Pseudozyma jejuensis sp. nov., a novel cutinolytic ustilaginomycetous yeast species that is able to degrade plastic waste

Enhancing biodegradation of PBAT through bio-stimulation using Pseudozyma jejuensis for effective plastic waste reduction

Polybutylene adipate-co-terephthalate (PBAT) is a flexible and biodegradable material that finds applications in mulching film and the food packaging industry. In this study, we aimed to address the global plastic waste problem by developing an improved biodegradation system for PBAT. Our focus was on utilizing the biodegradation capabilities of Pseudozyma jejuensis, a microorganism known for its ability to decompose Polycaprolactam (PCL). Through bio-stimulation, we aimed to enhance the growth mechanism of P. jejuensis and optimize PBAT biodegradation. Our results demonstrated significant structural changes in the PBAT film, as revealed by FT-IR analysis. Moreover, FE-SEM imaging exhibited evident surface erosion and pitting, indicating physical alterations due to biodegradation. These findings provide strong evidence for the efficiency of our developed biodegradation system. To fully harness the potential of this system and enable its practical implementation, further research is warranted to optimize and scale up the process. Our work contributes to the ongoing efforts to combat the global plastic waste crisis, offering a valuable solution for the efficient biodegradation of PBAT.

Bacterial degradation kinetics of poly(Ɛ-caprolactone) (PCL) film by Aquabacterium sp. CY2-9 isolated from plastic-contaminated landfill

Despite the identification of numerous bioplastic-degrading bacteria, the inconsistent rate of bioplastic degradation under differing cultivation conditions limits the intercomparison of results on biodegradation kinetics. In this study, we isolated a poly (Ɛ-caprolactone) (PCL)-degrading bacterium from a plastic-contaminated landfill and determined the principle-based biodegradation kinetics in a confined model system of varying cultivation conditions. Bacterial degradation of PCL films synthesized by different polymer number average molecular weights (M_n) and concentrations (% w/v) was investigated using both solid and liquid media at various temperatures. As a result, the most active gram-negative bacterial strain at ambient temperature (28 °C), designated CY2-9, was identified as Aquabacterium sp. Based on 16 S rRNA gene analysis. A clear zone around the bacterial colony was apparently exhibited during solid cultivation, and the diameter sizes increased with incubation time. During biodegradation processes in the PCL film, the thermal stability declined (determined by TGA; weight changes at critical temperature), whereas the crystalline proportion increased (determined by DSC; phase transition with temperature increment), implying preferential degradation of the amorphous region in the polymer structure. The surface morphologies (determined by SEM; electron optical system) were gradually hydrolyzed, creating destruction patterns as well as alterations in functional groups on film surfaces (determined by FT-IR; infrared spectrum of absorption or emission). In the kinetic study based on the weight loss of the PCL film (4.5 × 10⁴ Da, 1% w/v), ∼1.5 (>±0.1) × 10^-1 day^-1 was obtained from linear regression for both solid and liquid media cultivation at 28 °C. The biodegradation efficiencies increased proportionally by a factor of 2.6-7.9, depending on the lower polymer number average molecular weight and lower concentration. Overall, our results are useful for measuring and/or predicting the degradation rates of PCL films by microorganisms in natural environments.

Biodegradation of Biodegradable Polymers in Mesophilic Aerobic Environments

Finding alternatives to diminish plastic pollution has become one of the main challenges of modern life. A few alternatives have gained potential for a shift toward a more circular and sustainable relationship with plastics. Biodegradable polymers derived from bio- and fossil-based sources have emerged as one feasible alternative to overcome inconveniences associated with the use and disposal of non-biodegradable polymers. The biodegradation process depends on the environment's factors, microorganisms and associated enzymes, and the polymer properties, resulting in a plethora of parameters that create a complex process whereby biodegradation times and rates can vary immensely. This review aims to provide a background and a comprehensive, systematic, and critical overview of this complex process with a special focus on the mesophilic range. Activity toward depolymerization by extracellular enzymes, biofilm effect on the dynamic of the degradation process, CO2 evolution evaluating the extent of biodegradation, and metabolic pathways are discussed. Remarks and perspectives for potential future research are provided with a focus on the current knowledge gaps if the goal is to minimize the persistence of plastics across environments. Innovative approaches such as the addition of specific compounds to trigger depolymerization under particular conditions, biostimulation, bioaugmentation, and the addition of natural and/or modified enzymes are state-of-the-art methods that need faster development. Furthermore, methods must be connected to standards and techniques that fully track the biodegradation process. More transdisciplinary research within areas of polymer chemistry/processing and microbiology/biochemistry is needed.

