Diversity of endophytic plant-growth microorganisms from Gentianella weberbaueri and Valeriana pycnantha, highland Peruvian medicinal plants

Diversity of endophytic bacteria with antimicrobial potential isolated from marine macroalgae from Yacila and Cangrejos beaches, Piura-Peru

Endophytic bacteria found in marine macroalgae have been studied for their potential antimicrobial activity, consequently, they could serve as a valuable source of bioactive compounds to control pathogenic bacteria, yeasts, and fungi. Algae endophytic bacteria were isolated from Caulerpa sp., Ulva sp., Ahnfeltiopsis sp., and Chondracantus chamissoi from Yacila and Cangrejo Beaches (Piura, Peru). Antimicrobial assays against pathogenic bacteria were evaluated using cross-culture, over-plate, and volatile organic compound tests. Afterward, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of selected crude extracts were determined, also ITS molecular analysis, antifungal activity, and PCR of iturin, fengycin, and surfactin genes were performed for bacteria strains exhibiting better activity. Forty-six algae endophytic bacteria were isolated from algae. Ten strains inhibited gram-positive pathogenic bacteria (Enterococcus faecalis, Staphylococcus epidermidis, S. aureus, and Listeria monocytogenes), and 12 inhibited gram-negative bacteria (Escherichia coli and Salmonella enteric sv typhimurium). Bacteria with better activity belong to Bacillus sp., Kluyvera ascorbata, Pantoea agglomerans, Leclercia adecarboxylata, and Enterobacter sp., which only four showed antifungal activities against Candida albicans, C. tropicalis, Colletotrichium sp., Fusarium sp., Fusarium oxysporum, and Alternaria sp. Furthermore, K. ascorbata YAFE21 and Bacillus sp. YCFE4 exhibited iturin and fengycin genes. The results indicate that the algae endophytic bacteria found in this study, particularly K. ascorbata YAFE21, Bacillus sp. YCFR6, L. adecarboxylata CUFE2, Bacillus sp. YUFE8, Enterobacter sp. YAFL1, and P. agglomerans YAFL6, could be investigated as potential producers of antimicrobial compounds due to their broad activity against various microorganisms.

Antitumor and antibacterial activity of metabolites of endophytic Colletotrichum siamense isolated from coffee (Coffea arabica L. cv IAPAR-59)

Endophytic fungi produce a range of known metabolites and several others, not yet explored, which present important biological activities from the pharmaceutical and industrial perspective. Several studies have reported the diversity of endophytes in Coffea arabica plants, although few have been described in organic cultures. In the current paper, we describe the chemical profile of specialized metabolites in the ethyl acetate phase in a strain of the endophytic fungus Colletotrichum siamense associated with coffee (Coffea arabica L.) (Rubiaceae) and its potential against tumor cells and bacteria of medical and food importance. Cytotoxicity assays in tumor cells MCF-7 and HepG2/C3A were performed by MTT and microdilution in broth to evaluate the antibacterial action of metabolic extract. The antiproliferative assay showed promising results after 24 h of treatment, with 50% injunction concentrations for the two cell types. UHPLC-MS/MS analyses with an electrospray ionization source were used to analyze the extracts and identify compounds of species Colletotrichum siamense, which is still little explored as a source of active metabolites. Many of these compounds observed in the endophytic need to be chemically synthesized in industry, at high costs, while production by the fungus becomes a chemically and economically more viable alternative. Pyrocatechol, gentisyl alcohol, and alpha-linolenic acid, associated with different mechanisms of action against tumor cells, were detected among the main compounds. The extract of the endophytic fungus Colletotrichum siamense presented several compounds with pharmacological potential and antibacterial activity, corroborating its potential in biotechnological applications.

