Indole-3-acetic acid-producing yeasts in the phyllosphere of the carnivorous plant Drosera indica L

Optimisation of indole acetic acid production by Neopestalotiopsis aotearoa endophyte isolated from Thymus vulgaris and its impact on seed germination of Ocimum basilicum

BACKGROUND

Microbial growth during plant tissue culture is a common problem that causes significant losses in the plant micro-propagation system. Most of these endophytic microbes have the ability to propagate through horizontal and vertical transmission. On the one hand, these microbes provide a rich source of several beneficial metabolites.

RESULTS

The present study reports on the isolation of fungal species from different in vitro medicinal plants (i.e., Breynia disticha major, Breynia disticha, Duranta plumieri, Thymus vulgaris, Salvia officinalis, Rosmarinus officinalis, and Ocimum basilicum l) cultures. These species were tested for their indole acetic acid (IAA) production capability. The most effective species for IAA production was that isolated from Thymus vulgaris plant (11.16 µg/mL) followed by that isolated from sweet basil plant (8.78 µg/mL). On screening for maximum IAA productivity, medium, "MOS + tryptophan" was chosen that gave 18.02 μg/mL. The macroscopic, microscopic examination and the 18S rRNA sequence analysis indicated that the isolate that given code T4 was identified as Neopestalotiopsis aotearoa (T4). The production of IAA by N. aotearoa was statistically modeled using the Box-Behnken design and optimized for maximum level, reaching 63.13 µg/mL. Also, IAA extract was administered to sweet basil seeds in vitro to determine its effect on plant growth traits. All concentrations of IAA extract boosted germination parameters as compared to controls, and 100 ppm of IAA extract exhibited a significant growth promotion effect for all seed germination measurements.

CONCLUSIONS

The IAA produced from N. aotearoa (T4) demonstrated an essential role in the enhancement of sweet basil (Ocimum basilicum) growth, suggesting that it can be employed to promote the plant development while lowering the deleterious effect of using synthetic compounds in the environment.

Effects of Environmental Stresses on Synthesis of 2-Phenylethanol and IAA by Enterobacter sp. CGMCC 5087

2-Phenylethanol (2-PE) and indole-3-acetic acid (IAA) are important secondary metabolites produced by microorganisms, and their production are closely linked to the growth state of microorganisms and environmental factors. Enterobacter CGMCC 5087 can produce both 2-PE and IAA depending on α-ketoacid decarboxylase KDC4427. This study aimed to investigate the effects of different environment factors including osmotic pressure, temperature, and pH on the synthesis of 2-PE and IAA in Enterobacter sp. CGMCC 5087. The bacteria exhibited an enhanced capacity for 2-PE synthesis while not affecting IAA synthesis under 5% NaCl and pH 4.5 stress conditions. In an environment with pH 9.5, the synthesis capacity of 2-PE remained unchanged while the synthesis capacity of IAA decreased. The synthesis ability of 2-PE was enhanced with an increase in temperature within the range of 25 °C to 37 °C, while the synthesis capacity of IAA was not affected significantly. Additionally, the expression of KDC4427 varied under stress conditions. Under 5% NaCl stress and decreased temperature, expression of the KDC4427 gene was increased. However, altering pH did not result in significant differences in gene expression levels, while elevated temperature caused a decrease in gene expression. Furthermore, molecular docking and molecular dynamics simulations suggested that these conditions may induce fluctuation in the geometry shape of binding cavity, binding energy, and especially the dαC-C- value, which played key roles in affecting the enzyme activity. These results provide insights and strategies for the synthesis of metabolic products 2-PE and IAA in bacterial fermentation, even under unfavorable conditions.

Cryptococcus neoformans: plant-microbe interactions and ecology

While the opportunistic human pathogens Cryptococcus neoformans and Cryptococcus gattii are often isolated from plants and plant-related material, evidence suggests that these Cryptococcus species do not directly infect plants. Studies find that plants are important for Cryptococcus mating and dispersal. However, these studies have not provided enough detail about how plants and these fungi interact, especially in ways that could show the fungi are capable of causing disease. This review synthesizes recent findings from studies utilizing different plant models associated with the ecology of C. neoformans and C. gattii. Unanswered questions about their environmental role are highlighted. Overall, current research indicates that Cryptococcus utilizes plants as a substrate rather than harming them, arguing against Cryptococcus as a genuine plant pathogen. We hypothesize that plants represent reservoirs that aid dispersal, not hosts vulnerable to infection.

Endophytic fungi: Unravelling plant-endophyte interaction and the multifaceted role of fungal endophytes in stress amelioration

Endophytic fungi colonize interior plant tissue and mostly form mutualistic associations with their host plant. Plant-endophyte interaction is a complex mechanism and is currently a focus of research to understand the underlying mechanism of endophyte asymptomatic colonization, the process of evading plant immune response, modulation of gene expression, and establishment of a balanced mutualistic relationship. Fungal endophytes rely on plant hosts for nutrients, shelter, and transmission and improve the host plant's tolerance against biotic stresses, including -herbivores, nematodes, bacterial, fungal, viral, nematode, and other phytopathogens. Endophytic fungi have been reported to improve plant health by reducing and eradicating the harmful effect of phytopathogens through competition for space or nutrients, mycoparasitism, and through direct or indirect defense systems by producing secondary metabolites as well as by induced systemic resistance (ISR). Additionally, for efficient crop improvement, practicing them would be a fruitful step for a sustainable approach. This review article summarizes the current research progress in plant-endophyte interaction and the fungal endophyte mechanism to overcome host defense responses, their subsequent colonization, and the establishment of a balanced mutualistic interaction with host plants. This review also highlighted the potential of fungal endophytes in the amelioration of biotic stress. We have also discussed the relevance of various bioactive compounds possessing antimicrobial potential against a variety of agricultural pathogens. Furthermore, endophyte-mediated ISR is also emphasized.

Molecular characterization of vermicompost-derived IAA-releasing bacterial isolates and assessment of their impact on the root improvement of banana during primary hardening

The hardening step of micropropagation is crucial to make the in vitro raised plants mature and further enhancing their survivability in the external environment. Auxin regulates various root physiological parameters in plant systems. Therefore, the present study aimed to assess the impact of three vermicompost-derived IAA-releasing microbial strains, designated S1, S2, and S3, as biofertilizers on in vitro raised banana plantlets during primary hardening. The High-Performance Thin-Layer Chromatography (HPTLC) analysis of these strains revealed a higher IAA content for S1 and S2 than that of S3 after 144 h of incubation. In total, seven different treatments were applied to banana plantlets, and significant variations were observed in all plant growth parameters for all treatments except autoclaved cocopeat (100%) mixed with autoclaved vermicompost (100%) at a 1:1 ratio. Among these treatments, the application of S3 biofertilizer: autoclaved cocopeat (1:1), followed by S2 biofertlizer: autoclaved cocopeat (1:1), was found to be better than other treatments for root numbers per plant, root length per plant, root volume, and chlorophyll content. These findings have confirmed the beneficial effects of microbial strains on plant systems and propose a link between root improvement and bacterial auxin. Further, these strains were identified at the molecular level as Bacillus sp. As per our knowledge, this is the first report of Bacillus strains isolated from vermicompost and applied as biofertilizer along with cocopeat for the primary hardening of banana. This unique approach may be adopted to improve the quality of plants during hardening, which increases their survival under abiotic stresses.

Biosynthetic Pathways and Functions of Indole-3-Acetic Acid in Microorganisms

Indole-3-acetic acid (IAA) belongs to the family of auxin indole derivatives. IAA regulates almost all aspects of plant growth and development, and is one of the most important plant hormones. In microorganisms too, IAA plays an important role in growth, development, and even plant interaction. Therefore, mechanism studies on the biosynthesis and functions of IAA in microorganisms can promote the production and utilization of IAA in agriculture. This mini-review mainly summarizes the biosynthesis pathways that have been reported in microorganisms, including the indole-3-acetamide pathway, indole-3-pyruvate pathway, tryptamine pathway, indole-3-acetonitrile pathway, tryptophan side chain oxidase pathway, and non-tryptophan dependent pathway. Some pathways interact with each other through common key genes to constitute a network of IAA biosynthesis. In addition, functional studies of IAA in microorganisms, divided into three categories, have also been summarized: the effects on microorganisms, the virulence on plants, and the beneficial impacts on plants.