Ten decadal advances in fungal biology leading towards human well-being

Fungi are an understudied resource possessing huge potential for developing products that can greatly improve human well-being. In the current paper, we highlight some important discoveries and developments in applied mycology and interdisciplinary Life Science research. These examples concern recently introduced drugs for the treatment of infections and neurological diseases; application of -OMICS techniques and genetic tools in medical mycology and the regulation of mycotoxin production; as well as some highlights of mushroom cultivaton in Asia. Examples for new diagnostic tools in medical mycology and the exploitation of new candidates for therapeutic drugs, are also given. In addition, two entries illustrating the latest developments in the use of fungi for biodegradation and fungal biomaterial production are provided. Some other areas where there have been and/or will be significant developments are also included. It is our hope that this paper will help realise the importance of fungi as a potential industrial resource and see the next two decades bring forward many new fungal and fungus-derived products.

Ecotoxicological and physiological risks of microplastics on fish and their possible mitigation measures

Microplastics (MPs) are widely distributed and extensively found within marine ecosystems, and approximately 8 million tons of plastics are being dumped into the sea annually. Once reached the marine environment, plastics tend to get fragmented into smaller particles through photo-degradation, mechanical and biological processes. These MPs have raised concerns globally due to their potential toxic impacts on a wide variety of aquatic fauna and humans. Ingested microplastics can cause severe health implications in fishes, including reduced feeding intensity, improper gill functioning, immuno-suppression, and compromised reproducibility. Several studies were also conducted to scrutinize MPs trophic transfer through the food chain from primary producers to top predators and their bioaccumulation. This paper briefly summarizes all the possible sources, routes, bioavailability, trophic transfer, and consequences of microplastics in fishes. The review article also intended to highlight various mitigation strategies like implementing Four R's concept (refuse, reduce, reuse, and recycle), integrated strategies, ban on single-use plastics, use bioplastics, and create behavioural changes with public awareness.

Simultaneous nitrification and denitrification by a novel isolated Pseudomonas sp. JQ-H3 using polycaprolactone as carbon source

The novel isolated strain JQ-H3 exhibited heterotrophic nitrification-aerobic denitrification (HN-AD) ability using poly (ε-caprolactone) (PCL) as a sole carbon source under aerobic conditions. This was the first time that a PCL-degrading bacterium was characterized to be with capability of nitrifying and denitrifying performances. Strain JQ-H3 removed approximately 95.40% of NH₄⁺-N (102.40 mg/L), about 91.1% of NO₃^--N (99.01 mg/L), with the maximum specific removal rates of 0.308 mg NH₄⁺-N/mg DCW/h and 0.220 mg NO₃^--N/mg DCW/h, respectively. The functional genes amoA, napA, nirS, cnorB, and nosZ were successfully expressed during the nitrogen removal process. An increasing PCL concentrations caused a decline in cell growth and nitrogen removal efficiency, which was attributed to the decrease in the rate of the PCL hydrolysis and the amount of dissolved organic carbon (DOC) release. These results demonstrated the strain as an ideal candidate for nitrogen removal from wastewater by using PCL as carbon source.

