common bacterial species, rhizospheric and endophytes bacteria, and their specific role in the pollutant removal process. The roots of plants release oxygen and exudates, which act as a substrate for microbial growth. The bacteria attach themselves to the roots and form biofilms to get nutrients from the plants. Along the plants, the microbial community also influences the performance of FTWs. The bacterial community contributes to the removal of nitrogen, phosphorus, toxic metals, hydrocarbon, and organic compounds. Plant–microbe interaction breaks down complex compounds into simple nutrients, mobilizes metal ions, and increases the uptake of pollutants by plants. The inoculation of the roots of plants with acclimatized microbes may improve the phytoremediation potential of FTWs. The bacteria also encourage plant growth and the bioavailability of toxic pollutants and can alleviate metal toxicity.