Biochemical and Biotechnological Insights into Fungus-Plant Interactions for Enhanced Sustainable Agricultural and Industrial Processes

The literature is full of studies reporting environmental and health issues related to using traditional pesticides in food production and storage. Fortunately, alternatives have arisen in the last few decades, showing that organic agriculture is possible and economically feasible. And in this scenario, fungi may be helpful. In the natural environment, when associated with plants, these microorganisms offer plant-growth-promoting molecules, facilitate plant nutrient uptake, and antagonize phytopathogens. It is true that fungi can also be phytopathogenic, but even they can benefit agriculture in some way-since pathogenicity is species-specific, these fungi are shown to be useful against weeds (as bioherbicides). Finally, plant-associated yeasts and molds are natural biofactories, and the metabolites they produce while dwelling in leaves, flowers, roots, or the rhizosphere have the potential to be employed in different industrial activities. By addressing all these subjects, this manuscript comprehensively reviews the biotechnological uses of plant-associated fungi and, in addition, aims to sensitize academics, researchers, and investors to new alternatives for healthier and more environmentally friendly production processes.

Organic Farming Allows Balanced Fungal and Oomycetes Communities

Conventional and organic farming systems affect soils differently, thereby influencing microbial diversity and composition. Organic farming, which relies on natural processes, biodiversity, and cycles adapted to local conditions, is generally known to improve soil texture and alleviate microbial diversity loss compared with that of conventional farming, which uses synthetic inputs such as chemical fertilisers, pesticides, and herbicides. Although they affect the health and productivity of host plants, the community dynamics of fungi and fungi-like oomycetes (under Chromista) in organic farmland are poorly understood. The present study aimed to determine the differences in the diversity and composition of fungi and oomycetes inhabiting organic and conventional farm soils using culture-based DNA barcoding and culture-independent environmental DNA (eDNA) metabarcoding. Four tomato farms with different farming practices were selected and investigated: mature pure organic (MPO) via non-pesticide and organic fertiliser, mature integrated organic (MIO) via non-pesticide and chemical fertiliser, mature conventional chemical (MCC) via both pesticide and chemical fertiliser, and young conventional chemical (YCC). Culture-based analysis revealed that different genera were dominant on the four farms: Linnemannia in MPO, Mucor in MIO, and Globisporangium in MCC and YCC. eDNA metabarcoding demonstrated that the fungal richness and diversity on the MPO farm were higher than that on other farms. Both conventional farms exhibited simpler fungal and oomycete network structures with lower phylogenetic diversity. Interestingly, a high richness of oomycetes was shown in YCC; in which, Globisporangium, a potential pathogenic group on tomato plants, was abundantly observed. Our findings indicate that organic farming enhances fungal and oomycete diversity, which may provide robust support for maintaining healthy and sustainable agricultural practices. This study contributes to our knowledge on the positive effects of organic farming on crop microbiomes and provides essential information for maintaining biological diversity.

Effective Microorganisms as Halal-Based Sources for Biofertilizer Production and Some Socio-Economic Insights: A Review

This paper aims to review the literature on 'Effective Microorganism (EM)' and 'Fertilizer' from the Scopus database and to discuss EMs using Halal-based sources for biofertilizer production from socio economic insights. Based on EM and fertilizer publications on the Scopus database, all the 17 papers reviewed provided no detailed information on the Halal-status of the biofertilizers inoculated with EM. The impacts of Halal-certified biofertilizers will trigger the Halal certification in food products by (a) catering for the increasing Halal food demand due to expectedly Muslim population expansion, (b) contributing to the sustainable buying behaviour of Halal products' consumers in the future, (c) catering for the increasing number of Muslim travellers around the world, (d) becoming a positive driver for higher production of more Halal foods that can enhance food safety, human health and well-being, and (e) creating a cost-effective and increasing food marketability. The later three points (c, d and e) play a very important role in a country's societal well-being and economic growth and development. Although Halal-status is not a must for the world's food marketing, Halal-certified biofertilizer for the Halal-status of food carries the greatest potential to enter the ever-expanding Muslim markets. Finally, it is postulated that the successful usage of EM using Halal-based sources for biofertilizer production will result in two major outcomes from the points of United Nations' Sustainable Development Goals # 9 (Industry, Innovation and Infrastructure) and # 12 (Responsible Consumption and Production). Hence, the presented review provides a starting point for future research considering sustainability and innovation as priorities.

Mycobiota of Mexican Maize Landraces with Auxin-Producing Yeasts That Improve Plant Growth and Root Development

Compared to agrochemicals, bioinoculants based on plant microbiomes are a sustainable option for increasing crop yields and soil fertility. From the Mexican maize landrace "Raza cónico" (red and blue varieties), we identified yeasts and evaluated in vitro their ability to promote plant growth. Auxin production was detected from yeast isolates and confirmed using Arabidopsis thaliana plants. Inoculation tests were performed on maize, and morphological parameters were measured. Eighty-seven yeast strains were obtained (50 from blue corn and 37 from red corn). These were associated with three families of Ascomycota (Dothideaceae, Debaryomycetaceae, and Metschnikowiaceae) and five families of Basidiomycota (Sporidiobolaceae, Filobasidiaceae, Piskurozymaceae, Tremellaceae, and Rhynchogastremataceae), and, in turn, distributed in 10 genera (Clavispora, Rhodotorula, Papiliotrema, Candida, Suhomyces, Soliccocozyma, Saitozyma Holtermaniella, Naganishia, and Aeurobasidium). We identified strains that solubilized phosphate and produced siderophores, proteases, pectinases, and cellulases but did not produce amylases. Solicoccozyma sp. RY31, C. lusitaniae Y11, R. glutinis Y23, and Naganishia sp. Y52 produced auxins from L-Trp (11.9-52 µg/mL) and root exudates (1.3-22.5 µg/mL). Furthermore, they stimulated the root development of A. thaliana. Inoculation of auxin-producing yeasts caused a 1.5-fold increase in maize plant height, fresh weight, and root length compared to uninoculated controls. Overall, maize landraces harbor plant growth-promoting yeasts and have the potential for use as agricultural biofertilizers.

Effects of Co-Inoculating Saccharomyces spp. with Bradyrhizobium japonicum on Atmospheric Nitrogen Fixation in Soybeans (Glycine max (L.))

Crop production encounters challenges due to the dearth of nitrogen (N) and phosphorus (P), while excessive chemical fertilizer use causes environmental hazards. The use of N-fixing microbes and P-solubilizing microbes (PSMs) can be a sustainable strategy to overcome these problems. Here, we conducted a greenhouse pot experiment following a completely randomized blocked design to elucidate the influence of co-inoculating N-fixing bacteria (Bradyrhizobium japonicum) and PSMs (Saccharomyces cerevisiae and Saccharomyces exiguus) on atmospheric N₂-fixation, growth, and yield. The results indicate a significant influence of interaction on Indole-3-acetic acid production, P solubilization, seedling germination, and growth. It was also found that atmospheric N₂-fixation, nodule number per plant, nodule dry weight, straw, and root dry weight per plant at different growth stages were significantly increased under dual inoculation treatments relative to single inoculation or no inoculation treatment. Increased seed yield and N and P accumulation were also noticed under co-inoculation treatments. Soil available N was highest under sole bacterial inoculation and lowest under the control treatment, while soil available P was highest under co-inoculation treatments and lowest under the control treatment. We demonstrated that the co-inoculation of N-fixing bacteria and PSMs enhances P bioavailability and atmospheric N₂-fixation in soybeans leading to improved soil fertility, raising crop yields, and promoting sustainable agriculture.

