Molecular analysis of endophytic bacteria from the genus Bacillus isolated from tropical maize (Zea mays L.)

Endophytic Bacteria Bacillus subtilis, Isolated from Zea mays, as Potential Biocontrol Agent against Botrytis cinerea

Simple Summary

Plant–microorganism associations date back more than 400 million years. Plants host microorganisms that establish many different relationships with them, some negative and others very positive for both organisms. A type of this relationship is established with microorganisms that live inside them, known as endophytic microorganisms; they can include bacteria, yeasts, and fungi. In this study, we isolate endophytic bacteria from maize plants, and we characterize them in order to check their potential for being used as biocontrol agents against Botrytis cinerea, one of the most important phytopathogenic fungi in the world. The endophytic bacteria showed this antagonistic effect during in vitro assay and also during in vivo assay in Phaseolus vulgaris. At the same time, they showed the capacity for promoting growth in Zea mays plants.

Abstract

Plant diseases are one of the main factors responsible for food loss in the world, and 20–40% of such loss is caused by pathogenic infections. Botrytis cinerea is the most widely studied necrotrophic phytopathogenic fungus. It is responsible for incalculable economic losses due to the large number of host plants affected. Today, B. cinerea is controlled mainly by synthetic fungicides whose frequent application increases risk of resistance, thus making them unsustainable in terms of the environment and human health. In the search for new alternatives for the biocontrol of this pathogen, the use of endophytic microorganisms and their metabolites has gained momentum in recent years. In this work, we isolated endophytic bacteria from Zea mays cultivated in Colombia. Several strains of Bacillus subtilis, isolated and characterized in this work, exhibited growth inhibition against B. cinerea of more than 40% in in vitro cultures. These strains were characterized by studying several of their biochemical properties, such as production of lipopeptides, potassium solubilization, proteolytic and amylolytic capacity, production of siderophores, biofilm assays, and so on. We also analyzed: (i) its capacity to promote maize growth (Zea mays) in vivo, and (ii) its capacity to biocontrol B. cinerea during in vivo infection in plants (Phaseolus vulgaris).

Identification and Characterisation of Endophytic Bacteria from Coconut (Cocos nucifera) Tissue Culture

The coconut is an important economic crop in the Philippines which currently ranks as the world's second largest producer. This study characterised and identified endophytes from coconut tissue culture in order to gain an initial understanding of their potential uses as sources of bioproducts. The isolates were evaluated using morphological, biochemical and molecular methods. Gram staining results revealed that four out of five bacteria isolated were Gram positive. Isolate CEB 1 fermented all three sugars in the Triple Sugar Iron Test while the other four did not. 16S rDNA gene fragments were amplified from genomic DNA using the universal primers 16F27 and 16R1542. The 16S rDNA sequence were found to be homologous to Bacillus subtilis and Pantoea dispersa. Phylogenetic analyses showed significant clustering of bacterial isolates together with archived DNA of B. subtilis and P. dispersa. All isolated bacteria matched the characteristics of their molecular homologies. Isolate CEB 5, identified as B. subtilis, produced red pigments which are possibly pulcherrimin. Literature reports that pulcherrimin possesses antimicrobial activity against yeast species, microscopic fungi, and postharvest pathogens. P. dispera, on the other hand, has been reported to convert insoluble phosphorus into soluble form to enable plants to take up more phosphorus. Determination of the bioactivities of endophytes reported in this study may enable the discovery of novel bioproducts.

Maize seed endophytic bacteria: dominance of antagonistic, lytic enzyme-producing Bacillus spp

Beneficial aspects of endophytic microorganisms have motivated researchers to explore plant endophytic world. The present study was aimed to isolate and characterize the seed-borne endophytic bacteria from diverse maize genotypes. Eighty maize seed endophytic bacteria (MSEB), isolated from 30 maize genotypes, were characterized using polyphasic approach. The dendrograms and phylogenetic tree generated on the basis of ARDRA analysis and metabolic profiling of endophytic bacteria revealed genotypic and biochemical diversity among MSEB. The 16S rDNA sequence analysis revealed Bacillus as the most dominant encountered genus affiliated with Phylum Firmicutes. Few isolates belonged to genus Staphylococcus, whereas one isolate was identified as Corynebacterium sp. under Phylum Actinobacteria. Majority of the MSEB isolates exhibited antagonism against phytopathogenic fungi, production of ammonia, and secretion of lytic enzymes; some isolates also exhibited indole acetic acid production, the traits of which can be helpful in endophytic establishment and advantageous to the host plant. Besides, many MSEB exhibited tolerance to salinity (10%), osmotic stress (40% PEG6000), and temperature (60 °C), indicating their possible application under stress conditions. Endophytic nature of the selected MSEB isolates was confirmed by tracking their presence in shoots, leaves, and roots of the host seedlings with the help of biochemical marker (rifampicin resistance). Thus, the MSEB identified in the present study can be explored as potential bioinputs for improving plant growth and productivity under stressed conditions, besides helping in understanding the plant-endophyte interactions.