Microbial degradation of high impact polystyrene (HIPS), an e-plastic with decabromodiphenyl oxide and antimony trioxide

Accumulation of electronic waste has increased catastrophically and out of that various plastic resins constitute one of the leading thrown out materials in the electronic machinery. Enrichment medium, containing high impact polystyrene (HIPS) with decabromodiphenyl oxide and antimony trioxide as sole carbon source, was used to isolate microbial cultures. The viability of these cultures in the e-plastic containing mineral medium was further confirmed by triphenyl tetrazolium chloride (TTC) reduction test. Four cultures were identified by 16S rRNA sequencing as Enterobacter sp., Citrobacter sedlakii, Alcaligenes sp. and Brevundimonas diminuta. Biodegradation experiments were carried out in flask level and gelatin supplementation (0.1% w/v) along with HIPS had increased the degradation rate to a maximum of 12.4% (w/w) within 30days. This is the first report for this kind of material. The comparison of FTIR, NMR, and TGA analysis of original and degraded e-plastic films revealed structural changes under microbial treatment. Polystyrene degradation intermediates in the culture supernatant were also detected using HPLC analysis. The gravity of biodegradation was validated by morphological changes under scanning electron microscope. All isolates displayed depolymerase activity to substantiate enzymatic degradation of e-plastic.

Yeast diversity and novel yeast D1/D2 sequences from corn phylloplane obtained by a culture-independent approach

Culture-independent techniques have recently been used for evaluation of microbial diversity in the environment since it addresses the problem of unculturable microorganisms. In this study, the diversity of epiphytic yeasts from corn (Zea mays Linn.) phylloplanes in Thailand was investigated using this technique and sequence-based analysis of the D1/D2 domains of the large subunit ribosomal DNA sequences. Thirty-seven samples of corn leaf were collected randomly from 10 provinces. The DNA was extracted from leaf washing samples and the D1/D2 domains were amplified. The PCR products were cloned and then screened by colony PCR. A total of 1049 clones were obtained from 37 clone libraries. From this total, 329 clones (213 sequences) were closely related to yeast strains in the GenBank database, and they were clustered into 77 operational taxonomic units (OTUs) with a similarity threshold of 99 %. The majority of sequences (98.5 %) were classified into the phylum Basidiomycota. Sixteen known yeast species were identified. Interestingly, more than 65 % of the D1/D2 sequences obtained by this technique were suggested to be sequences from new yeast taxa. The predominant yeast sequences detected belonged to the order Ustilaginales with relative frequency of 68.0 %. The most common known yeast species detected on the leaf samples were Pseudozyma hubeiensis pro tem. and Moesziomyces antarcticus with frequency of occurrence of 24.3 and 21.6 %, respectively.

Insights into the plant polysaccharide degradation potential of the xylanolytic yeast Pseudozyma brasiliensis

In second-generation (2G) bioethanol production, plant cell-wall polysaccharides are broken down to release fermentable sugars. The enzymes of this process are classified as carbohydrate-active enzymes (CAZymes) and contribute substantially to the cost of biofuel production. A novel basidiomycete yeast species, Pseudozyma brasiliensis, was recently discovered. It produces an endo-β-1,4-xylanase with a higher specific activity than other xylanases. This enzyme is essential for the hydrolysis of biomass-derived xylan and has an important role in 2G bioethanol production. In spite of the P. brasiliensis biotechnological potential, there is no information about how it breaks down polysaccharides. For the first time, we characterized the secretome of P. brasiliensis grown on different carbon sources (xylose, xylan, cellobiose and glucose) and also under starvation conditions. The growth and consumption of each carbohydrate and the activity of the CAZymes of culture supernatants were analyzed. The CAZymes found in its secretomes, validated by enzymatic assays, have the potential to hydrolyze xylan, mannan, cellobiose and other polysaccharides. The data show that this yeast is a potential source of hydrolases, which can be used for biomass saccharification.