Ecology and functional potential of phyllosphere yeasts

The phyllosphere (i.e., the aerial parts of plants) harbors a rich microbial life, including bacteria, fungi, viruses, and yeasts. Current knowledge of yeasts stems primarily from industrial and medical research on Saccharomyces cerevisiae and Candida albicans, both of which can be found on plant tissues. For most other yeasts found in the phyllosphere, little is known about their ecology and functions. Here, we explore the diversity, dynamics, interactions, and genomics of yeasts associated with plant leaves and how tools and approaches developed for model yeasts can be adopted to disentangle the ecology and natural functions of phyllosphere yeasts. A first genomic survey exemplifies that we have only scratched the surface of the largely unexplored functional potential of phyllosphere yeasts.

Phosphate solubilization and indole acetic acid production by rhizosphere yeast Torulaspora globosa: improvement of culture conditions for better performance in vitro

The rhizosphere yeast Torulaspora globosa is known to produce indole acetic acid (IAA) and to solubilize minerals. Due to the prospective use of this yeast as a biostimulant for agricultural applications, this work aimed to optimize the cultural conditions for both IAA production and phosphate solubilization. For phosphate solubilization, the temperature (20, 25 and 30 °C), initial medium pH (3.0, 5.0, and 7.0), and shaker speed (without mixing, 100 rpm, 150 rpm, and 200 rpm) were considered using the one-factor-at-a-time (OFAT) design. Temperature of 25 °C, initial medium pH 7.0, and static cultures were the conditions of greatest phosphate solubilization, with 40% of the total phosphorus content solubilized from calcium phosphate (419.86 mg L-1) after 48 h. By using the response surface methodology, the maximum IAA production (217.73 µg mL-1) was obtained with the highest initial pH 7.0, the lowest nitrogen, and glucose concentrations (5 g L-1 and 10 g L-1, respectively) and the lowest agitator speed (100 rpm). Further tests indicated that nitrogen affected significantly IAA production and the absence of nitrogen in the medium promoted higher IAA production (457 µg mL-1). The results obtained here may contribute to the scaling up for industrial and agricultural applications of a yeast-based product with T. globosa.

Extracellular Metabolites of Heterotrophic Auxenochlorella protothecoides: A New Source of Bio-Stimulants for Higher Plants

The biodiversity of microalgal species is enormous, and their versatile metabolism produces a wide diversity of compounds that can be used in food, healthcare, and other applications. Microalgae are also a potential source of bio-stimulants that enhance nutrition efficiency, abiotic stress tolerance, and/or crop quality traits. In this study, the extracellular metabolites of Auxenochlorella protothecoides (EAp) were prepared using three different culture strategies, and their effects on plant growth were examined. Furthermore, the composition of EAp was analyzed by GC-MS. The elongation of lateral roots and the cold-tolerance of Arabidopsis thaliana and Nicotiana benthamiana were promoted by EAp. Moreover, EAp from high-cell-density fermentation stimulated the growth of the leafy vegetables Brassica rapa and Lactuca sativa at dilutions as high as 500- and 1000-fold. Three major groups of compounds were identified by GC-MS, including organic acids or organic acid esters, phenols, and saccharides. Some of these compounds have known plant–stimulating effects, while the rest requires further investigation in the future. Our study demonstrates that EAp is a potential bio-stimulant, while also providing an environmentally friendly and economical microalgae fermentation process.

Complementary Effects of Dark Septate Endophytes and Trichoderma Strains on Growth and Active Ingredient Accumulation of Astragalus mongholicus under Drought Stress

Drought is a major abiotic stress factor affecting plant growth and production, while utilizing beneficial endophytic fungi is one of the most promising strategies for enhancing plant growth and drought tolerance. In the current study, a pot experiment was conducted to investigate the beneficial effects of dark septate endophyte (DSE) (Macrophomina pseudophaseolina, Paraphoma radicina) and Trichoderma (Trichoderma afroharzianum, Trichoderma longibrachiatum) inoculum on Astragalus mongholicus grown in sterile soil under drought stress, alone, or in combination. The addition of Trichoderma enhanced the DSE colonization in roots regardless of the water condition. Under well-watered conditions, M. pseudophaseolina inoculation significantly enhanced the biomass and root length of A. mongholicus. The two DSE and Trichoderma inoculum significantly improved calycosin-7-O-β-D-glucoside content. However, M. pseudophaseolina + T. afroharzianum inoculation better promoted root growth, whereas co-inoculation had higher active ingredient contents compared with single inoculation, except for P. radicina + T. afroharzianum. Under drought stress, DSE and Trichoderma inoculum significantly improved root biomass, root length, calycosin-7-O-β-D-glucoside content, and activities of nitrate reductase and soil urease. P. radicina + T. afroharzianum and P. radicina + T. longibrachiatum better increased root length, and all combinations of DSE and Trichoderma had a greater impact on the increase in formononetin content compared with the single treatments. Additionally, Trichoderma relies on antioxidant enzymes, growth hormones, and the redox system (ascorbic acid−glutathione) to resist drought, while DSE strains have an additional osmotic regulation system in addition to the drought resistance function possessed by Trichoderma, and the effect of co-inoculation (especially M. pseudophaseolina + T. longibrachiatum and P. radicina + T. afroharzianum) on plant physiological parameters was greater than that of single inoculation. This study provides a new research direction for the effects of DSE and Trichoderma on medicinal plant cultivated in dryland.

Actinomucor elegans and Podospora bulbillosa Positively Improves Endurance to Water Deficit and Salinity Stresses in Tomato Plants

Fungal strains isolated from the rhizosphere of healthy Solanum lycopersicum were examined to mitigate symptoms of drought and salinity stresses. The fungal strains were identified as Actinomucor elegans and Podospora bulbillosa based on their DNA sequencing and morphological analysis. Additionally, the fungal strains were assayed for a number of plant growth promoting traits and abiotic stresses on solid media. Moreover, a greenhouse experiment was conducted and tomato seedlings were treated with 25% PEG or 1.5% NaCl for 12 days, and the impact of plant growth promoting fungi (PGPF) on tomato seedling performance under these conditions was examined. PGPF application raised the survival of the stressed tomato plants, which was evidenced by higher physiological and biochemical processes. The PGPF-inoculated plants exhibited higher chlorophyll, carotenoid, protein, amino acid, antioxidant activities, salicylic acid, glucose, fructose, and sucrose contents, and showed lower hydrogen peroxide, and lipid metabolism relative to control plants under stress. Analysis using gene expression showed enhanced expression of SlF3H gene and reduced expression of SlNCED1, SlDEAD31, SlbZIP38, and SlGRAS10 genes following PGPFs application. Overall, the outcomes of this study elucidate the function of these fungal strains and present candidates with potential implementation as biofertilizers and in promoting plant stress endurance.

Seed-Borne Probiotic Yeasts Foster Plant Growth and Elicit Health Protection in Black Gram (Vigna mungo L.)

Black gram is one of the most indispensable components of the world food basket and the growth and health of the crop get influenced by biotic and abiotic factors. Beneficial phyto-microbes are one among them that influence the crop growth, more particularly the seed borne microbes are comparatively beneficial, that they pass from generation to generation and are associated with the plants from establishment to development. In the present study, twenty seed-borne yeasts were characterized and tested for growth promotion of black gram and their antagonism against black gram phytopathogens. Two yeasts, Pichia kudriavzevii POY5 and Issatchenkia terricola GRY4, produced indole acetic acid (IAA), siderophore, 1-amino cyclopropane-1-carboxylic acid deaminase (ACCD), and plant defense enzymes. They solubilized phosphate and zinc and fixed atmospheric nitrogen. Inoculation of these two yeast isolates and Rhizobium BMBS1 improved the seed germination, physiological parameters and yield of black gram. Inoculation of Rhizoctonia solani-challenged plants with plant growth-promoting yeasts, resulted in the synthesis of defense-related enzymes such as peroxidases (POD), chitinases, catalase (CAT), and polyphenol oxidases (PPO). Thus, the seed-borne yeasts, Pichia kudriavzevii POY5 and Issatchenkia terricola GRY4, could be used as plant probiotics for black gram.

