Extracellular esterases of phylloplane yeast Pseudozyma antarctica induce defect on cuticle layer structure and water-holding ability of plant leaves

Enhanced biodegradable polyester film degradation in soil by sequential cooperation of yeast-derived esterase and microbial community

The degradation of biodegradable plastics poses a significant environmental challenge and requires effective solutions. In this study, an esterase derived from a phyllosphere yeast Pseudozyma antarctica (PaE) enhanced the degradation and mineralization of poly(butylene succinate-co-adipate) (PBSA) film in soil. PaE was found to substitute for esterases from initial degraders and activate sequential esterase production from soil microbes. The PBSA film pretreated with PaE (PBSA-E) rapidly diminished and was mineralized in soil until day 55 with high CO2 production. Soil with PBSA-E maintained higher esterase activities with enhancement of microbial abundance, whereas soil with inactivated PaE-treated PBSA film (PBSA-inact E) showed gradual degradation and time-lagged esterase activity increases. The fungal genera Arthrobotrys and Tetracladium, as possible contributors to PBSA-film degradation, increased in abundance in soil with PBSA-inact E but were less abundant in soil with PBSA-E. The dominance of the fungal genus Fusarium and the bacterial genera Arthrobacter and Azotobacter in soil with PBSA-E further supported PBSA degradation. Our study highlights the potential of PaE in addressing concerns associated with biodegradable plastic persistence in agricultural and environmental contexts.

Accelerated degradation of plastic products via yeast enzyme treatment

Biodegradable plastics can solve the problem of unwanted plastics accumulating in the environment if they can be given the contradictory properties of durability in use and rapid degradation after use. Commercially available agricultural biodegradable mulch films are made from formulations containing polybutylene adipate-co-terephthalate (PBAT) to provide mechanical and UV resistance during the growing season. Although used films are ploughed into the soil using a tiller to promote decomposition, it is difficult if they remain durable. We showed that an enzyme produced by the leaf surface yeast Pseudozyma antarctica (PaE) degrades PBAT-containing films. In laboratory studies, PaE randomly cleaved the PBAT polymer chain and induced erosion of the film surface. In the field, commercial biodegradable films containing PBAT placed on ridges were weakened in both the warm and cold seasons by spraying the culture filtrate of P. antarctica. After the field was ploughed the next day, the size and total weight of residual film fragments decreased significantly (p < 0.05). Durable biodegradable plastics used in the field are degraded using PaE treatment and are broken down into small fragments by the plough. The resultant degradation products can then be more readily assimilated by many soil microorganisms.

Production of Mannosylerythritol Lipids Using Oils from Oleaginous Microalgae: Two Sequential Microorganism Culture Approach

Mannosylerythritol lipids (MELs) are biosurfactants with excellent biochemical properties and a wide range of potential applications. However, most of the studies focusing on MELs high titre production have been relying in the use of vegetable oils with impact on the sustainability and process economy. Herein, we report for the first time MELs production using oils produced from microalgae. The bio-oil was extracted from Neochloris oleoabundans and evaluated for their use as sole carbon source or in a co-substrate strategy, using as an additional carbon source D-glucose, on Moesziomyces spp. cultures to support cell growth and induce the production of MELs. Both Moesziomyces antarcticus and M. aphidis were able to grow and produce MELs using algae-derived bio-oils as a carbon source. Using a medium containing as carbon sources 40 g/L of D-glucose and 20 g/L of bio-oils, Moesziomyces antarcticus and M. aphidis produced 12.47 ± 0.28 and 5.72 ± 2.32 g/L of MELs, respectively. Interestingly, there are no significant differences in productivity when using oils from microalgae or vegetable oils as carbon sources. The MELs productivities achieved were 1.78 ± 0.04 and 1.99 ± 0.12 g/L/h, respectively, for M. antarcticus fed with algae-derived or vegetable oils. These results open new perspectives for the production of MELs in systems combining different microorganisms.

Detection and diversity of the mannosylerythritol lipid (MEL) gene cluster and lipase A and B genes of Moesziomyces antarcticus isolated from terrestrial sites chronically contaminated with crude oil in Trinidad

BACKGROUND

Mannosylerythritol lipids (MELs) belong to the class of glycolipid biosurfactants and are produced by members of the Ustilago and Moesziomyces genera. Production of MELs is regulated by a biosynthetic gene cluster (MEL BGC). Extracellular lipase activity is also associated with MEL production. Most microbial glycolipid-producers are isolated from oil-contaminated environments. MEL-producing yeast that are capable of metabolizing crude oil are understudied, and there is very limited data on indigenous strains from tropical climates. Analysis of the MEL BGC and lipase genes in Trinidad M. antarcticus strains, using a gene-targeted approach, revealed a correlation between their intrinsic capability to degrade crude oil and their adaptation to survive in a chronically polluted terrestrial environment.