Diverse biological activities and secondary metabolites profile of Penicillium brevicompactum HE19ct isolated from the high-Andean medicinal plant Perezia coerulescens

Endophytic fungi produced attractive primary and secondary metabolites for industries, pharmacology, and biotechnology. The bioactive potential of HE19ct, identified as Penicillium brevicompactum according to ITS-BenA-caM, was addressed. Antimicrobial and antioxidant activities and secondary metabolite contents using four culture media in Agar-plate (ApF) and Submerged (SmF) fermentation were evaluated. Some plant growth-promoting (PGP) traits and their related genes were tested. HE19ct exhibited antimicrobial activity against Staphylococcus aureus, Enterococcus faecalis, Candida albicans, C. tropicalis, Fusarium sp., Geotrichum candidum, and Alternaria sp. All cultures showed DPPH scavenging activity and phenolic compounds, where ethyl acetate extract of SmF with malt extract showed higher activity and SmF/ApF with potato-dextrose exhibited higher yield, respectively. HE19ct solubilized tricalcium-phosphate and produced siderophore, endoglucanase, proteinase, and amylase. It enhanced the alfalfa's germination at 15 °C, root development, and phenols production at 15 and 24 °C. Phenols, tannins, anthraquinones, triterpenoids/steroids, and alkaloids production were detected depending on culture media. Polyketide synthase type I gene (PksI), subtilisin-like protease prb 1 (Pbr), and siderophore D (sidD) were PCR-amplified. Finally, HE19CT could be a promising source of interesting bioactive compounds for pharmacology and agriculture mainly in extreme conditions, then metabolomic and functional genetic research must be performed to support their appropriate application.

Reprogramming of microbial community in barley root endosphere and rhizosphere soil by polystyrene plastics with different particle sizes

Polystyrene plastics is an emerging pollutant affecting plant performance and soil functioning. However, little information is available on the effects of microplastics and nanoplastics on plant root endophytic and rhizospheric soil microbial communities. Here, barley plants were grown in microplastics/nanoplastics -treated soil and the diversity, composition and function of bacteria and fungi in the root and rhizosphere soil were examined. At the seedling stage, greater changes of root endophytes were found compared with rhizosphere microorganisms under the plastic treatments. Nanoplastics decreased the richness and diversity of the fungal community, while microplastics increased the diversity of the root endophytic bacterial community. The network of the bacterial community under nanoplastics showed higher vulnerability while lower complexity than that under the control. However, the bacterial community under microplastics had a relatively higher resistance than the control. For the rhizosphere microbial community, no significant effect of plastics was found on the α-diversity index at the seedling stage. In addition, the nanoplastics resulted in higher sensitivity in the relative abundance and function of rhizosphere soil microbes than root endophytic microbes at the mature stage. Treatments of polystyrene plastics with different particle sizes reprogramed the rhizosphere and root endophytic microbial communities. Different effects of microplastics and nanoplastics were found on the diversity, composition, network structure and function of bacteria and fungi, which might be due to the variation in particle sizes. These results lay a foundation for learning the effects of polystyrene plastics with different particle sizes on the microorganisms in rhizosphere soil and plant roots, which may have important implications for the adaptation of plant-microbial holobiont in polystyrene plastics-polluted soils.

Assessment of nitrogen-fixing endophytic and mineral solubilizing rhizospheric bacteria as multifunctional microbial consortium for growth promotion of wheat and wild wheat relative Aegilops kotschyi

Microbes play crucial functions in maintaining the health and growth of the plants directly or indirectly by supplying nutrients. These microbes could be used as biofertilizers for the enhancement of soil health and growth of crops. In preset investigation, potential microbes from endophytic and rhizospheric region of Aegilops kotschyi growing in green slopes of Shivaliks, Himachal Pradesh were sorted out and screened for plant growth promoting attributes including phosphorus and potassium solubilization. The potential bacterial strains were identified through 16S rRNA gene sequencing and developed as microbial consortium for the plant growth of wheat and wild wheat relative Aegilops kotschyi. A total 125 isolates of bacteria were sorted out and among them 36 were found as P-solubilizers and 19 showed K-solubilization attribute and two highly potential bacterial strain were identified as Bacillus tropicus EU-ARP-44 (P-solubilizer; 270.5 ± 0.00 mg L^-1) and B. megaterium EU-ARK-23 (K-Solubilizer; 51.3 ± 1.7 mg mL^-1). The microbial consortium of Rahnella sp. strain EU-A3SNfb (N-fixer; MN294545), B. tropicus EU-ARP-44 (P-solubilizer) and B. megaterium EU-ARK-23 (K-solubilizer) evaluation in Aegilops kotschyi and wheat crop resulted in the enhancement of growth as well as physiological parameter including shoot/root length, fresh/dry weight and chlorophyll, carotenoid, total soluble sugar content, phenolic and flavonoid content as compared to un-inoculated control. Microbial consortium consisting of potential plant growth promoting (PGP) bacterial strains could be used as biofertilizer and bioinoculants in cereals crop growing in hilly region.