Paul A. Endophytic bacteria with plant growth promoting abilities from Ophioglossum reticulatum L

Endophytic bacteria colonizing the internal tissues of plants are known to improve plant growth by a wide variety of mechanisms. This study envisages the isolation and evaluation of plant growth promoting attributes of bacterial endophytes in perennial fern Ophioglossum reticulatum L. A total of 20 phenotypically distinguishable bacterial endophytes were isolated from surface sterilized leaf lamina, petiole, rhizome and spike of O. reticulatum L. The Shannon-Weaver diversity index showed that the rhizome (1.54) harbor more diverse types of endophytic bacteria than in its petiole, leaf lamina and spike. The isolated endophytes were characterized on the basis of micromorphological and physio-biochemical characters and tentatively assigned to the genus Bacillus, Pseudomonas and Staphylococcus. The isolates showed distinct variations in their enzymatic activities, sugar fermentation and antibiotic sensitivity profile. A number of endophytic isolates showed plant growth promoting activities like production of indole-3-acetic acid (IAA) and siderophore, growth in nitrogen-free medium and solubilization of phosphate. Time course of growth and IAA production by the potent isolate Bacillus OPR 7 have been determined. Exploitation of such plant growth promoting endophytes appears to be one of the best options in increasing biomass yield and improving plant fitness and productivity.

Isolation of Mexican Bacillus Species and Their Effects in Promoting Growth of Chili Pepper (Capsicum annuum L. cv Jalapeño)

The purpose of this work was to isolate and identify native bacteria from plants collected in the State of Yucatán, México with the ability to promote growth of chili pepper (Capsicum annuum L. cv Jalapeño). We identified nine bacterial isolates that belong to five species of Bacillus (i.e. Bacillus subtilis, B. flexus, B. cereus, B. megaterium and B. endophyticus) that produced indoleacetic acid (4.0-24.3 µg/mL) with solubilization index of 1.3-1.6. All the bacterial isolates were evaluated based on their ability to promote growth of chili pepper. Plants inoculated with B. subtilis ITC-N67 showed an increase in stem diameter and root volume, whereas inoculation with B. cereus ITC-BL18 increased the number of flower buds, fresh biomass of roots and total fresh biomass. Conversely, B. flexus ITC-P4 and B. flexus ITC-P22 showed deleterious effect on root volume and total biomass. In summary, our data showed that native B. cereus TC-BL18 and B. subtilis ITC-N67 have potential to be used as growth promoting microorganism for chili pepper, particularly in the state of Yucatán, México.

Developmental Peculiarities and Seed-Borne Endophytes in Quinoa: Omnipresent, Robust Bacilli Contribute to Plant Fitness

Among potential climate change-adapted crops for future agriculture, quinoa (Chenopodium quinoa), a facultative halophyte plant with exceptional nutritional properties, stands out as a prime candidate. This work examined how quinoa deals with extreme situations during seed rehydration. Quinoa distinguishes itself from other plants in multiple ways. It germinates within minutes, even under extremely hostile conditions. Broken seeds/split embryos are able to regenerate. Furthermore, quinoa seedlings are resurrection-competent. These peculiarities became in part explainable upon discovery of seed-borne microorganisms. 100% of quinoa seeds, from different sources, are inhabited by diverse members of the genus Bacillus. These endophytes are motile and reside in all seedling organs, indicating vertical transmission. Owing to their high catalase activities and superoxide contents the bacteria potentially manipulate the host's redox status. Superoxide-driven cell expansion enables quinoa to overcome a critical period in development, seedling establishment. Quinoa's immediate confrontation with "foreign" reactive oxygen species and bacterial elicitors likely induces a naturally primed state, enabling plants to withstand extreme situations. The endophytic bacteria, which are cultivable and highly robust themselves, have high potential for application in agriculture, food (amylase) and cosmetics (catalase) industry. This work also discusses the potential of transferring quinoa's microbiome to improve stress resistance in other plant species.

Seasonal variation of bacterial endophytes in urban trees

Bacterial endophytes, non-pathogenic bacteria residing within plants, contribute to the growth and development of plants and their ability to adapt to adverse conditions. In order to fully exploit the capabilities of these bacteria, it is necessary to understand the extent to which endophytic communities vary between species and over time. The endophytes of Acer negundo, Ulmus pumila, and Ulmus parvifolia were sampled over three seasons and analyzed using culture dependent and independent methods (culture on two media, terminal restriction fragment length polymorphism, and tagged pyrosequencing of 16S ribosomal amplicons). The majority of culturable endophytes isolated were Actinobacteria, and all the samples harbored Bacillus, Curtobacterium, Frigoribacterium, Methylobacterium, Paenibacilllus, and Sphingomonas species. Regardless of culture medium used, only the culturable communities obtained in the winter for A. negundo could be distinguished from those of Ulmus spp. In contrast, the nonculturable communities were dominated by Proteobacteria and Actinobacteria, particularly Erwinia, Ralstonia, and Sanguibacter spp. The presence and abundance of various bacterial classes and phyla changed with the changing seasons. Multivariate analysis on the culture independent data revealed significant community differences between the endophytic communities of A. negundo and Ulmus spp., but overall season was the main determinant of endophytic community structure. This study suggests studies on endophytic populations of urban trees should expect to find significant seasonal and species-specific community differences and sampling should proceed accordingly.