The assessment of epiphytic yeast diversity in sugarcane phyllosphere in Thailand by culture-independent method

The diversity of epiphytic yeasts from sugarcane (Saccharum officinarum Linn.) phyllospheres in Thailand was investigated by culture-independent method based on the analysis of the D1/D2 domains of the large subunit rRNA gene sequences. Forty-five samples of sugarcane leaf were collected randomly from ten provinces in Thailand. A total of 1342 clones were obtained from 45 clone libraries. 426 clones (31.7 %) were closely related to yeast strains in the GenBank database, and they were clustered into 31 operational taxonomic units (OTUs) with a similarity threshold of 99 %. All OTU sequences were classified in phylum Basidiomycota which were closely related to 11 yeast species in seven genera including Cryptococcus flavus, Hannaella coprosmaensis, Rhodotorula taiwanensis, Jaminaea angkoreiensis, Malassezia restricta, Pseudozyma antarctica, Pseudozyma aphidis, Pseudozyma hubeiensis, Pseudozyma prolifica, Pseudozyma shanxiensis, and Sporobolomyces vermiculatus. The most predominant yeasts detected belonged to Ustilaginales with 89.4 % relative frequency and the prevalent yeast genus was Pseudozyma. However, the majority were unable to be identified as known yeast species and these sequences may represent the sequences of new yeast taxa. In addition, The OTU that closely related to P. prolifica was commonly detected in sugarcane phyllosphere.

Assessment of epiphytic yeast diversity in rice (Oryza sativa) phyllosphere in Thailand by a culture-independent approach

The epiphytic yeast diversity in rice phyllosphere in Thailand was investigated by a culture-independent technique based on the RFLP pattern and the sequence of the D1/D2 domain of the large subunit rRNA gene. Forty-four samples of rice leaf were collected randomly from six provinces. The DNA was extracted from leaf washing samples and the D1/D2 domain was amplified using PCR technique. The PCR products were cloned and then screened by colony PCR. Of total 1121 clones, 451 clones (40.2 %) revealed the D1/D2 domain sequences closely related to sequences of yeasts in GenBank, and they were clustered into 45 operational taxonomic units (OTUs) at 99 % homology. Of total yeast related clones, 329 clones (72.9 %) were identified as nine known yeast species, which consisted of 314 clones (8 OTUs) in the phylum Basidiomycota including Bullera japonica, Pseudozyma antarctica, Pseudozyma aphidis, Sporobolomyces blumeae, Sporobolomyces carnicolor and Sporobolomyces oryzicola and 15 clones (6 OTUs) in the phylum Ascomycota including Metschnikowia koreensis, Meyerozyma guilliermondii and Wickerhamomyces anomalus. The D1/D2 sequences (122 clones) that could not be identified as known yeast species were closest to 3 and 14 species in Ascomycota and Basidiomycota, respectively, some of which may be new yeast species. The most predominant species detected was P. antarctica (42.6 %) followed by B. japonica (25.9 %) with 63.6 and 22.7 % frequency of occurrence, respectively. The results of OTU richness of each sampling location revealed that climate condition and sampling location could affect epiphytic yeast diversity in rice phyllosphere.

Biodegradation of poly (ε-caprolactone) (PCL) film and foam plastic by Pseudozyma japonica sp. nov., a novel cutinolytic ustilaginomycetous yeast species

Aliphatic polyesters poly (ε-caprolactone) (PCL) and foam plastic have been shown to be biodegradable by microorganisms, which possess cutinolytic enzymes. Pseudozyma japonica-Y7-09, showed both high growth and enzyme activity on Yeast malt (YM) medium fed with PCL film than on YM medium. The hydrolytic enzyme activity of the culture on p-nitrophenyl butyrate indicated the occurrence of cutinase enzyme. This activity was confirmed by the degradation of PCL film which reached to the maximum (93.33 %) at 15 days and the degradation of foam plastic which reached 43.2 % at 30 days. These results suggest that the extracellular cutinase enzyme of Pseudozyma japonica-Y7-09 may be useful for the biological degradation of plastic wastes.

