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  1. Article: The genome sequence of the commercially cultivated mushroom Agrocybe aegerita reveals a conserved repertoire of fruiting-related genes and a versatile suite of biopolymer-degrading enzymes

    Rühl, Martin / SHARMA, RAHUL / Thines, Marco

    BMC genomics, 19:48

    2018  

    Abstract: BACKGROUND: Agrocybe aegerita is an agaricomycete fungus with typical mushroom features, which is commercially cultivated for its culinary use. In nature, it is a saprotrophic or facultative pathogenic fungus causing a white-rot of hardwood in forests of ...

    Institution Senckenberg Biodiversität und Klima Forschungszentrum
    Abstract BACKGROUND: Agrocybe aegerita is an agaricomycete fungus with typical mushroom features, which is commercially cultivated for its culinary use. In nature, it is a saprotrophic or facultative pathogenic fungus causing a white-rot of hardwood in forests of warm and mild climate. The ease of cultivation and fructification on solidified media as well as its archetypal mushroom fruit body morphology render A. aegerita a well-suited model for investigating mushroom developmental biology. RESULTS: Here, the genome of the species is reported and analysed with respect to carbohydrate active genes and genes known to play a role during fruit body formation. In terms of fruit body development, our analyses revealed a conserved repertoire of fruiting-related genes, which corresponds well to the archetypal fruit body morphology of this mushroom. For some genes involved in fruit body formation, paralogisation was observed, but not all fruit body maturation-associated genes known from other agaricomycetes seem to be conserved in the genome sequence of A. aegerita. In terms of lytic enzymes, our analyses suggest a versatile arsenal of biopolymer-degrading enzymes that likely account for the flexible life style of this species. Regarding the amount of genes encoding CAZymes relevant for lignin degradation, A. aegerita shows more similarity to white-rot fungi than to litter decomposers, including 18 genes coding for unspecific peroxygenases and three dye-decolourising peroxidase genes expanding its lignocellulolytic machinery. CONCLUSIONS: The genome resource will be useful for developing strategies towards genetic manipulation of A. aegerita, which will subsequently allow functional genetics approaches to elucidate fundamentals of fruiting and vegetative growth including lignocellulolysis.
    Keywords Comparative genomics ; Carbohydrate active enzymes ; Agaricales ; Basidiomycetes ; Developmental biology ; Fruit body ; Mushroom ; White-rot
    Language English
    Document type Article
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  2. Article ; Online: Identification of volatile producing enzymes in higher fungi: Combining analytical and bioinformatic methods.

    Orban, Axel M / Rühl, Martin

    Methods in enzymology

    2022  Volume 664, Page(s) 221–242

    Abstract: Filamentous fungi harbor the genetic potential for the biosynthesis of several secondary metabolites including various volatile organic compounds (VOCs). Nonetheless, under standard laboratory conditions, many of these VOCs are not formed. Furthermore, ... ...

    Abstract Filamentous fungi harbor the genetic potential for the biosynthesis of several secondary metabolites including various volatile organic compounds (VOCs). Nonetheless, under standard laboratory conditions, many of these VOCs are not formed. Furthermore, little is known about enzymes involved in the production of fungal VOCs. To tap these interesting topics, we developed an approach to identify enzymes putatively involved in the fungal VOC biosynthesis. In this chapter, we highlight different fungal cultivation methods and techniques for the extraction of VOCs, including a method that allows the noninvasive analysis of VOCs. In addition using terpene synthases as an example, it is depicted how enzymes putatively involved in VOC synthesis can be identified by means of bioinformatic approaches. Transcriptomic data of chosen genes combined with volatilome data obtained during different developmental stages is demonstrated as a powerful tool to identify enzymes putatively involved in fungal VOC biosynthesis. Especially with regard to subsequent enzyme characterization, this procedure is a target-oriented way to save time and efforts by considering only the most important enzymes.
    MeSH term(s) Computational Biology ; Fungi/genetics ; Fungi/metabolism ; Volatile Organic Compounds/metabolism
    Chemical Substances Volatile Organic Compounds
    Language English
    Publishing date 2022-01-19
    Publishing country United States
    Document type Journal Article
    ISSN 1557-7988
    ISSN (online) 1557-7988
    DOI 10.1016/bs.mie.2021.12.007
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Protein- and Carbohydrate-Rich Supplements in Feeding Adult Black Soldier Flies (