RESULTS

M. antarcticus was isolated from naturally-occurring crude oil seeps and an asphaltic mud volcano in Trinidad; these are habitats that have not been previously reported for this species. Genus identification was confirmed by the large-subunit (LSU) and the small-subunit (SSU) sequence comparisons and species identification was confirmed by ITS sequence comparisons and phylogenetic inference. The essential genes (Emt1, Mac1, Mac2, Mmf1) of the MEL BGC were detected with gene-specific primers. Emt1p, Mac1p and Mmf1p sequence analyses confirmed that the Trinidad strains harboured novel synonymous amino acid (aa) substitutions and structural comparisons revealed different regions of disorder, specifically for the Emt1p sequence. Functionality of each protein sequence was confirmed through motif mining and mutation prediction. Phylogenetic relatedness was inferred for Emt1p, Mac1p and Mmf1p sequences. The Trinidad strains clustered with other M. antarcticus sequences, however, the representative Trinidad M. antarcticus sequences consistently formed a separate, highly supported branch for each protein. Similar phylogenetic placement was indicated for LipA and LipB nucleotide and protein sequences. The Trinidad strains also demonstrated lipolytic activity in culture, with an ability to utilize different carbon sources. Comparative evolution of MEL BGC and LipA gene suggested early and late duplication events, depending on the gene, followed by a number of speciation events within Ustilaginaceae. M. antarcticus and M. aphidis were separated from all other members of Ustilaginaceae and two gene homologues were detected, one for each species.

CONCLUSIONS

Sequence analyses was based on a novel gene-targeted approach to analyze the essential genes of the MEL BGC and LipA and LipB genes of M. antarcticus strains from Trinidad. The findings indicated that these strains accumulated nucleotide mutations to a threshold level that did not affect the function of specific proteins encoded by the MEL BGC and LipA and LipB genes. The biosurfactant and lipase enzymes secreted by these Trinidad M. antarcticus strains facilitated their survival in oil-contaminated terrestrial environments. These findings suggest that the Trinidad strains should be explored as promising candidates for the commercial production of MEL biosurfactants and lipase enzymes.

Cutinase-like biodegradable plastic-degrading enzymes from phylloplane yeasts have cutinase activity

Phylloplane yeast genera Pseudozyma and Cryptococcus secrete biodegradable plastic (BP)-degrading enzymes, termed cutinase-like enzymes (CLEs). Although CLEs contain highly conserved catalytic sites, the whole protein exhibits ≤30% amino acid sequence homology with cutinase. In this study, we analyzed whether CLEs exhibit cutinase activity. Seventeen Cryptococcus magnus strains, which degrade BP at 15 °C, were isolated from leaves and identified the DNA sequence of the CLE in one of the strains. Cutin was prepared from tomato leaves and treated with CLEs from 3 Cryptococcus species (C. magnus, Cryptococcus flavus, and Cryptococcus laurentii) and Pseudozyma antarctia (PaE). A typical cutin monomer, 10,16-dihydroxyhexadecanoic acid, was detected in extracts of the reaction solution via gas chromatography-mass spectrometry, showing that cutin was indeed degraded by CLEs. In addition to the aforementioned monomer, separation analysis via thin-layer chromatography detected high-molecular-weight products resulting from the breakdown of cutin by PaE, indicating that PaE acts as an endo-type enzyme.

Targeted transcriptomic study of the implication of central metabolic pathways in mannosylerythritol lipids biosynthesis in Pseudozyma antarctica T-34

Pseudozyma antarctica is a nonpathogenic phyllosphere yeast known as an excellent producer of industrial lipases and mannosylerythritol lipids (MELs), which are multi-functional glycolipids. The fungus produces a much higher amount of MELs from vegetable oil than from glucose, whereas its close relative, Ustilago maydis UM521, produces a lower amount of MELs from vegetable oil. In the present study, we used previous gene expression profiles measured by DNA microarray analyses after culturing on two carbon sources, glucose and soybean oil, to further characterize MEL biosynthesis in P. antarctica T-34. A total of 264 genes were found with induction ratios and expression intensities under oily conditions with similar tendencies to those of MEL cluster genes. Of these, 93 were categorized as metabolic genes using the Eukaryotic Orthologous Groups classification. Within this metabolic category, amino acids, carbohydrates, inorganic ions, and secondary metabolite metabolism, as well as energy production and conversion, but not lipid metabolism, were enriched. Furthermore, genes involved in central metabolic pathways, such as glycolysis and the tricarboxylic acid cycle, were highly induced in P. antarctica T-34 under oily conditions, whereas they were suppressed in U. maydis UM521. These results suggest that the central metabolism of P. antarctica T-34 under oily conditions contributes to its excellent oil utilization and extracellular glycolipid production.

The phylloplane yeast Pseudozyma: a rich potential for biotechnology

Basidiomycetous yeast Pseudozyma strains are often isolated from leaf surfaces. Here, we describe the sources of Pseudozyma yeasts and their useful secreted products, including enzymes and biosurfactants. We then outline the life of Pseudozyma on the leaf surface and introduce studies to verify ecological functions of their useful products. In addition, the function of Pseudozyma in maintaining the health of plants is briefly explained. Finally, the gene manipulation techniques necessary for future research and development of technological applications of Pseudozyma are described.

