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Journal of Fungi (Basel, Switzerland) Sep 2022The genus belongs to the class Ascomycota and the family Coniochaetaceae. Some of the species are plant and animal pathogens, while others are known to be primarily...
The genus belongs to the class Ascomycota and the family Coniochaetaceae. Some of the species are plant and animal pathogens, while others are known to be primarily involved in human diseases. In the last few decades, case reports of human infections with have increased, mainly in immunocompromised hosts. We have described and characterised a new species in the genus , here named (PMML0158), which was isolated from a clinical sample. Species identification and thorough description were based on apposite and reliable phylogenetic and phenotypic approaches. The phylogenetic methods included multilocus phylogenetic analyses of four genomic regions: ITS (rRNA Internal Transcribed Spacers 1 and 2), TEF-1α (Translation Elongation Factor-1alpha), B-tub2 (β-tubulin2), and D1/D2 domains (28S large subunit rRNA). The phenotypic characterisation consisted, first, of a physiological analysis using both EDX (energy-dispersive X-ray spectroscopy) and Biolog advanced phenotypic technology for fixing the chemical mapping and carbon-source oxidation/assimilation profiles. Afterwards, morphological characteristics were highlighted by optical microscopy and scanning electron microscopy. The in vitro antifungal susceptibility profile was characterised using the E-test exponential gradient method. The molecular analysis revealed the genetic distance between the novel species (PMML0158) and other known taxa, and the phenotypic analysis confirmed its unique chemical and physiological profile when compared with all other species of this genus.
PubMed: 36294564
DOI: 10.3390/jof8100999 -
MycoKeys 2021Lichens are the result of a symbiotic interaction between fungi (mycobionts) and algae (phycobionts). Aside from mycobionts, lichen thalli can also contain...
Lichens are the result of a symbiotic interaction between fungi (mycobionts) and algae (phycobionts). Aside from mycobionts, lichen thalli can also contain non-lichenised fungal species, such as lichenicolous and endolichenic fungi. For this study, three surveys were conducted in China's Yunnan Province and Inner Mongolia Autonomous Region between 2017 and 2020. Several samples of four lichen species were collected during these surveys: , , and . Six isolates of were recovered from these four lichen species. The phylogenetic and morphological analyses revealed that two of these isolates were previously identified species, and . Those remaining were from potentially unknown species. We used molecular and morphological data to describe these previously-unknown species as , and The findings of this study significantly improve our understanding of the variety and habitat preferences of in China and globally.
PubMed: 34602840
DOI: 10.3897/mycokeys.83.71140 -
Microbiological Research Dec 2023The urgent need for better disposal and recycling of plastics has motivated a search for microbes with the ability to degrade synthetic polymers. While microbes capable...
The urgent need for better disposal and recycling of plastics has motivated a search for microbes with the ability to degrade synthetic polymers. While microbes capable of metabolizing polyurethane and polyethylene terephthalate have been discovered and even leveraged in enzymatic recycling approaches, microbial degradation of additive-free polypropylene (PP) remains elusive. Here we report the isolation and characterization of two fungal strains with the potential to degrade pure PP. Twenty-seven fungal strains, many isolated from hydrocarbon contaminated sites, were screened for degradation of commercially used textile plastic. Of the candidate strains, two identified as Coniochaeta hoffmannii and Pleurostoma richardsiae were found to colonize the plastic fibers using scanning electron microscopy (SEM). Further experiments probing degradation of pure PP films were performed using C. hoffmannii and P. richardsiae and analyzed using SEM, Raman spectroscopy and Fourier transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR). The results showed that the selected fungi were active against pure PP, with distinct differences in the bonds targeted and the degree to which each was altered. Whole genome and transcriptome sequencing was conducted for both strains and the abundance of carbohydrate active enzymes, GC content, and codon usage bias were analyzed in predicted proteomes for each. Enzymatic assays were conducted to assess each strain's ability to degrade naturally occurring compounds as well as synthetic polymers. These investigations revealed potential adaptations to hydrocarbon-rich environments and provide a foundation for further investigation of PP degrading activity in C. hoffmannii and P. richardsiae.