Tobacco Plant Growth-Promoting and Antifungal Activities of Three Endophytic Yeast Strains

In this research, the biosynthetic and biocontrol potential of endophytic yeast to improve the growth and development of tobacco has been elucidated. Three yeast strains were enriched and isolated from different plant tissues. Partial sequence analysis of ITS5-5.8-ITS4 region of the nuclear ribosomal DNA with universal primers identified YD5, YE1, and YSW1 as Saccharomyces cerevisiae (S. cerevisiae), Zygosaccharomyces bailii (Z. bailii), and Saccharomyces kudriavzevii (S. kudriavzevii), respectively. When cultivated in a medium supplemented with 0.1% L-tryptophan, isolated yeast strains produced indole-3-acetic acid (IAA). The capacities of those strains to improve the mobility of phosphorus and synthesize siderophores has been proven. Their antimicrobial activities against several Solanaceae plant pathogenic fungi (Alternaria solani pathovar. tobacco, Rhizoctonia solani, and Fusarium solani pathovar. phaseoli) were determined. S. cerevisiae YD5, Z. bailii YE1, and S. kudriavzevii YSW1 inhibited the growth of all tested pathogens. Yeast strains were tested for endophytic colonization of tobacco by two different inoculation methods: soil drench (SD) and leaf spraying (LS). To establish colonization in the various tissues of tested tobacco (Nicotiana tabaccum L.) plants, samples were taken on the seventh, fourteenth, and twenty-first days after treatment (DAT), and explants were inoculated on yeast malt agar (YMA). Both techniques of inoculation showed a high frequency of colonization from 83.33% to 100%. To determine the effectiveness of the microbial endophytes, their effect on some physiological processes in the plant were analyzed, such as photosynthesis, stomatal conductivity, and transpiration intensity. The effect of single and double treatment with yeast inoculum on the development and biochemical parameters of tobacco was reported. Plants have the ability of structural and functional adaptation to stress effects of different natures. All treated plants had a higher content of photosynthetic pigments compared to the control. Photosynthesis is probably more intense, and growth stimulation has been observed. The chlorophyll a/b ratio remained similar, and the total chlorophyll/carotenoid ratio slightly increased as a result of elevated chlorophyll levels. The most significant stimulating effect was recorded in tobacco plants treated by foliar spraying with Z. bailii YE1 and S. cerevisiae YD5. In contrast, S. kudriavzevii YSW1 had a better effect when applied as a soil drench. Thus, S. cerevisiae YD5, Z. bailii YE1, and S. kudriavzevii YSW1 have a high potential to be used as a biocontrol agents in organic agriculture.

Exogenous Indole-3-Acetic Acid Induced Ethanol Tolerance in Phylogenetically Diverse Saccharomycetales Yeasts

Indole-3-acetic acid (IAA) is an exogenous growth regulatory signal that is produced by plants and various microorganisms. Microorganisms have been suggested to cross-communicate with each other through IAA-mediated signaling mechanisms. The IAA-induced tolerance response has been reported in several microorganisms, but has not yet been described in Saccharomycetales yeasts. In the present study, three common stressors (heat, osmotic pressure, and ethanol) were examined in relation to the influence of a pretreatment with IAA on stress tolerance in 12 different lineages of Saccharomyces cerevisiae. The pretreatment with IAA had a significant effect on the induction of ethanol tolerance by reducing the doubling time of S. cerevisiae growth without the pretreatment. However, the pretreatment did not significantly affect the induction of thermo- or osmotolerance. The IAA pretreatment decreased the lethal effects of ethanol on S. cerevisiae cells. Although yeasts produce ethanol to outcompete sympatric microorganisms, IAA is not a byproduct of this process. Nevertheless, the accumulation of IAA indicates an increasing number of microorganisms, and, thus, greater competition for resources. Since the “wine trait” is shared by both phylogenetically related and distinct lineages in Saccharomycetales, we conclude that IAA-induced ethanol tolerance is not specific to S. cerevisiae; it may be widely detected in both pre-whole genome duplication (WGD) and post-WGD yeasts belonging to several genera of Saccharomycetales.

Non-target impacts of fungicide disturbance on phyllosphere yeasts in conventional and no-till management

Fungicides reduce fungal pathogen populations and are essential to food security. Understanding the impacts of fungicides on crop microbiomes is vital to minimizing unintended consequences while maintaining their use for plant protection. However, fungicide disturbance of plant microbiomes has received limited attention, and has not been examined in different agricultural management systems. We used amplicon sequencing of fungi and prokaryotes in maize and soybean microbiomes before and after foliar fungicide application in leaves and roots from plots under long-term no-till and conventional tillage management. We examined fungicide disturbance and resilience, which revealed consistent non-target effects and greater resiliency under no-till management. Fungicides lowered pathogen abundance in maize and soybean and decreased the abundance of Tremellomycetes yeasts, especially Bulleribasidiaceae, including core microbiome members. Fungicide application reduced network complexity in the soybean phyllosphere, which revealed altered co-occurrence patterns between yeast species of Bulleribasidiaceae, and Sphingomonas and Hymenobacter in fungicide treated plots. Results indicate that foliar fungicides lower pathogen and non-target fungal abundance and may impact prokaryotes indirectly. Treatment effects were confined to the phyllosphere and did not impact belowground microbial communities. Overall, these results demonstrate the resilience of no-till management to fungicide disturbance, a potential novel ecosystem service provided by no-till agriculture.

Functional characterization of culturable fungi from microbiomes of the "conical cobs" Mexican maize (Zea mays L.) landrace

Mexican maize landraces, produced for local consumption, are adapted to different environmental conditions, and their yield is affected by abiotic and biotic factors, including the use of agrochemicals. The search for sustainable alternatives to agrochemicals includes the study of the culturable microbial communities. In this study, the fungal communities associated with 2 Mexican maize landraces reddish and bluish "conical cobs" were found to be comprised of Ascomycota fungi, represented by 89 strains within 6 orders (Pleosporales, Hypocreales, Onygenales, Capnodiales, Helotiales, and Eurotiales) and 16 genera. Cellulases and metallophores production were the primary enzymatic products and plant growth-promoting activities were detected among the isolates. Penicillium, Didymella, and Fusarium strains had the most active enzymatic and plant growth promoting activities, however, Aspergillus sp. HES2-2.2, Talaromyces sp. RS1-7, and Penicillium sp. HFS3-3 showed antagonistic activity against the four phytopathogenic Fusarium strains Fusarium oxysporum, Fusarium sambucinum, Fusarium fujikuroi and Fusarium incarnatum-equiseti and also a high and diverse production of enzymatic and plant growth promoting activities; here we identified fungal strains as candidates to promote maize growth.

Phyllosphere microbiome: Diversity and functions

Phyllosphere or aerial surface of plants represents the globally largest and peculiar microbial habitat that inhabits diverse and rich communities of bacteria, fungi, viruses, cyanobacteria, actinobacteria, nematodes, and protozoans. These hyperdiverse microbial communities are related to the host's specific functional traits and influence the host's physiology and the ecosystem's functioning. In the last few years, significant advances have been made in unravelling several aspects of phyllosphere microbiology, including diversity and microbial community composition, dynamics, and functional interactions. This review highlights the current knowledge about the assembly, structure, and composition of phyllosphere microbial communities across spatio-temporal scales, besides functional significance of different microbial communities to the plant host and the surrounding environment. The knowledge will help develop strategies for modelling and manipulating these highly beneficial microbial consortia for furthering scientific inquiry into their interactions with the host plants and also for their useful and economic utilization.