Diversity and characterization of culturable bacterial endophytes from Zea mays and their potential as plant growth-promoting agents in metal-degraded soils

In this study, we evaluated the phylogenetic diversity of culturable bacterial endophytes of Zea mays plants growing in an agricultural soil contaminated with Zn and Cd. Endophytic bacterial counts were determined in roots and shoots, and isolates were grouped by random amplified polymorphic DNA and identified by 16S ribosomal RNA (rRNA) gene sequencing. Endophytes were further characterized for the production of plant growth-promoting (PGP) substances, such as NH3, siderophores, indol-3-acetic acid (IAA), hydrogen cyanide and extracellular enzymes, and for the capacity to solubilize phosphate. The endophytes producing higher amounts of IAA were screened for their tolerance to Zn and Cd and used as bioinoculants for maize seedlings grown in the Zn/Cd-contaminated soil. The counts of endophytes varied between plant tissues, being higher in roots (6.48 log10 g(-1) fresh weight) when compared to shoots (5.77 log10 g(-1) fresh weight). Phylogenetic analysis showed that endophytes belong to three major groups: α-Proteobacteria (31 %), γ-Proteobacteria (26 %) and Actinobacteria (26 %). Pseudomonas, Agrobacterium, Variovorax and Curtobacterium were among the most represented genera. Endophytes were well-adapted to high Zn/Cd concentrations (up to 300 mg Cd l(-1) and 1,000 mg Zn l(-1)) and showed ability to produce several PGP traits. Strains Ochrobactrum haematophilum ZR 3-5, Acidovorax oryzae ZS 1-7, Frigoribacterium faeni ZS 3-5 and Pantoea allii ZS 3-6 increased root elongation and biomass of maize seedlings grown in soil contaminated with Cd and Zn. The endophytes isolated in this study have potential to be used in bioremediation/phytoremediation strategies.

Isolation of endophytic bacteria from arboreal species of the Amazon and identification by sequencing of the 16S rRNA encoding gene

Endophytic bacteria from three arboreal species native to the Amazon (Carapa guianenses, Ceiba pentandra, and Swietenia macrophylla), were isolated and identified, through partial sequencing of the 16S rRNA encoding gene. From these, 16 isolates were obtained, although, when compared to sequences deposited in GenBank, only seven had produced identifiable fragments. Bacillus, Pantoea and two non-culturable samples were identified. Results obtained through sequence analysis revealed low genetic diversity across the isolates, even when analyzing different species and plant structures. This is the first report concerning the isolation and identification of endophytic bacteria in these plant species.

Conservation and diversity of seed associated endophytes in Zea across boundaries of evolution, ethnography and ecology

Endophytes are non-pathogenic microbes living inside plants. We asked whether endophytic species were conserved in the agriculturally important plant genus Zea as it became domesticated from its wild ancestors (teosinte) to modern maize (corn) and moved from Mexico to Canada. Kernels from populations of four different teosintes and 10 different maize varieties were screened for endophytic bacteria by culturing, cloning and DNA fingerprinting using terminal restriction fragment length polymorphism (TRFLP) of 16S rDNA. Principle component analysis of TRFLP data showed that seed endophyte community composition varied in relation to plant host phylogeny. However, there was a core microbiota of endophytes that was conserved in Zea seeds across boundaries of evolution, ethnography and ecology. The majority of seed endophytes in the wild ancestor persist today in domesticated maize, though ancient selection against the hard fruitcase surrounding seeds may have altered the abundance of endophytes. Four TRFLP signals including two predicted to represent Clostridium and Paenibacillus species were conserved across all Zea genotypes, while culturing showed that Enterobacter, Methylobacteria, Pantoea and Pseudomonas species were widespread, with γ-proteobacteria being the prevalent class. Twenty-six different genera were cultured, and these were evaluated for their ability to stimulate plant growth, grow on nitrogen-free media, solubilize phosphate, sequester iron, secrete RNAse, antagonize pathogens, catabolize the precursor of ethylene, produce auxin and acetoin/butanediol. Of these traits, phosphate solubilization and production of acetoin/butanediol were the most commonly observed. An isolate from the giant Mexican landrace Mixteco, with 100% identity to Burkholderia phytofirmans, significantly promoted shoot potato biomass. GFP tagging and maize stem injection confirmed that several seed endophytes could spread systemically through the plant. One seed isolate, Enterobacter asburiae, was able to exit the root and colonize the rhizosphere. Conservation and diversity in Zea-microbe relationships are discussed in the context of ecology, crop domestication, selection and migration.