Topics: Plastics; Polypropylenes; Ascomycota; Fungi; Biodegradation, Environmental
PubMed: 37793281
DOI: 10.1016/j.micres.2023.127507 -
BMC Microbiology Apr 2022Symbiotic associations of endophytic fungi have been proved by possessing an ability to produce hormones and metabolites for their host plant. Members of the Orchidaceae...
BACKGROUND
Symbiotic associations of endophytic fungi have been proved by possessing an ability to produce hormones and metabolites for their host plant. Members of the Orchidaceae are obligate mycorrhizal species but a non-mycorrhizal association needs more investigation for their ability to promote plant growth and produce plant growth hormones. In the present study, endophytic fungi were isolated from the roots of Dendrobium longicornu Lindl., to investigate the root colonizing activity and role in plant growth and development.
RESULTS
Among 23 fungal isolates were identified both by morphological and molecular technique as Penicillium sp., Fusarium sp., Coniochaeta sp., Alternaria sp., and Cladosporium sp. The dominate species were Coniochaeta sp. and Cladosporium sp. The dominant species as per the isolation was Coniochaeta sp. These fungal strains were screened for growth-promoting activity of Cymbidium aloifolium (plantlet) consider as cross genus interaction and Dendrobium longicornu (protocorms) as a host plant in in-vitro condition. Importantly, Cladosporium sp., and Coniochaeta sp. showed successful colonization and peloton formation with roots of C. aloifolium. Moreover, it also enhanced acclimatization of plantlets. Fungal elicitors from nine fungal isolates enhanced the growth of the in vitro grown protocorms of D. longicornu. Key bioactive compounds detected in the fungal colonized plant extract were 2H-pyran-2-one, Cyclopropanecarboxylic acid, Oleic Acid and d-Mannitol, which may have a potential role in plant-microbe interaction. All fungal endophytes were able to synthesize the indole acetic acid (IAA) in presence of tryptophan. Moreover, fungal extract DLCCR7 treated with DL-tryptophan yielded a greater IAA concentration of 43 μg per ml than the other extracts. The iaaM gene involved in IAA synthesis pathway was amplified using iaaM gene primers successfully from Alternaria sp., Cladosporium sp., and Coniochaeta sp.
CONCLUSIONS
Hence, this study confirms the production of IAA by endophytes and demonstrated their host as well as cross-genus plant growth-promoting potential by producing metabolites required for the growth of the plant.
Topics: Alternaria; Ascomycota; Endophytes; Fungi; Hormones; Indoleacetic Acids; Orchidaceae; Phylogeny; Plant Growth Regulators; Tryptophan
PubMed: 35418028
DOI: 10.1186/s12866-022-02507-z -
Microbial Cell Factories Jul 2020Two marine fungi, a Trichoderma sp. and a Coniochaeta sp., which can grow on D-galacturonic acid and pectin, were selected as hosts to engineer for mucic acid...
BACKGROUND
Two marine fungi, a Trichoderma sp. and a Coniochaeta sp., which can grow on D-galacturonic acid and pectin, were selected as hosts to engineer for mucic acid production, assessing the suitability of marine fungi for production of platform chemicals. The pathway for biotechnologcial production of mucic (galactaric) acid from D-galacturonic acid is simple and requires minimal modification of the genome, optimally one deletion and one insertion. D-Galacturonic acid, the main component of pectin, is a potential substrate for bioconversion, since pectin-rich waste is abundant.
RESULTS
Trichoderma sp. LF328 and Coniochaeta sp. MF729 were engineered using CRISPR-Cas9 to oxidize D-galacturonic acid to mucic acid, disrupting the endogenous pathway for D-galacturonic acid catabolism when inserting a gene encoding bacterial uronate dehydrogenase. The uronate dehydrogenase was expressed under control of a synthetic expression system, which fucntioned in both marine strains. The marine Trichoderma transformants produced 25 g L mucic acid from D-galacturonic acid in equimolar amounts: the yield was 1.0 to 1.1 g mucic acid [g D-galacturonic acid utilized]. D-Xylose and lactose were the preferred co-substrates. The engineered marine Trichoderma sp. was more productive than the best Trichoderma reesei strain (D-161646) described in the literature to date, that had been engineered to produce mucic acid. With marine Coniochaeta transformants, D-glucose was the preferred co-substrate, but the highest yield was 0.82 g g: a portion of D-galacturonic acid was still metabolized. Coniochaeta sp. transformants produced adequate pectinases to produce mucic acid from pectin, but Trichoderma sp. transformants did not.