Large scale production of indole-3-acetic acid and evaluation of the inhibitory effect of indole-3-acetic acid on weed growth

Indole-3-acetic acid (IAA) is the most common plant hormone of the auxin class and regulates various plant growth processes. The present study investigated IAA production by the basidiomycetous yeast Rhodosporidiobolus fluvialis DMKU-CP293 using the one-factor-at-a-time (OFAT) method and response surface methodology (RSM). IAA production was optimized in shake-flask culture using a cost-effective medium containing 4.5% crude glycerol, 2% CSL and 0.55% feed-grade l-tryptophan. The optimized medium resulted in a 3.3-fold improvement in IAA production and a 3.6-fold reduction in cost compared with those obtained with a non-optimized medium. Production was then scaled up to a 15-L bioreactor and to a pilot-scale (100-L) bioreactor based on the constant impeller tip speed (V_tip) strategy. By doing so, IAA was successfully produced at a concentration of 3569.32 mg/L at the pilot scale. To the best of our knowledge, this is the first report of pilot-scale IAA production by microorganisms. In addition, we evaluated the effect of crude IAA on weed growth. The results showed that weed (Cyperus rotundus L.) growth could be inhibited by 50 mg/L of crude IAA. IAA therefore has the potential to be developed as a herbicidal bioproduct to replace the chemical herbicides that have been banned in various countries, including Thailand.

Plant growth-promoting traits of yeasts isolated from the tank bromeliad Vriesea minarum L.B. Smith and the effectiveness of Carlosrosaea vrieseae for promoting bromeliad growth

Yeasts can play important roles in promoting plant growth; however, little information is available in this regard for yeasts in water of bromeliad tanks. Here, we characterize the ability of 79 yeast isolates from tank bromeliad Vriesea minarum, an endangered species, to solubilize phosphate, secrete siderophores, and synthesize indole-3-acetic acid (IAA). The results showed that 67.8% of all assayed yeast isolates mobilized inorganic phosphate; 40.0% secreted siderophores; and 89.9% synthetized IAA and IAA-like compounds. Among the species studied, Carlosrosaea vrieseae UFMG-CM-Y6724 is highlighted for producing IAA (76.1 μg mL^-1) and siderophores, and solubilizing phosphate. In addition, evaluation of the effects of filtrate containing IAA-like compounds produced by the C. vrieseae on the development and photosynthetic performance of V. minarum seedlings found it to improve seedling growth equal to that of commercial IAA. These results demonstrate that C. vrieseae can produce compounds with great potential for future use as biofertilizer agents.

Culturable Yeasts as Biofertilizers and Biopesticides for a Sustainable Agriculture: A Comprehensive Review

The extensive use of synthetic fertilizers and pesticides has negative consequences in terms of soil microbial biodiversity and environmental contamination. Faced with this growing concern, a proposed alternative agricultural method is the use of microorganisms as biofertilizers. Many works have been focused on bacteria, but the limited literature on yeasts and their potential ability to safely promote plant growth is gaining particular attention in recent years. Thus, the objective of this review is to highlight the application of yeasts as biological agents in different sectors of sustainable agricultural practices through direct or indirect mechanisms of action. Direct mechanisms include the ability of yeasts to provide soluble nutrients to plants, produce organic acids and phytohormones (indole-3-acetic acid). Indirect mechanisms involve the ability for yeasts to act as biocontrol agents through their high antifungal activity and lower insecticidal and herbicidal activity, and as soil bioremediating agents. They also act as protective agents against extreme environmental factors by activating defense mechanisms. It is evident that all the aspects that yeasts offer could be useful in the creation of quality biofertilizers and biopesticides. Hence, extensive research on yeasts could be promising and potentially provide an environmentally friendly solution to the increased crop production that will be required with a growing population.

Features of basidiomycetous yeasts from grapes and apples associated with crop environment and fermenting juice

AIMS

The characterization of grape and apple yeasts was carried out to investigate the ecology of basidiomycetes associated with crop environment and fermenting juice.

METHODS AND RESULTS

A total of 15 basidiomycetous strains were analysed for plant-growth promoting properties, sensitivity to fungicides and features related to their survival in fermenting juice (low pH, SO₂ and ethanol sensitivity). Only one strain displayed 1-aminocyclopropane-1-carboxylate deaminase activity, whereas other strains were able to produce ammonia and indole-3-acetic acid, solubilize calcium phosphate, and display catalase activity and antagonism against Botrytis cinerea. Strains presented great variability in their sensitivity to fungicides. Rhodotorula mucilaginosa Yl26 and Sporobolomyces agrorum PYCC 8108^T displayed low sensitivity to all fungicides, with high tolerance to SO₂ and ethanol, and were able to survive in fermenting grape and apple juice.

CONCLUSIONS

This study revealed the diversity of basidiomycetous yeasts in the important physiological traits that affect their growth, either in the crop environment or in fermenting juice.

SIGNIFICANCE AND IMPACT OF THE STUDY

Identify the possibility of selective effects of fungicide treatments on basidiomycetous yeasts that could offer benefits for grapevines and apple trees, as well as the survival of strains that are better adapted to fermenting juice and that potentially have a role in the aroma of beverages.

Indole-3-acetic acid is a physiological inhibitor of TORC1 in yeast

Indole-3-acetic acid (IAA) is the most common, naturally occurring phytohormone that regulates cell division, differentiation, and senescence in plants. The capacity to synthesize IAA is also widespread among plant-associated bacterial and fungal species, which may use IAA as an effector molecule to define their relationships with plants or to coordinate their physiological behavior through cell-cell communication. Fungi, including many species that do not entertain a plant-associated life style, are also able to synthesize IAA, but the physiological role of IAA in these fungi has largely remained enigmatic. Interestingly, in this context, growth of the budding yeast Saccharomyces cerevisiae is sensitive to extracellular IAA. Here, we use a combination of various genetic approaches including chemical-genetic profiling, SAturated Transposon Analysis in Yeast (SATAY), and genetic epistasis analyses to identify the mode-of-action by which IAA inhibits growth in yeast. Surprisingly, these analyses pinpointed the target of rapamycin complex 1 (TORC1), a central regulator of eukaryotic cell growth, as the major growth-limiting target of IAA. Our biochemical analyses further demonstrate that IAA inhibits TORC1 both in vivo and in vitro. Intriguingly, we also show that yeast cells are able to synthesize IAA and specifically accumulate IAA upon entry into stationary phase. Our data therefore suggest that IAA contributes to proper entry of yeast cells into a quiescent state by acting as a metabolic inhibitor of TORC1.

Auxins are a major group of plant phytohormones that are critical for growth and development. Amongst the auxins, indole-3-acetic acid (IAA) is the most common, naturally occurring phytohormone that regulates cell division, differentiation, and senescence in plants. Interestingly, the capacity to synthesize and secrete IAA is also widespread among fungi, including the budding yeast Saccharomyces cerevisiae, but the role of IAA in fungi has largely remained unknown. Here, we confirm an earlier observation that IAA inhibits growth of budding yeast and show by diverse genetic and biochemical means that IAA restrains budding yeast growth by inhibiting the target of rapamycin complex 1 (TORC1), a highly conserved eukaryotic regulator of growth. Intriguingly, budding yeast cells accumulate IAA specifically when limited for nutrients, which suggests that IAA plays a hitherto unknown physiological role in contributing to the establishment of cellular quiescence by acting as a metabolic inhibitor of TORC1.

Shaping the leaf microbiota: plant-microbe-microbe interactions

The aerial portion of a plant, namely the leaf, is inhabited by pathogenic and non-pathogenic microbes. The leaf's physical and chemical properties, combined with fluctuating and often challenging environmental factors, create surfaces that require a high degree of adaptation for microbial colonization. As a consequence, specific interactive processes have evolved to establish a plant leaf niche. Little is known about the impact of the host immune system on phyllosphere colonization by non-pathogenic microbes. These organisms can trigger plant basal defenses and benefit the host by priming for enhanced resistance to pathogens. In most disease resistance responses, microbial signals are recognized by extra- or intracellular receptors. The interactions tend to be species specific and it is unclear how they shape leaf microbial communities. In natural habitats, microbe-microbe interactions are also important for shaping leaf communities. To protect resources, plant colonizers have developed direct antagonistic or host manipulation strategies to fight competitors. Phyllosphere-colonizing microbes respond to abiotic and biotic fluctuations and are therefore an important resource for adaptive and protective traits. Understanding the complex regulatory host-microbe-microbe networks is needed to transfer current knowledge to biotechnological applications such as plant-protective probiotics.