    Klüber, Patrick / Arous, Emna / Zorn, Holger / Rühl, Martin

    Life (Basel, Switzerland)

    2023  Volume 13, Issue 2

    Abstract: The black soldier fly, ...

    Abstract The black soldier fly,
    Language English
    Publishing date 2023-01-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662250-6
    ISSN 2075-1729
    ISSN 2075-1729
    DOI 10.3390/life13020355
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  4. Article ; Online: A Novel

    Brescia, Fabio Francesco / Korf, Lukas / Essen, Lars-Oliver / Zorn, Holger / Ruehl, Martin

    Journal of agricultural and food chemistry

    2024  Volume 72, Issue 12, Page(s) 6471–6480

    Abstract: Increasing consumer aversion to non-natural flavoring substances is prompting a heightened interest in enzymatic processes for flavor production. This includes methylation reactions, which are often performed by using hazardous chemicals. By correlation ... ...

    Abstract Increasing consumer aversion to non-natural flavoring substances is prompting a heightened interest in enzymatic processes for flavor production. This includes methylation reactions, which are often performed by using hazardous chemicals. By correlation of aroma profile data and transcriptomic analysis, a novel
    MeSH term(s) Methyltransferases/metabolism ; Escherichia coli/metabolism ; Pleurotus/metabolism ; Benzaldehydes
    Chemical Substances Methyltransferases (EC 2.1.1.-) ; 4-hydroxybenzaldehyde (O1738X3Y38) ; 4-anisaldehyde (9PA5V6656V) ; Benzaldehydes
    Language English
    Publishing date 2024-03-10
    Publishing country United States
    Document type Journal Article
    ZDB-ID 241619-0
    ISSN 1520-5118 ; 0021-8561
    ISSN (online) 1520-5118
    ISSN 0021-8561
    DOI 10.1021/acs.jafc.3c08849
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  5. Article: Enzymatic Oxidation of Ca-Lignosulfonate and Kraft Lignin in Different Lignin-Laccase-Mediator-Systems and MDF Production.

    Euring, Markus / Ostendorf, Kolja / Rühl, Martin / Kües, Ursula

    Frontiers in bioengineering and biotechnology

    2022  Volume 9, Page(s) 788622

    Abstract: Laccase-mediator-oxidized lignin offers replacement for conventional chemical binders to produce fiberboards. Compared to the previously reported laccase-mediator system (LMS), a lignin-laccase-mediator-system (LLMS) has an advantage in that it requires ... ...

    Abstract Laccase-mediator-oxidized lignin offers replacement for conventional chemical binders to produce fiberboards. Compared to the previously reported laccase-mediator system (LMS), a lignin-laccase-mediator-system (LLMS) has an advantage in that it requires much shorter fiber-enzyme incubation time due to significantly increased redox reactions. However, the cost of regularly applying laccase on an industrial scale is currently too high. We have employed
    Language English
    Publishing date 2022-01-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2719493-0
    ISSN 2296-4185
    ISSN 2296-4185
    DOI 10.3389/fbioe.2021.788622
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  6. Book ; Article ; Online: Identification of volatile producing enzymes in higher fungi

    Orban, Axel Martin / Rühl, Martin

    Combining analytical and bioinformatic methods

    2022  

    Abstract: 221 ... 242 ... Filamentous fungi harbor the genetic potential for the biosynthesis of several secondary metabolites including various volatile organic compounds (VOCs). Nonetheless, under standard laboratory conditions, many of these VOCs are not formed. ... ...