CONCLUSIONS
Both marine species were successfully engineered using CRISPR-Cas9 and the synthetic expression system was functional in both species. Although Coniochaeta sp. transformants produced mucic acid directly from pectin, the metabolism of D-galacturonic acid was not completely disrupted and mucic acid amounts were low. The D-galacturonic pathway was completely disrupted in the transformants of the marine Trichoderma sp., which produced more mucic acid than a previously constructed T. reesei mucic acid producing strain, when grown under similar conditions. This demonstrated that marine fungi may be useful as production organisms, not only for native enzymes or bioactive compounds, but also for other compounds.
Topics: Aquatic Organisms; Ascomycota; Biotechnology; CRISPR-Cas Systems; Hexuronic Acids; Metabolic Engineering; Sugar Acids; Trichoderma
PubMed: 32736636
DOI: 10.1186/s12934-020-01411-3 -
Biotechnology For Biofuels 2019Particular species of the genus (Sordariomycetes) exhibit great potential for bioabatement of furanic compounds and have been identified as an underexplored source of...
BACKGROUND
Particular species of the genus (Sordariomycetes) exhibit great potential for bioabatement of furanic compounds and have been identified as an underexplored source of novel lignocellulolytic enzymes, especially . However, there is a lack of information about their genomic features and metabolic capabilities. Here, we report the first in-depth genome/transcriptome survey of a species (strain 2T2.1).
RESULTS
The genome of sp. strain 2T2.1 has a size of 74.53 Mbp and contains 24,735 protein-encoding genes. Interestingly, we detected a genome expansion event, resulting ~ 98% of the assembly being duplicated with 91.9% average nucleotide identity between the duplicated regions. The lack of gene loss, as well as the high divergence and strong genome-wide signatures of purifying selection between copies indicates that this is likely a recent duplication, which arose through hybridization between two related -like species (allopolyploidization). Phylogenomic analysis revealed that 2T2.1 is related sp. PMI546 and sp. AK0013, which both occur endophytically. Based on carbohydrate-active enzyme (CAZy) annotation, we observed that even after in silico removal of its duplicated content, the 2T2.1 genome contains exceptional lignocellulolytic machinery. Moreover, transcriptomic data reveal the overexpression of proteins affiliated to CAZy families GH11, GH10 (endoxylanases), CE5, CE1 (xylan esterases), GH62, GH51 (α-l-arabinofuranosidases), GH12, GH7 (cellulases), and AA9 (lytic polysaccharide monoxygenases) when the fungus was grown on wheat straw compared with glucose as the sole carbon source.
CONCLUSIONS
We provide data that suggest that a recent hybridization between the genomes of related species may have given rise to sp. 2T2.1. Moreover, our results reveal that the degradation of arabinoxylan, xyloglucan and cellulose are key metabolic processes in strain 2T2.1 growing on wheat straw. Different genes for key lignocellulolytic enzymes were identified, which can be starting points for production, characterization and/or supplementation of enzyme cocktails used in saccharification of agricultural residues. Our findings represent first steps that enable a better understanding of the reticulate evolution and "eco-enzymology" of lignocellulolytic species.
PubMed: 31572496
DOI: 10.1186/s13068-019-1569-6 -
Fungal Systematics and Evolution Jun 2021An order, family and genus are validated, seven new genera, 35 new species, two new combinations, two epitypes, two lectotypes, and 17 interesting new host and / or...