Indole-3-acetic acid synthesized through the indole-3-pyruvate pathway promotes Candida tropicalis biofilm formation

We previously found that the elevated abundance of the fungus Candida tropicalis is positively correlated with the bacteria Escherichia coli and Serratia marcescens in Crohn’s disease patients and the three pathogens, when co-cultured, form a robust mixed-species biofilm. The finding suggests that these three pathogens communicate and promote biofilm formation, possibly through secretion of small signaling molecules. To identify candidate signaling molecules, we carried out a metabolomic analysis of the single-species and triple-species cultures of the three pathogens. This analysis identified 15 metabolites that were highly increased in the triple-species culture. One highly induced metabolite was indole-3-acetic acid (IAA), which has been shown to induce filamentation of certain fungi. We thus tested the effect of IAA on biofilm formation of C. tropicalis and demonstrated that IAA promotes biofilm formation of C. tropicalis. Then, we carried out isotope tracing experiments using ¹³C-labeled-tryptophan as a precursor to uncover the biosynthesis pathway of IAA in C. tropicalis. The results indicated that C. tropicalis synthesizes IAA through the indole-3-pyruvate pathway. Further studies using inhibitors of the indole-3-pyruvate pathway are warranted to decipher the mechanisms by which IAA influences biofilm formation.

Plant growth-promoting traits of yeasts isolated from Spanish vineyards: benefits for seedling development

It is known that some microorganisms can enhance plant development. However, the use of yeasts as growth-promoting agents has been poorly investigated. The aim of this study was the characterisation of a collection of 69 yeast strains isolated from Spanish vineyards. Phytobeneficial attributes such as solubilisation of nutrients, synthesis of active biomolecules and cell wall-degrading enzyme production were analysed. Strains that revealed multiple growth-promoting characteristics were identified. The in vitro co-culture of Nicotiana benthamiana with yeast isolates showed enhancement of plant growth in 10 strains (up to 5-fold higher shoot dry weight in the case of Hyphopichia pseudoburtonii Hp-54), indicating a beneficial direct yeast-plant interaction. In addition, 18 out of the 69 strains increased dry weight and the number of roots per seedling when tobacco seeds were inoculated. Two of these, Pichia dianae Pd-2 and Meyerozyma guilliermondii Mg-11, also increased the chlorophyll content. The results in tobacco were mostly reproduced in lettuce with these two strains, which demonstrates that the effect of the yeast-plant interaction is not species-specific. In addition, the yeast collection was evaluated in maize seedlings grown in soil in a phytotron. Three isolates (Debaryomyces hansenii Dh-67, Lachancea thermotolerans Lt-69 and Saccharomyces cerevisiae Sc-6) promoted seedling development (increases of 10 % in dry weight and chlorophyll content). In conclusion, our data confirm that several yeast strains can promote plant growth and could be considered for the development of biological fertiliser treatments.

Evaluation of Multifarious Plant Growth Promoting Trials of Yeast Isolated from the Soil of Assam Tea (Camellia sinensis var. assamica) Plantations in Northern Thailand

Some soil microorganisms, especially bacteria and mycorrhizal fungi, play a role in the promotion of plant growth. However, plant growth promotion involving yeasts in soil has not yet been extensively investigated. This study aimed to isolate and identify yeast strains obtained from soils of the Assam tea plant (Camellia sinensis var. assamica) in northern Thailand and to investigate their plant growth promoting capabilities. A total of 42 yeast strains were obtained and identified by analysis of the D1/D2 domain of the large subunit ribosomal RNA gene. We identified 35 strains of six species belonging to the phylum Ascomycota, namely Aureobasidium melanogenum, Kazachstania aquatica, Saturnispora diversa, Saturnispora sekii, Schwanniomyces pseudopolymorphus and Wickerhamomyces anomalus, and six species were determined to belong to the phylum Basidiomycota, namely Apiotrichum scarabaeorum, Curvibasidium pallidicorallinum, Papiliotrema laurentii, Rhodosporidiobolus ruineniae, Trichosporon asahii and Trichosporon coremiiforme. Seven strains were representative of potential new species and belonged to the genera Galactomyces and Wickerhamomyces. A total of 28 strains were found to produce indole-3-acetic acid (IAA) in a range of 2.12 to 37.32 mg/L, with the highest amount of IAA produced by R. ruineniae SDBR-CMU-S1-03. All yeast strains were positive in terms of ammonia production, and only eight strains were positive for siderophore production. Two yeast species, P. laurentii and W. anomalus, were able to solubilize the insoluble form of calcium and zinc. The ability to produce amylase, endogulcanase, lipase, pectinase, protease and xylanase was dependent upon the yeast species and strain involved.

Expression of SidD gene and physiological characterization of the rhizosphere plant growth-promoting yeasts

There is increasing evidence that rhizosphere microbes contribute to the stress mitigation process, but the mechanisms of this plant-microbe interaction are not yet understood. Siderophores-producing microorganisms have been considered important for enhancing metal tolerance in plants. In this study, rhizosphere yeasts were isolated from wheat (Triticum aestivum L.) and examined for siderophores production and heavy metal resistance. Out of thirty-five isolates, only eight yeast strains showed heavy metal-resistance and plant-growth promotion properties. The highest inorganic phosphate-solubilization was shown by Trichosporon ovoides IFM 63839 (2.98 mg ml⁻¹) and Saccharomyces cerevisiae FI25-1F (2.54 mg ml⁻¹). Two strains, namely YEAST-6 and YEAST-16 showed high siderophore production and heavy metal-resistance, were investigated for sidD gene expression under different levels of Cd²⁺ and Pb²⁺ toxicity stress. The heavy metal-resistant yeast strains were characterized and identified based on the phenotypic characteristics and their 18S rRNA genes sequence. SidD gene expression was induced by yeasts growing under iron-limiting conditions and excess of other heavy metal, suggesting that expression of sidD gene increases in the presence of 600–800 μM heavy metal but under iron limitation. Extensive studies of the microbe-plant micronutrient interactions will enrich our understanding of the rhizosphere role in the terms of plant growth promotion.

Rice siR109944 suppresses plant immunity to sheath blight and impacts multiple agronomic traits by affecting auxin homeostasis

Plant small RNAs (sRNAs) play significant roles in regulating various developmental processes and hormone signalling pathways involved in plant responses to a wide range of biotic and abiotic stresses. However, the functions of sRNAs in response to rice sheath blight remain unclear. We screened rice (Oryza sativa) sRNA expression patterns against Rhizoctonia solani and found that Tourist-miniature inverted-repeat transposable element (MITE)-derived small interfering RNA (siRNA) (here referred to as siR109944) expression was clearly suppressed upon R. solani infection. One potential target of siR109944 is the F-Box domain and LRR-containing protein 55 (FBL55), which encode the transport inhibitor response 1 (TIR1)-like protein. We found that rice had significantly enhanced susceptibility when siR109944 was overexpressed, while FBL55 OE plants showed resistance to R. solani challenge. Additionally, multiple agronomic traits of rice, including root length and flag leaf inclination, were affected by siR109944 expression. Auxin metabolism-related and signalling pathway-related genes were differentially expressed in the siR109944 OE and FBL55 OE plants. Importantly, pre-treatment with auxin enhanced sheath blight resistance by affecting endogenous auxin homeostasis in rice. Furthermore, transgenic Arabidopsis overexpressing siR109944 exhibited early flowering, increased tiller numbers, and increased susceptibility to R. solani. Our results demonstrate that siR109944 has a conserved function in interfering with plant immunity, growth, and development by affecting auxin homeostasis in planta. Thus, siR109944 provides a genetic target for plant breeding in the future. Furthermore, exogenous application of indole-3-acetic acid (IAA) or auxin analogues might effectively protect field crops against diseases.