Production and Functionalities of Specialized Metabolites from Different Organic Sources

Medicinal plants are rich sources of specialized metabolites that are of great importance to plants, animals, and humans. The usefulness of active biological compounds cuts across different fields, such as agriculture, forestry, food processing and packaging, biofuels, biocatalysts, and environmental remediation. In recent years, research has shifted toward the use of microbes, especially endophytes (bacteria, fungi, and viruses), and the combination of these organisms with other alternatives to optimize the production and regulation of these compounds. This review reinforces the production of specialized metabolites, especially by plants and microorganisms, and the effectiveness of microorganisms in increasing the production/concentration of these compounds in plants. The study also highlights the functions of these compounds in plants and their applications in various fields. New research areas that should be explored to produce and regulate these compounds, especially in plants and microbes, have been identified. Methods involving molecular studies are yet to be fully explored, and next-generation sequencing possesses an interesting and reliable approach.

Assembly, Core Microbiota, and Function of the Rhizosphere Soil and Bark Microbiota in Eucommia ulmoides

Medicinal plants are inhabited by diverse microbes in every compartment, and which play an essential role in host growth and development, nutrient absorption, synthesis of secondary metabolites, and resistance to biological and abiotic stress. However, the ecological processes that manage microbiota assembly and the phenotypic and metabolic characteristics of the core microbiota of Eucommia ulmoides remain poorly explored. Here, we systematically evaluated the effects of genotypes, compartment niches, and environmental conditions (climate, soil nutrition, and secondary metabolites) on the assembly of rhizosphere soil and bark associated bacterial communities. In addition, phenotypic and metabolic characteristics of E. ulmoides core microbiota, and their relationship with dominant taxa, rare taxa, and pharmacologically active compounds were deciphered. Results suggested that microbiota assembly along the two compartments were predominantly shaped by the environment (especially pH, relative humidity, and geniposide acid) and not by host genotype or compartment niche. There were 690 shared genera in the rhizosphere soil and bark, and the bark microbiota was mainly derived from rhizosphere soil. Core microbiota of E. ulmoides was a highly interactive “hub” microbes connecting dominant and rare taxa, and its phenotypic characteristics had a selective effect on compartment niches. Metabolic functions of the core microbiota included ammonia oxidation, nitrogen fixation, and polyhydroxybutyrate storage, which are closely related to plant growth or metabolism. Moreover, some core taxa were also significantly correlated with three active compounds. These findings provide an important scientific basis for sustainable agricultural management based on the precise regulation of the rhizosphere soil and bark microbiota of E. ulmoides.

Ecology and potential functions of plant-associated microbial communities in cold environments

Complex microbial communities are associated with plants and can improve their resilience under harsh environmental conditions. In particular, plants and their associated communities have developed complex adaptation strategies against cold stress. Although changes in plant-associated microbial community structure have been analysed in different cold regions, scarce information is available on possible common taxonomic and functional features of microbial communities across cold environments. In this review, we discuss recent advances in taxonomic and functional characterization of plant-associated microbial communities in three main cold regions, such as alpine, Arctic and Antarctica environments. Culture-independent and culture-dependent approaches are analysed, in order to highlight the main factors affecting the taxonomic structure of plant-associated communities in cold environments. Moreover, biotechnological applications of plant-associated microorganisms from cold environments are proposed for agriculture, industry and medicine, according to biological functions and cold adaptation strategies of bacteria and fungi. Although further functional studies may improve our knowledge, the existing literature suggest that plants growing in cold environments harbor complex, host-specific and cold-adapted microbial communities, which may play key functional roles in plant growth and survival under cold conditions.

The Potential Role of Microbial Biostimulants in the Amelioration of Climate Change-Associated Abiotic Stresses on Crops

Crop plants are more often exposed to abiotic stresses in the current age of fast-evolving climate change. This includes exposure to extreme and unpredictable changes in climatic conditions, phytosanitary hazards, and cultivation conditions, which results in drastic losses in worldwide agricultural productions. Plants coexist with microbial symbionts, some of which play key roles in the ecosystem and plant processes. The application of microbial biostimulants, which take advantage of symbiotic relationships, is a long-term strategy for improving plant productivity and performance, even in the face of climate change-associated stresses. Beneficial filamentous fungi, yeasts, and bacteria are examples of microbial biostimulants, which can boost the growth, yield, nutrition and stress tolerance in plants. This paper highlights recent information about the role of microbial biostimulants and their potential application in mitigating the abiotic stresses occurring on crop plants due to climate change. A critical evaluation for their efficient use under diverse climatic conditions is also made. Currently, accessible products generally improve cultural conditions, but their action mechanisms are mostly unknown, and their benefits are frequently inconsistent. Thus, further studies that could lead to the more precisely targeted products are discussed.