An order, family and genus are validated, seven new genera, 35 new species, two new combinations, two epitypes, two lectotypes, and 17 interesting new host and / or geographical records are introduced in this study. Validated order, family and genus: and (based on . New genera: (based on ); (based on ); (based on ); (based on ); (based on ); (based on ); (based on ). New species: on dead culms of (Netherlands); on dead culms of (Spain); on leaves of sp. (Australia); from submerged leaf litter (Singapore); on leaves of sp. (Malaysia); on leaves of sp. (South Africa); from soil (Netherlands); on branches of (Vietnam); on dead culm of sp. (France); on leaf sheath of sp. (Germany); from soil (Netherlands); from soil (Chile); on dead stems of (South Africa); on leaves of sp. (Angola); on dead leaves of (Germany); on seed capsules of (South Africa); on dead leaves of (Namibia); from soil (Netherlands); on dead wood of (Czech Republic); on leaves of (Ukraine); from soil (Netherlands); on masonry and plastering (France); on leaves of (South Africa); from soil (Netherlands); from soil (Netherlands); on leaves of (South Africa); on leaves of (USA); from soil (Netherlands); in sporocarp of on wood (Netherlands); on (Netherlands); on (Netherlands); on leaf of (Australia); from human eye specimen (USA); on twig of (Germany), and on twigs of (Spain). Crous PW, Hernández-Restrepo M, Schumacher RK, Cowan DA, Maggs-Kölling G, Marais E, Wingfield MJ, Yilmaz N, Adan OCG, Akulov A, Álvarez Duarte E, Berraf-Tebbal A, Bulgakov TS, Carnegie AJ, de Beer ZW, Decock C, Dijksterhuis J, Duong TA, Eichmeier A, Hien LT, Houbraken JAMP, Khanh TN, Liem NV, Lombard L, Lutzoni FM, Miadlikowska JM, Nel WJ, Pascoe IG, Roets F, Roux J, Samson RA, Shen M, Spetik M, Thangavel R, Thanh HM, Thao LD, van Nieuwenhuijzen EJ, Zhang JQ, Zhang Y, Zhao LL, Groenewald JZ (2021). New and Interesting Fungi. 4. 255-343. doi: 10.3114/fuse.2021.07.13.
PubMed: 34124627
DOI: 10.3114/fuse.2021.07.13 -
Frontiers in Microbiology 2022Endophytic fungi are microorganisms with the ability to colonize plants for the entire or at least a significant part of their life cycle asymptomatically, establishing...
Endophytic fungi are microorganisms with the ability to colonize plants for the entire or at least a significant part of their life cycle asymptomatically, establishing a plant-fungus association. They play an important role in balancing ecosystems, as well as benefiting host through increasing plant growth, and protecting the host plants from abiotic and biotic stresses using various strategies. In the present study, endophytic fungi were isolated from wild and endemic apple cultivars, followed by characterizing their antifungal effect against . To characterize the endophytic fungi, 417 fungal strains were separated from 210 healthy fruit, leaf, and branch samples collected from the north of Iran. Among the purified fungal isolates, 33 fungal genera were identified based on the morphological characteristics, of which 38 species were detected according to the morphological features and molecular data of ITS, , and genomic regions (related to the genus). The results represented that most of the endophytic fungi belonged to Ascomycota (67.8%), 31.4% of isolates were mycelia sterilia, while the others were Basidiomycota (0.48%) and Mucoromycota (0.24%). Additionally, , , and were determined as the dominant genera. The antifungal properties of the identified isolates were evaluated against to determine the release of media-permeable metabolites, Volatile Organic Compounds (VOCs), chitinase, and cellulase as antifungal mechanisms, as well as producing phosphate solubilisation as growth-promoting effect. Based on the results of metabolite and VOC tests, the six isolates of GO13S1, 55S2, 61S2, 7F2, 2S1 and 3 L2 were selected for greenhouse tests. Further, 55S2 and 61S2 could solubilize inorganic phosphate. All isolates except 3 L2 exhibited cellulase activity, while chitinase activity was observed in 2S1, 3 L2, and 61S2. Finally, 55S2 and 2S1 completely controlled the disease on the apple seedling leaves under greenhouse conditions.
