Global nutrient profiling by Phenotype MicroArrays: a tool complementing genomic and proteomic studies in conidial fungi

Atanasova, Lea; Druzhinina, Irina S.

doi:10.1631/jzus.b1000007

Cited by 54 publications

(50 citation statements)

References 94 publications

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“…A total of 90 l of the conidial suspension was dispensed into each of the wells of the Biolog FF microplates and incubated at 28°C in darkness and with a 12-h ligh-dark cycle. The OD 750 (for detection of mycelial growth) was measured after 18,24,42,48,66,72,90, and 96 h using a microplate reader. The growth rate of each strain was assessed based on the averaged mycelial density, measured on all 95 carbon sources after 0, 24, 48, and 72 h of incubation in darkness.…”

Section: Methodsmentioning

confidence: 99%

The Polyketide Synthase Gene pks4 of Trichoderma reesei Provides Pigmentation and Stress Resistance

et al. 2013

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Species of the fungal genus Trichoderma (Hypocreales, Ascomycota) are well-known for their production of various secondary metabolites. Nonribosomal peptides and polyketides represent a major portion of these products. In a recent phylogenomic investigation of Trichoderma polyketide synthase (PKS)-encoding genes, the pks4 from T. reesei was shown to be an orthologue of pigment-forming PKSs involved in synthesis of aurofusarin and bikaverin in Fusarium spp. In this study, we show that deletion of this gene in T. reesei results in loss of green conidial pigmentation and in pigmentation alteration of teleomorph structures. It also has an impact on conidial cell wall stability and the antagonistic abilities of T. reesei against other fungi, including formation of inhibitory metabolites. In addition, deletion of pks4 significantly influences the expression of other PKS-encoding genes of T. reesei. To our knowledge, this is the first indication that a low-molecular-weight pigment-forming PKS is involved in defense, mechanical stability, and stress resistance in fungi. The economically important genus Trichoderma (Hypocreales, Ascomycota, Dikarya) is well-known for its mycotrophic lifestyle and for the broad range of biotrophic interactions with plants and animals. Moreover, it contains several cosmopolitan species characterized by their outstanding environmental opportunism. These properties have given rise to the use of several species in agriculture as biopesticides and biofertilizers, while T. reesei is utilized for production of bioenergy-related enzymes (1).The molecular basis for the opportunistic success of Trichoderma is not yet well understood. While there is some evidence for a role of some secreted proteins (2, 3), less is known about a possible role(s) of secondary metabolites. In this respect, Trichoderma spp. are probably best known for production of peptaibols, which are nonribosomal peptides with antimicrobial and plant defensestimulating activities (4). However, the role of polyketide synthases (PKSs) in Trichoderma ecophysiology is not well studied. Trichoderma spp. polyketides are produced by iterative PKSs, multifunctional enzymes consisting of several active sites capable of catalyzing the fusion of variable numbers of coenzyme A (CoA)-linked acyl monomers, such as acetyl-CoA and malonylCoA, into polymers known as polyketides. They can be further grouped into nonreducing (NR) and reducing (RD) PKSs according to their domain organization (5). Recently, Baker et al. (6) used a phylogenomic approach to study the PKS repertoire in T. reesei, T. atroviride, and T. virens, and their findings enabled the putative in silico prediction of some of the respective products. A total of 11 PKS-encoding genes were found in the T. reesei genome, among which 2 occur only in T. reesei and 9 have orthologues in T. virens or/and T. atroviride PKSs (6). pks4 (Trire2: 82208, Triat2:79, and Trive2:77826 in T. reesei, T. atroviride, and T. virens, respectively), which encodes an enzyme of the nonreducing type (clade I)...

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Section: Methodsmentioning

confidence: 99%

The Polyketide Synthase Gene pks4 of Trichoderma reesei Provides Pigmentation and Stress Resistance

et al. 2013

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“…1a). The use of Biolog™ plates has focused on the characterization of bacteria and their communities, though fungi and diverse communities have also been characterized [8] (Fig. 1b).…”

Section: Applicationsmentioning

confidence: 99%

“…A wavelength around 660 nm is correlated with cell counts in yeast [16]. A wavelength of 700 nm was used for the measurement of fungal hyphae [8]. See Notes for use in algae.…”

Section: For Cell Density Approximationmentioning

confidence: 99%

Phenotyping Microarrays for the Characterization of Environmental Microorganisms

Low‐Décarie

Lofano

Samani

2015

Springer Protocols Handbooks

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Culture-based methods for the characterization of microorganisms remain essential to advances in microbiology. Phenotyping arrays and microplates in which each well represents a different selective growth environment are important tools (1) in the identification of microbial isolates, (2) in the characterization of the phenotypic fingerprint of microbial communities, (3) for linking specific functions with specific organisms or genes, and (4) for the identification of evolutionary trade-offs in the establishment of phenotypes. The use of phenotyping arrays in the study of hydrocarbon and lipid degradation by microbial isolates or communities is an emerging application. The application of phenotyping arrays requires careful selection of substrates, growth medium, and dyes and consideration of the intrinsic limitations of the approach. The use of phenotyping arrays leads to the production of large amounts of data, which require specific approaches for summarization and analysis. Liquid handling automation will increase the feasibility of custom phenotyping arrays that include hydrocarbons and lipids.

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“…Nevertheless, the enumeration of total number of fungi as their occurrence ascertainment is also a recognized and an important method in microbiological state evaluation of food products [12]. Identification for phenetic differences of fungi based on nutrient (within carbon sources) profiling 1 3 might be a useful tool for food microbial contamination circumscription [13]. The Biolog FF (filamentous fungi) is the rapid spectrophotometric method for metabolic potential assessment of fungi and yeast.…”

Section: Introductionmentioning

confidence: 99%

Quality assessment of goji fruits, cranberries, and raisins using selected markers

Jeszka-Skowron

Oszust

Zgoła‐Grześkowiak

et al. 2018

Eur Food Res Technol

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The aim of the study was to determine the antioxidant activity, total phenolic content, and total carotenoid content of dried fruit extracts prepared from goji fruits, cranberries, and raisins. Ergosterol content of samples-as a marker of fungal contamination-was measured by LC-MS/MS technique. For the goji fruit samples, fungal community-level physiological profiling and fungal isolate catabolic diversity were tested to evaluate more precisely their fungal contamination. The highest antioxidant activity and total phenolic content were determined for dried goji fruits. Simultaneously, the dried goji fruits were contaminated by ergosterol − 3.8 µg g −1 of dried fruit and the bulk goji fruits were contaminated by heat-resistant fungi. The study of fungal community as a fungal contamination marker of dried goji fruits was performed by a combination of the Biolog FF plates and traditional culture methods which is the first application of this composite analytical approach. Ergosterol content could be an indicator of fungal growth on dried fruits. The Biolog FF microplates can be used as a quick, easy, cheap, and effective method for the detection of heat-resistant fungi in dried fruits.

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Global nutrient profiling by Phenotype MicroArrays: a tool complementing genomic and proteomic studies in conidial fungi

Cited by 54 publications

References 94 publications

The Polyketide Synthase Gene pks4 of Trichoderma reesei Provides Pigmentation and Stress Resistance

The Polyketide Synthase Gene pks4 of Trichoderma reesei Provides Pigmentation and Stress Resistance

Phenotyping Microarrays for the Characterization of Environmental Microorganisms

Quality assessment of goji fruits, cranberries, and raisins using selected markers

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