Pseudozyma brasiliensis sp. nov., a xylanolytic, ustilaginomycetous yeast species isolated from an insect pest of sugarcane roots

A novel ustilaginomycetous yeast isolated from the intestinal tract of an insect pest of sugarcane roots in Ribeirão Preto, São Paulo State, Brazil, represents a novel species of the genus Pseudozyma based on molecular analyses of the D1/D2 rDNA large subunit and the internal transcribed spacer (ITS1+ITS2) regions. The name Pseudozyma brasiliensis sp. nov. is proposed for this species, with GHG001(T) ( = CBS 13268(T) = UFMG-CM-Y307(T)) as the type strain. P. brasiliensis sp. nov. is a sister species of Pseudozyma vetiver, originally isolated from leaves of vetiver grass and sugarcane in Thailand. P. brasiliensis sp. nov. is able to grow well with xylan as the sole carbon source and produces high levels of an endo-1,4-xylanase that has a higher specific activity in comparison with other eukaryotic xylanases. This enzyme has a variety of industrial applications, indicating the great biotechnological potential of P. brasiliensis.

Genome and transcriptome analysis of the basidiomycetous yeast Pseudozyma antarctica producing extracellular glycolipids, mannosylerythritol lipids

Pseudozyma antarctica is a non-pathogenic phyllosphere yeast known as an excellent producer of mannosylerythritol lipids (MELs), multi-functional extracellular glycolipids, from vegetable oils. To clarify the genetic characteristics of P. antarctica, we analyzed the 18 Mb genome of P. antarctica T-34. On the basis of KOG analysis, the number of genes (219 genes) categorized into lipid transport and metabolism classification in P. antarctica was one and a half times larger than that of yeast Saccharomyces cerevisiae (140 genes). The gene encoding an ATP/citrate lyase (ACL) related to acetyl-CoA synthesis conserved in oleaginous strains was found in P. antarctica genome: the single ACL gene possesses the four domains identical to that of the human gene, whereas the other oleaginous ascomycetous species have the two genes covering the four domains. P. antarctica genome exhibited a remarkable degree of synteny to U. maydis genome, however, the comparison of the gene expression profiles under the culture on the two carbon sources, glucose and soybean oil, by the DNA microarray method revealed that transcriptomes between the two species were significantly different. In P. antarctica, expression of the gene sets relating fatty acid metabolism were markedly up-regulated under the oily conditions compared with glucose. Additionally, MEL biosynthesis cluster of P. antarctica was highly expressed regardless of the carbon source as compared to U. maydis. These results strongly indicate that P. antarctica has an oleaginous nature which is relevant to its non-pathogenic and MEL-overproducing characteristics. The analysis and dataset contribute to stimulate the development of improved strains with customized properties for high yield production of functional bio-based materials.

Pseudozyma vetiver sp. nov., a novel anamorphic ustilaginomycetous yeast species isolated from the phylloplane in Thailand

Three strains representing one novel yeast species were isolated from the phylloplanes of the vetiver grasses (DMKU-LV90 and DMKU-LV99(T)) and sugarcane (DMKU-SP260) collected in Thailand by leaf washing followed by a plating technique. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics and the sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer region (ITS), the three strains were found to represent a single novel anamorphic ustilaginomycetous yeast species in the genus Pseudozyma. The name Pseudozyma vetiver sp. nov. is proposed for this novel species. The type strain is DMKU-LV99(T) (BCC 61021 = CBS 12824). The novel species showed phylogenetic relationships to the other members of the genus Pseudozyma and to teleomorphic fungal genera, namely Ustilago, Sporisorium and Anomalomyces in Ustilaginaceae, Ustilaginales. The three strains showed identical sequences both in the D1/D2 and ITS regions. The Pseudozyma species closest to the novel species in terms of pairwise sequence similarity in the D1/D2 region was Pseudozyma pruni but with 2.3 % nucleotide substitutions (14 nucleotide substitutions and no gaps out of 606 nt). The novel species and P. pruni differed by 10.9 % nucleotide substitutions (75 nucleotide substitutions and 31 gaps out of 691 nt) in the ITS region. The phylogenetic analysis based on the combined sequences of the ITS region and the D1/D2 region of the LSU rRNA gene showed that the novel species was found to be most closely related to Pseudozyma fusiformata but with 2.9 % nucleotide substitutions in the D1/D2 region and 7.4 % nucleotide substitutions in the ITS region.