PubMed: 36419433
DOI: 10.3389/fmicb.2022.1024001 -
Biotechnology For Biofuels and... Mar 2023In a previous study, shaking speed was found to be an important factor affecting the population dynamics and lignocellulose-degrading activities of a synthetic...
BACKGROUND
In a previous study, shaking speed was found to be an important factor affecting the population dynamics and lignocellulose-degrading activities of a synthetic lignocellulolytic microbial consortium composed of the bacteria Sphingobacterium paramultivorum w15, Citrobacter freundii so4, and the fungus Coniochaeta sp. 2T2.1. Here, the gene expression profiles of each strain in this consortium were examined after growth at two shaking speeds (180 and 60 rpm) at three time points (1, 5 and 13 days).
RESULTS
The results indicated that, at 60 rpm, C. freundii so4 switched, to a large extent, from aerobic to flexible (aerobic/microaerophilic/anaerobic) metabolism, resulting in continued slow growth till late stage. In addition, Coniochaeta sp. 2T2.1 tended to occur to a larger extent in the hyphal form, with genes encoding adhesion proteins being highly expressed. Much like at 180 rpm, at 60 rpm, S. paramultivorum w15 and Coniochaeta sp. 2T2.1 were key players in hemicellulose degradation processes, as evidenced from the respective CAZy-specific transcripts. Coniochaeta sp. 2T2.1 exhibited expression of genes encoding arabinoxylan-degrading enzymes (i.e., of CAZy groups GH10, GH11, CE1, CE5 and GH43), whereas, at 180 rpm, some of these genes were suppressed at early stages of growth. Moreover, C. freundii so4 stably expressed genes that were predicted to encode proteins with (1) β-xylosidase/β-glucosidase and (2) peptidoglycan/chitinase activities, (3) stress response- and detoxification-related proteins. Finally, S. paramultivorum w15 showed involvement in vitamin B2 generation in the early stages across the two shaking speeds, while this role was taken over by C. freundii so4 at late stage at 60 rpm.
CONCLUSIONS
We provide evidence that S. paramultivorum w15 is involved in the degradation of mainly hemicellulose and in vitamin B2 production, and C. freundii so4 in the degradation of oligosaccharides or sugar dimers, next to detoxification processes. Coniochaeta sp. 2T2.1 was held to be strongly involved in cellulose and xylan (at early stages), next to lignin modification processes (at later stages). The synergism and alternative functional roles presented in this study enhance the eco-enzymological understanding of the degradation of lignocellulose in this tripartite microbial consortium.
PubMed: 36991472
DOI: 10.1186/s13068-023-02289-0 -
Microorganisms May 2023The main purpose of this study was to degrade total petroleum hydrocarbons (TPHs) from contaminated soil in batch microcosm reactors. Native soil fungi isolated from the...
The main purpose of this study was to degrade total petroleum hydrocarbons (TPHs) from contaminated soil in batch microcosm reactors. Native soil fungi isolated from the same petroleum-polluted soil and ligninolytic fungal strains were screened and applied in the treatment of soil-contaminated microcosms in aerobic conditions. The bioaugmentation processes were carried out using selected hydrocarbonoclastic fungal strains in mono or co-cultures. Results demonstrated the petroleum-degrading potential of six fungal isolates, namely KBR1 and KBR8 (indigenous) and KBR1-1, KB4, KB2 and LB3 (exogenous). Based on the molecular and phylogenetic analysis, KBR1 and KB8 were identified as [MW699896] and [MW699895], while KBR1-1, KB4, KB2 and LB3 were affiliated with the genera sp. [MZ817958], [MW699897], [MZ817957] and sp. [MW699893], respectively. The highest rate of TPH degradation was recorded in soil microcosm treatments (SMT) after 60 days by inoculation with 97 ± 2.54%, followed by bioaugmentation with the native strain (92 ± 1.83%) and then by the fungal consortium (84 ± 2.21%). The statistical analysis of the results showed significant differences.
PubMed: 37317325
DOI: 10.3390/microorganisms11051351