Fungal pretreatment of lignocellulosic biomass for the production of plant hormone by Pichia fermentans under submerged conditions

The study was designed to evaluate the production of auxin by eukaryotic unicellular organism Pichia fermentans. Different media formulations were used for the production of indole-3-acetic acid (IAA) under broth and submerged conditions. Wheat straw-based production medium was formulated and optimized using statistical approach. The IAA production was significantly enhanced by nine folds, when the wheat straw was pretreated with Phanerochaete chrysosporium (150 µg/ml) as compared to untreated wheat straw (16.44 µg/ml). Partial purification of IAA was carried out by silica gel column chromatography and further confirmed by high-performance liquid chromatography. Exogenous application of crude and partially purified IAA positively influenced the Vigna radiata seedling growth. The number of lateral roots in the growing seedlings was significantly higher as compared to the control seeds. Thus, the present findings point towards an efficient production of plant hormone by yeast and white rot fungus using abundantly available wheat straw, which may lead to the development of cost-effective production of such metabolites and their further use in agricultural field to reduce the negative impact of chemical fertilizers.

Effects of auxin derivatives on phenotypic plasticity and stress tolerance in five species of the green alga Desmodesmus (Chlorophyceae, Chlorophyta)

Green microalgae of the genus Desmodesmus are characterized by a high degree of phenotypic plasticity (i.e. colony morphology), allowing them to be truly cosmopolitan and withstand environmental fluctuations. This flexibility enables Desmodesmus to produce a phenotype–environment match across a range of environments broader compared to algae with more fixed phenotypes. Indoles and their derivatives are a well-known crucial class of heterocyclic compounds and are widespread in different species of plants, animals, and microorganisms. Indole-3-acetic acid (IAA) is the most common, naturally occurring plant hormone of the auxin class. IAA may behave as a signaling molecule in microorganisms, and the physiological cues of IAA may also trigger phenotypic plasticity responses in Desmodesmus. In this study, we demonstrated that the changes in colonial morphs (cells per coenobium) of five species of the green alga Desmodesmus were specific to IAA but not to the chemically more stable synthetic auxins, naphthalene-1-acetic acid and 2,4-dichlorophenoxyacetic acid. Moreover, inhibitors of auxin biosynthesis and polar auxin transport inhibited cell division. Notably, different algal species (even different intraspecific strains) exhibited phenotypic plasticity different to that correlated to IAA. Thus, the plasticity involving individual-level heterogeneity in morphological characteristics may be crucial for microalgae to adapt to changing or novel conditions, and IAA treatment potentially increases the tolerance of Desmodesmus algae to several stress conditions. In summary, our results provide circumstantial evidence for the hypothesized role of IAA as a diffusible signal in the communication between the microalga and microorganisms. This information is crucial for elucidation of the role of plant hormones in plankton ecology.

Biosynthetic pathway of indole-3-acetic acid in ectomycorrhizal fungi collected from northern Thailand

Indole-3-acetic acid (IAA) is an imperative phytohormone for plant growth and development. Ectomycorrhizal fungi (ECM) are able to produce IAA. However, only a few studies on IAA biosynthesis pathways in ECM fungi have been reported. This study aimed to investigate the IAA biosynthesis pathway of six ECM cultures including Astraeus odoratus, Gyrodon suthepensis, Phlebopus portentosus, Pisolithus albus, Pisolithus orientalis and Scleroderma suthepense. The results showed that all ECM fungi produced IAA in liquid medium that had been supplemented with L-tryptophan. Notably, fungal IAA levels vary for different fungal species. The detection of indole-3-lactic acid and indole-3-ethanol in the crude culture extracts of all ECM fungi indicated an enzymatic reduction of indole-3-pyruvic acid and indole-3-acetaldehyde, respectively in the IAA biosynthesis via the indole-3-pyruvic acid pathway. Moreover, the tryptophan aminotransferase activity confirmed that all ECM fungi synthesize IAA through the indole-3-pyruvic acid pathway. Additionally, the elongation of rice and oat coleoptiles was stimulated by crude culture extract. This is the first report of the biosynthesis pathway of IAA in the tested ECM fungi.

The effect of Saccharomyces cerevisiae on antioxidant system of grape leaves infected by downy mildew

In this article, results of the comparative analysis and assessment of resistance of two grape cultivars Vostorg and Muscat blanc against downy mildew disease (Plasmopara viticola) with or without the symbiote Saccharomyces cerevisiae (vine yeast) were shown. The highly resistant cultivar Vostorg with yeast pre-treatment demonstrated a high defensive capability to the pathogen due to the fast immune response. On the first day after inoculation with downy downy mildew the rapid increase in the hydrogen peroxide, which is involved the first step of the grape’s defense system induction, was observed. At the same time, the upregulation of the relative expression of the PR2 protein (β-1,3-gluconase), a key gene involved in the plant’s resistance to pathogens. The oxidative burst was not detected in the susceptible cultivar Muscat blanc for the couple of hours after inoculation with downy mildew pathogen. The significant increase of the total phenols content and expression of stilbene synthase, which is an enzyme involved in the synthesis of phytoalexins, was observed in leaves of Muscat blanc. It was shown that pre-treatment of grape leaves with natural symbiote S. cerevisiae enhanced the immune response of the resistant cultivar Vostorg and inducted phytoalexins synthesis in the susceptible cultivar Muscat blanc.

Biosynthetic Pathway of Indole-3-Acetic Acid in Basidiomycetous Yeast Rhodosporidiobolus fluvialis

IAA biosynthetic pathways in a basidiomycetous yeast, Rhodosporidiobolus fluvialis DMKU-CP293, were investigated. The yeast strain showed tryptophan (Trp)-dependent IAA biosynthesis when grown in tryptophan supplemented mineral salt medium. Gas chromatography-mass spectrometry was used to further identify the pathway intermediates of Trp-dependent IAA biosynthesis. The results indicated that the main intermediates produced by R. fluvialis DMKU-CP293 were tryptamine (TAM), indole-3-acetic acid (IAA), and tryptophol (TOL), whereas indole-3-pyruvic acid (IPA) was not found. However, supplementation of IPA to the culture medium resulted in IAA peak detection by high-performance liquid chromatography analysis of the culture supernatant. Key enzymes of three IAA biosynthetic routes, i.e., IPA, IAM and TAM were investigated to clarify the IAA biosynthetic pathways of R. fluvialis DMKU-CP293. Results indicated that the activities of tryptophan aminotransferase, tryptophan 2-monooxygenase, and tryptophan decarboxylase were observed in cell crude extract. Overall results suggested that IAA biosynthetic in this yeast strain mainly occurred via the IPA route. Nevertheless, IAM and TAM pathway might be involved in R. fluvialis DMKU-CP293.

The plant growth-promoting potential of the mesophilic wood-rot mushroom Pleurotus pulmonarius

AIMS

To demonstrate the plant growth-promoting potential of a wood-decay mushroom.

METHODS AND RESULTS

A wild strain of a white rot fungus (Pleurotus pulmonarius) was found to convert 10 mmol l^-1 L-tryptophan (TRP) to approximately 15 μg ml^-1 indole-3-acetic acid (IAA) under the optimal growth conditions of 30°C and pH 5 for 15 days. Results of gas chromatography-mass spectrometry indicated IAA synthesis through the indole-3-pyruvic acid pathway when using cellulose as a sole carbon source. The mycelium as well as the culture filtrate promoted the growth and chlorophyll content of seedlings. In a monocotyledonous plant (rice), the number of lateral roots was increased experimentally, whereas in a dicotyledonous plant (tomato), the fungus led to an increased length of shoots and roots.

CONCLUSIONS

TRP-dependent IAA production was demonstrated for the first time for P. pulmonarius and may be responsible for enhancing plant growth in vitro.

SIGNIFICANCE AND IMPACT OF THE STUDY

Synthesis of IAA as the most prevalent phytohormone in plants has been demonstrated for soil microfungi. Pleurotus pulmonarius is reported as an IAA-producing wood-decay macrofungus. The higher temperature optimum of P. pulmonarius isolated from subtropical environment compared to other Pleurotus species from temperate regions makes it more suitable for application in subtropical/tropical regions.