Witches' broom resistant genotype CCN51 shows greater diversity of symbiont bacteria in its phylloplane than susceptible genotype catongo

Background

Theobroma cacao L. (cacao) is a perennial tropical tree, endemic to rainforests of the Amazon Basin. Large populations of bacteria live on leaf surfaces and these phylloplane microorganisms can have important effects on plant health. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated studies of the phylloplane microbiome. In this study, we characterized the bacterial microbiome of the phylloplane of the catongo genotype (susceptible to witch’s broom) and CCN51 (resistant). Bacterial microbiome was determined by sequencing the V3-V4 region of the bacterial 16S rRNA gene.

Results

After the pre-processing, a total of 1.7 million reads were considered. In total, 106 genera of bacteria were characterized. Proteobacteria was the predominant phylum in both genotypes. The exclusive genera of Catongo showed activity in the protection against UV radiation and in the transport of substrates. CCN51 presented genus that act in the biological control and inhibition in several taxonomic groups. Genotype CCN51 presented greater diversity of microorganisms in comparison to the Catongo genotype and the total community was different between both. Scanning electron microscopy analysis of leaves revealed that on the phylloplane, many bacterial occur in large aggregates in several regions of the surface and isolated nearby to the stomata.

Conclusions

We describe for the first time the phylloplane bacterial communities of T. cacao. The Genotype CCN51, resistant to the witch’s broom, has a greater diversity of bacterial microbioma in comparison to Catongo and a greater amount of exclusive microorganisms in the phylloplane with antagonistic action against phytopathogens.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1339-9) contains supplementary material, which is available to authorized users.

Disease severity enhancement by an esterase from non-phytopathogenic yeast Pseudozyma antarctica and its potential as adjuvant for biocontrol agents

The phylloplane yeast Pseudozyma antarctica secretes an esterase, named PaE, and xylanase when cultivated with xylose. We previously observed that the lipophilic layer of Micro-Tom tomato leaves became thinner after the culture filtrate treatment. The leaves developed reduced water-holding ability and became wilted. In this study, the purified enzymes were spotted on Micro-Tom leaves. PaE, but not xylanase, thinned the lipophilic layer of leaves and decreased leaf resistance to the phytopathogenic fungus Botrytis cinerea. Disease severity increased significantly in detached leaves and potted plants treated with the culture filtrate and B. cinerea spores compared with those treated with inactivated enzyme and B. cinerea alone. Spore germination ratios, numbers of penetrating fungal hyphae in the leaves, and fungal DNA contents also increased significantly on the detached leaves. Japanese knotweed (Fallopia japonica), a serious invasive alien weed in Europe and North America, also became susceptible to infection by the rust pathogen Puccinia polygoni-amphibii var. tovariae following the culture filtrate treatment. The culture filtrate treatment increased disease development in plants induced by both phytopathogenic fungi. Our results suggest that P. antarctica culture filtrate could be used as an adjuvant for sustainable biological weed control using phytopathogenic fungi.

Endophytic Fungi from Frankincense Tree Improves Host Growth and Produces Extracellular Enzymes and Indole Acetic Acid

Boswellia sacra, an economically important frankincense-producing tree found in the desert woodlands of Oman, is least known for its endophytic fungal diversity and the potential of these fungi to produce extracellular enzymes and auxins. We isolated various fungal endophytes belonging to Eurotiales (11.8%), Chaetomiaceae (17.6%), Incertae sadis (29.5%), Aureobasidiaceae (17.6%), Nectriaceae (5.9%) and Sporomiaceae (17.6%) from the phylloplane (leaf) and caulosphere (stem) of the tree. Endophytes were identified using genomic DNA extraction, PCR amplification and sequencing the internal transcribed spacer regions, whereas a detailed phylogenetic analysis of the same gene fragment was made with homologous sequences. The endophytic colonization rate was significantly higher in the leaf (5.33%) than the stem (0.262%). The Shannon-Weiner diversity index was H′ 0.8729, while Simpson index was higher in the leaf (0.583) than in the stem (0.416). Regarding the endophytic fungi’s potential for extracellular enzyme production, fluorogenic 4-methylumbelliferone standards and substrates were used to determine the presence of cellulases, phosphatases and glucosidases in the pure culture. Among fungal strains, Penicillum citrinum BSL17 showed significantly higher amounts of glucosidases (62.15±1.8 μM^-1min^-1mL) and cellulases (62.11±1.6 μM^-1min^-1mL), whereas Preussia sp. BSL10 showed significantly higher secretion of glucosidases (69.4±0.79 μM^-1min^-1mL) and phosphatases (3.46±0.31μM^-1min^-1mL) compared to other strains. Aureobasidium sp. BSS6 and Preussia sp. BSL10 showed significantly higher potential for indole acetic acid production (tryptophan-dependent and independent pathways). Preussia sp. BSL10 was applied to the host B. sacra tree saplings, which exhibited significant improvements in plant growth parameters and accumulation of photosynthetic pigments. The current study concluded that endophytic microbial resources producing extracellular enzymes and auxin could establish a unique niche for ecological adaptation during symbiosis with the host Frankincense tree.