Function-driven design of Bacillus kochii and Filobasidium magnum co-culture to improve quality of flue-cured tobacco

Flue-cured tobacco (FCT) is an economical raw material whose quality affects the quality and cost of the derived product. However, the time-consuming and inefficient spontaneous aging is the primary process for improving the FCT quality in the industry. In this study, a function-driven co-culture with functional microorganisms was built in response to the quality-driven need for less irritation and more aroma in FCT. The previous study has found that Bacillus kochii SC could degrade starch and protein to reduce tobacco irritation and off-flavors. The Filobasidium magnum F7 with high lipoxygenase activity was screened out for degrading higher fatty acid esters and terpenoids to promote the aroma and flavor of FCT. Co-cultivation with strain SC and F7 obtained better quality improvement than mono-culture at an initial inoculation ratio of 1:3 for 2 days, representing a significant breakthrough in efficiency and a reduction in production costs compared to the more than 2 years required for the spontaneous aging process. Through the analysis of microbial diversity, predicted flora functions, enzyme activities and volatile compositions within the mono- and co-cultivation, our study showed the formation of a function-driven co-culture between two strains through functional division of labor and nutritional feeding. Herein, the function-driven co-culture via bioaugmentation will become an increasingly implemented approach for the tobacco industry.

Functional and morphological analysis of isolates of phylloplane and rhizoplane endophytic bacteria interacting in different cocoa production systems in the Amazon

Endophytic bacteria colonize different internal tissues of plants without damaging their cells. They can establish themselves in the same niche as other microorganisms and develop antagonistic activities against phytopathogens. There is little research on the functional and morphological characterization of these bacteria in production systems in the Amazon. Thus, the objective of this work was to functionally and morphologically characterize endophytic bacteria isolated from cocoa trees (Theobroma cacao L.) and evaluate their antagonistic potential against phytopathogens. A total of 197 endophytic bacteria isolates were obtained from leaves and roots of cocoa plants with different production systems and at different times of the year. The characterization of functional groups consisted of proteolytic, amylolytic and cellulolytic activity and ability to fix nitrogen and solubilize phosphate. Morphological diversity was evaluated mainly according to the following parameters: shape, color, size and elevation of the colony. Thirteen isolates of endophytic bacteria, selected by cluster analysis, were used to evaluate the antagonistic potential in paired trials against four species of phytopathogenic fungi. The largest amount of endophytic bacteria was isolated from the root (95.9%), in the dry season. The most expressive activities with regards to the enzyme index were amylolytic (71.9%), proteolytic (70.2%) and nitrogen fixing (38.6%), respectively. The similarity analysis formed two clusters with isolates CS R 2.4 and CS R 2.25 exhibiting 100% similarity. Five isolates displayed inhibitory activity against phytopathogenic fungi, most notably isolate TS R 2.19, which exhibited antagonistic activity against all fungi and mycelial growth inhibition rates between 25.7% and 50.7%. Understanding the interaction between endophytes in cocoa plants is important as a possible additional tool in biological control. Our studies are incipient and the first to be carried out in different cocoa production systems in the state of Pará, Brazil.

Fungi-Bacteria Associations in Wilt Diseased Rhizosphere and Endosphere by Interdomain Ecological Network Analysis

In the plant rhizosphere and endosphere, some fungal and bacterial species regularly co-exist, however, our knowledge about their co-existence patterns is quite limited, especially during invasion by bacterial wilt pathogens. In this study, the fungal communities from soil to endophytic compartments were surveyed during an outbreak of tobacco wilt disease caused by Ralstonia solanacearum. It was found that the stem endophytic fungal community was significantly altered by pathogen invasion in terms of community diversity, structure, and composition. The associations among fungal species in the rhizosphere and endosphere infected by R. solanacearum showed more complex network structures than those of healthy plants. By integrating the bacterial dataset, associations between fungi and bacteria were inferred by Inter-Domain Ecological Network (IDEN) approach. It also revealed that infected samples, including both the rhizosphere and endosphere, had more complex interdomain networks than the corresponding healthy samples. Additionally, the bacterial wilt pathogenic Ralstonia members were identified as the keystone genus within the IDENs of both root and stem endophytic compartments. Ralstonia members was negatively correlated with the fungal genera Phoma, Gibberella, and Alternaria in infected roots, as well as Phoma, Gibberella, and Diaporthe in infected stems. This suggested that those endophytic fungi may play an important role in resisting the invasion of R. solanacearum.