Phyllosphere yeasts rapidly break down biodegradable plastics

The use of biodegradable plastics can reduce the accumulation of environmentally persistent plastic wastes. The rate of degradation of biodegradable plastics depends on environmental conditions and is highly variable. Techniques for achieving more consistent degradation are needed. However, only a few microorganisms involved in the degradation process have been isolated so far from the environment. Here, we show that Pseudozyma spp. yeasts, which are common in the phyllosphere and are easily isolated from plant surfaces, displayed strong degradation activity on films made from poly-butylene succinate or poly-butylene succinate-co-adipate. Strains of P. antarctica isolated from leaves and husks of paddy rice displayed strong degradation activity on these films at 30°C. The type strain, P. antarctica JCM 10317, and Pseudozyma spp. strains from phyllosphere secreted a biodegradable plastic-degrading enzyme with a molecular mass of about 22 kDa. Reliable source of biodegradable plastic-degrading microorganisms are now in our hands.

Isolation of Pseudozyma churashimaensis sp. nov., a novel ustilaginomycetous yeast species as a producer of glycolipid biosurfactants, mannosylerythritol lipids

An ustilaginomycetous anamorphic yeast species isolated from the leaves of Saccharum officinarum (sugarcane) in Okinawa, Japan, was identified as a novel Pseudozyma species based on morphological and physiological aspects and molecular taxonomic analysis using the D1/D2 domains of the large subunit (26S) rRNA gene and the internal transcribed spacer 1 (ITS1)-5.8S-ITS2 regions. The name Pseudozyma churashimaensis sp. nov. was proposed for the novel species, with JCM 16988(T) as the type strain. Interestingly, P. churashimaensis was found to produce glycolipid biosurfactants, a mixture of mannosylerythritol lipids (MELs), including a novel tri-acetylated derivative (MEL-A2), from glucose. The observed critical micelle concentration (CMC) and the surface tension at CMC of MEL-A2 were 1.7 × 10⁻⁶ M and 29.2 mN/m, respectively. Moreover, on a water-penetration scan, MEL-A2 efficiently formed different lyotropic liquid crystalline phases, including the lamella phase at a wide range of concentrations, indicating its excellent surface-active and self-assembling properties. The novel strain of the genus Pseudozyma should thus facilitate the application of glycolipid biosurfactants in combination with other MEL producers.

Structural and functional studies of Aspergillus oryzae cutinase: enhanced thermostability and hydrolytic activity of synthetic ester and polyester degradation

Cutinases are responsible for hydrolysis of the protective cutin lipid polyester matrix in plants and thus have been exploited for hydrolysis of small molecule esters and polyesters. Here we explore the reactivity, stability, and structure of Aspergillus oryzae cutinase and compare it to the well-studied enzyme from Fusarium solani. Two critical differences are highlighted in the crystallographic analysis of the A. oryzae structure: (i) an additional disulfide bond and (ii) a topologically favored catalytic triad with a continuous and deep groove. These structural features of A. oryzae cutinase are proposed to result in an improved hydrolytic activity and altered substrate specificity profile, enhanced thermostability, and remarkable reactivity toward the degradation of the synthetic polyester polycaprolactone. The results presented here provide insight into engineering new cutinase-inspired biocatalysts with tailor-made properties.

Pseudozyma pruni sp. nov., a novel ustilaginomycetous anamorphic fungus from flowers in Taiwan

Two ustilaginomycetous anamorphic strains were isolated from flowers in Taiwan. Phylogenetic analysis based on the combined rRNA gene sequence of internal transcribed spacer 1 (ITS1)-5.8S-ITS2 and large-subunit D1/D2 domains indicated that the closest recognized species was Pseudozyma fusiformata. The results of DNA-DNA hybridization and physiological characteristics showed that the two strains represent a novel species within the genus Pseudozyma. The name Pseudozyma pruni sp. nov. is proposed, with FIRDI 005(T) (=BCRC 34227(T) =CBS 10937(T)) as the type strain.