Leaf-associated microbiomes of grafted tomato plants

Bacteria and fungi form complex communities (microbiomes) in above- and below-ground organs of plants, contributing to hosts' growth and survival in various ways. Recent studies have suggested that host plant genotypes control, at least partly, plant-associated microbiome compositions. However, we still have limited knowledge of how microbiome structures are determined in/on grafted crop plants, whose above-ground (scion) and below-ground (rootstock) genotypes are different with each other. By using eight varieties of grafted tomato plants, we examined how rootstock genotypes could determine the assembly of leaf endophytic microbes in field conditions. An Illumina sequencing analysis showed that both bacterial and fungal community structures did not significantly differ among tomato plants with different rootstock genotypes: rather, sampling positions in the farmland contributed to microbiome variation in a major way. Nonetheless, a further analysis targeting respective microbial taxa suggested that some bacteria and fungi could be preferentially associated with particular rootstock treatments. Specifically, a bacterium in the genus Deinococcus was found disproportionately from ungrafted tomato individuals. In addition, yeasts in the genus Hannaella occurred frequently on the tomato individuals whose rootstock genotype was "Ganbarune". Overall, this study suggests to what extent leaf microbiome structures can be affected/unaffected by rootstock genotypes in grafted crop plants.

Isolation and Properties of Enterobacter sp. LX3 Capable of Producing Indoleacetic Acid

Indoleacetic acid (IAA) can act as a phytohormone to modulate plant growth and development, thus persistent search for IAA-producing microbes is underway for a potential application in promoting plant growth. In this paper, an IAA-producing bacterium was obtained from maize rhizosphere in biochar-amending field. This strain is a Gram-negative and facultative anaerobic rod. Phenotypic examination and 16S rRNA gene sequencing suggest that this strain is a new strain of the Enterobacter species. We designated this strain LX3. LX3 produced up to 200 mg/L of IAA in nutrient broth and promoted barley development and increased plant chlorophyll level. This suggests that LX3 has potential as a biofertilizer.

Biosynthetic pathway and optimal conditions for the production of indole-3-acetic acid by an endophytic fungus, Colletotrichum fructicola CMU-A109

Endophytic fungi are known to produce indole-3-acetic acid (IAA), which can stimulate plant growth. Twenty-seven isolates of endophytic fungi were isolated from Coffea arabica in northern Thailand. Only one isolate (CMU-A109) produced IAA in vitro. This isolate was identified as Colletotrichum fructicola based on morphological characteristics and molecular phylogenetic analysis of a combined five loci (internal transcribed spacer of ribosomal DNA, actin, β-tubulin 2, chitin synthase and glyceraldehyde-3-phosphate dehydrogenase genes). Identification of a fungal IAA production obtained from indole 3-acetamide (IAM) and tryptophan 2-monooxygenase activity is suggestive of IAM routed IAA biosynthesis. The highest IAA yield (1205.58±151.89 μg/mL) was obtained after 26 days of cultivation in liquid medium supplemented with 8 mg/mL L-tryptophan at 30°C. Moreover, the crude fungal IAA could stimulate coleoptile elongation of maize, rice and rye. This is the first report of IAA production by C. fructicola and its ability to produce IAA was highest when compared with previous reports on IAA produced by fungi.

Influence of Light on Plant-Phyllosphere Interaction

Plant-phyllosphere interactions depend on microbial diversity, the plant host and environmental factors. Light is perceived by plants and by microorganisms and is used as a cue for their interaction. Photoreceptors respond to narrow-bandwidth wavelengths and activate specific internal responses. Light-induced plant responses include changes in hormonal levels, production of secondary metabolites, and release of volatile compounds, which ultimately influence plant-phyllosphere interactions. On the other hand, microorganisms contribute making some essential elements (N, P, and Fe) biologically available for plants and producing growth regulators that promote plant growth and fitness. Therefore, light directly or indirectly influences plant-microbe interactions. The usage of light-emitting diodes in plant growth facilities is helping increasing knowledge in the field. This progress will help define light recipes to optimize outputs on plant-phyllosphere communications. This review describes research advancements on light-regulated plant-phyllosphere interactions. The effects of full light spectra and narrow bandwidth-wavelengths from UV to far-red light are discussed.

Characterization of indole-3-pyruvic acid pathway-mediated biosynthesis of auxin in Neurospora crassa

Plants, bacteria and some fungi are known to produce indole-3-acetic acid (IAA) by employing various pathways. Among these pathways, the indole-3-pyruvic acid (IPA) pathway is the best studied in green plants and plant-associated beneficial microbes. While IAA production circuitry in plants has been studied for decades, little is known regarding the IAA biosynthesis pathway in fungal species. Here, we present the first data for IAA-producing genes and the associated biosynthesis pathway in a non-pathogenic fungus, Neurospora crassa. For this purpose, we used a computational approach to determine the genes and outlined the IAA production circuitry in N. crassa. We then validated these data with experimental evidence. Here, we describe the homologous genes that are present in the IPA pathway of IAA production in N. crassa. High-performance liquid chromatography and thin-layer chromatography unambiguously identified IAA, indole-3-lactic acid (ILA) and tryptophol (TOL) from cultures supplemented with tryptophan. Deletion of the gene (cfp) that encodes the enzyme indole-3-pyruvate decarboxylase, which converts IPA to indole-3-acetaldehyde (IAAld), results in an accumulation of higher levels of ILA in the N. crassa culture medium. A double knock-out strain (Δcbs-3;Δahd-2) for the enzyme IAAld dehydrogenase, which converts IAAld to IAA, shows a many fold decrease in IAA production compared with the wild type strain. The Δcbs-3;Δahd-2 strain also displays slower conidiation and produces many fewer conidiospores than the wild type strain.

Environmental Metabarcoding Reveals Contrasting Belowground and Aboveground Fungal Communities from Poplar at a Hg Phytomanagement Site

Characterization of microbial communities in stressful conditions at a field level is rather scarce, especially when considering fungal communities from aboveground habitats. We aimed at characterizing fungal communities from different poplar habitats at a Hg-contaminated phytomanagement site by using Illumina-based sequencing, network analysis approach, and direct isolation of Hg-resistant fungal strains. The highest diversity estimated by the Shannon index was found for soil communities, which was negatively affected by soil Hg concentration. Among the significant correlations between soil operational taxonomic units (OTUs) in the co-occurrence network, 80% were negatively correlated revealing dominance of a pattern of mutual exclusion. The fungal communities associated with Populus roots mostly consisted of OTUs from the symbiotic guild, such as members of the Thelephoraceae, thus explaining the lowest diversity found for root communities. Additionally, root communities showed the highest network connectivity index, while rarely detected OTUs from the Glomeromycetes may have a central role in the root network. Unexpectedly high richness and diversity were found for aboveground habitats, compared to the root habitat. The aboveground habitats were dominated by yeasts from the Lalaria, Davidiella, and Bensingtonia genera, not detected in belowground habitats. Leaf and stem habitats were characterized by few dominant OTUs such as those from the Dothideomycete class producing mutual exclusion with other OTUs. Aureobasidium pullulans, one of the dominating OTUs, was further isolated from the leaf habitat, in addition to Nakazawaea populi species, which were found to be Hg resistant. Altogether, these findings will provide an improved point of reference for microbial research on inoculation-based programs of tailings dumps.

Environmental Factors Can Influence Mitochondrial Inheritance in the Saccharomyces Yeast Hybrids

Mitochondria play a critical role in the generation of metabolic energy and are crucial for eukaryotic cell survival and proliferation. In most sexual eukaryotes, mitochondrial DNA (mtDNA) is inherited from only one parent in non-Mendelian inheritance in contrast to the inheritance of nuclear DNA. The model organism Saccharomyces cerevisiae is commonly used to study mitochondrial biology. It has two mating types: MATa and MATα. Previous studies have suggested that the mtDNA inheritance patterns in hybrid diploid cells depend on the genetic background of parental strains. However, the underlying mechanisms remain unclear. To elucidate the mechanisms, we examined the effects of environmental factors on the mtDNA inheritance patterns in hybrids obtained by crossing S. cerevisiae with its close relative S. paradoxus. The results demonstrated that environmental factors can influence mtDNA transmission in hybrid diploids, and that the inheritance patterns are strain dependent. The fitness competition assay results showed that the fitness differences can explain the mtDNA inheritance patterns under specific conditions. However, in this study, we found that fitness differences cannot fully be explained by mitochondrial activity in hybrids under stress conditions.