Characterization of siderophore-producing microorganisms associated to plants from high-Andean heavy metal polluted soil from Callejón de Huaylas (Ancash, Perú)

Endophytic and rhizospheric microorganisms associated with six native plants adapted to heavy metal polluted soil from Punta Olímpica and Chahuapampa, located in Callejón de Huaylas mountains, were evaluated as potential candidates for technologies to clean polluted ecosystems. It was selected 14 bacteria and 9 fungi strains by their iron and/or aluminum siderophore production trait, where BEP17-Dm showed higher production. According to the 16S rDNA analysis, bacteria belong to Pseudomonas, Bacillus, and Achromobacter genera, whereas by ITS analysis fungi belong to Talaromyces, Hypoxylon, Tolypocladium, and Penicillium. All bacteria strains tolerated lead (2-8 mM) and eigth tolerated cadmium (1-6 mM); also all fungi tolerated lead (9-70 mM) and cadmium (3-10 mM). Two bacteria and six fungi solubilized cadmium carbonate, while eleven bacteria and two fungi solubilized tricalcium phosphate, where P. japonica BEP18-Dm and B. subtilis BRU16-Sr exhibited higher solubilization index. None strains solubilized lead carbonate. BEP18-Dm produced higher concentration of IAA (53.42 μgml^-1); while six bacteria and all fungi strains produced a low concentration of auxins. Medicago sativa seedlings inoculated with BEP17-Dm, BEP18-Dm, or BRU16-Sr showed more surviving percentage under in vitro culture in presence of Cd, Pb (0.5-1.0 mM), or Al (2.5-5.0 mM). Finally, it is the first report of siderophore-producing microorganisms from polluted soil of Callejón de Huaylas highlands, interestedly they displayed metabolic properties useful to enhance phytoremediation and biotechnology application.

Medicinal Plants and Their Bacterial Microbiota: A Review on Antimicrobial Compounds Production for Plant and Human Health

Medicinal plants (MPs) have been used since antiquity in traditional and popular medicine, and they represent a very important source of bioactive molecules, including antibiotic, antiviral, and antifungal molecules. Such compounds are often of plant origin, but in some cases, an origin or a modification from plant microbiota has been shown. Actually, the research continues to report the production of bioactive molecules by plants, but the role of plant–endophytic interaction is emerging. Classic examples are mainly concerned with fungal endophytes; however, it has been recently shown that bacterial endophytes can also play an important role in influencing the plant metabolism related to the synthesis of bioactive compounds. In spite of this, a deep investigation on the power of MP bacterial endophytes is lacking. Here, an overview of the studies on MP bacterial microbiota and its role in the production of plant antimicrobial compounds contributing to prime host defense system and representing a huge resource for biotech and therapeutic applications is provided.

Root fungal endophytes: identity, phylogeny and roles in plant tolerance to metal stress

Metal trace elements accumulate in soils mainly because of anthropic activities, leading living organisms to develop strategies to handle metal toxicity. Plants often associate with root endophytic fungi, including nonmycorrhizal fungi, and some of these organisms are associated with metal tolerance. The lack of synthetic analyses of plant-endophyte-metal tripartite systems and the scant consideration for taxonomy led to this review aiming (1) to inventory non-mycorrhizal root fungal endophytes described with respect to their taxonomic diversity and (2) to determine the mutualistic roles of these plant-fungus associations under metal stress. More than 1500 species in 100 orders (mainly Hypocreales and Pleosporales) were reported from a wide variety of environments and hosts. Most reported endophytes had a positive effect on their host under metal stress, but with various effects on metal uptake or translocation and no clear taxonomic consistency. Future research considering the functional patterns and dynamics of these associations is thus encouraged.