    Abstract 221

    242

    Filamentous fungi harbor the genetic potential for the biosynthesis of several secondary metabolites including various volatile organic compounds (VOCs). Nonetheless, under standard laboratory conditions, many of these VOCs are not formed. Furthermore, little is known about enzymes involved in the production of fungal VOCs. To tap these interesting topics, we developed an approach to identify enzymes putatively involved in the fungal VOC biosynthesis. In this chapter, we highlight different fungal cultivation methods and techniques for the extraction of VOCs, including a method that allows the noninvasive analysis of VOCs. In addition using terpene synthases as an example, it is depicted how enzymes putatively involved in VOC synthesis can be identified by means of bioinformatic approaches. Transcriptomic data of chosen genes combined with volatilome data obtained during different developmental stages is demonstrated as a powerful tool to identify enzymes putatively involved in fungal VOC biosynthesis. Especially with regard to subsequent enzyme characterization, this procedure is a target-oriented way to save time and efforts by considering only the most important enzymes.
    Keywords Aroma biosynthesis ; Filamentous fungi ; Genome mining ; Mushroom ; Terpene synthases ; VOCs
    Subject code 572
    Language English
    Publishing country de
    Document type Book ; Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Protein- and Carbohydrate-Rich Supplements in Feeding Adult Black Soldier Flies (Hermetia illucens) Affect Life History Traits and Egg Productivity

    Klüber, Patrick / Arous, Emna / Zorn, Holger / Ruhl, Martin

    2023  

    Abstract: 1 ... 25 ... The black soldier fly, Hermetia illucens (BSF; Diptera: Stratiomyidae), has come into the focus of research over the past decade since its larvae are polyphagous feeders with an exceptional substrate range, making them a promising candidate for ... ...

    Abstract 1

    25

    The black soldier fly, Hermetia illucens (BSF; Diptera: Stratiomyidae), has come into the focus of research over the past decade since its larvae are polyphagous feeders with an exceptional substrate range, making them a promising candidate for the bioconversion of various organic side streams into valuable insect protein. While larval nutritional requirements have been studied in detail, basic information on adult feeding is still lacking. The reproduction of adult flies is a bottleneck and key determinant in rearing BSF, which has extensive potential for improvement. In the present study, we examined the impact of different carbohydrate (honey and d-glucose) and protein sources (Spirulina and Chlorella powder) on a variety of life history traits using a highly standardized single pair approach. Feeding a 5% honey solution was shown to make females live 2.8 d longer, become more fecund (9 egg clutches per 10 females), lay more eggs (increasing 1.7-fold to 182.4 mg per 10 females), reduce the number of failed oviposition events 3-fold and increase multiple oviposition events from 2 to 15. Additionally, female longevity after oviposition improved 1.7-fold from 6.7 to 11.5 d. In order to further optimize adult feeding, mixtures of proteins and carbohydrates with varying ratios should be tested.

    13

    2
    Keywords black soldier fly ; feeding behavior ; insect rearing ; life history traits ; longevity ; mating ; oviposition ; rearing method ; reproduction
    Subject code 590
    Language English
    Publishing country de
    Document type Article ; Online
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  8. Article: Engineering a lipoxygenase from cyclocybe aegerita towards long chain polyunsaturated fatty acids.

    Karrer, Dominik / Gand, Martin / Rühl, Martin

    AMB Express

    2021  Volume 11, Issue 1, Page(s) 37

    Abstract: The basidiomycetous lipoxygenase Lox1 from Cyclocybe aegerita catalyzes the oxygenation of polyunsaturated fatty acids (PUFAs) with a high preference towards the C18-PUFA linoleic acid (C18:2 (ω-6)). In contrast, longer PUFAs, generally not present in ... ...

    Abstract The basidiomycetous lipoxygenase Lox1 from Cyclocybe aegerita catalyzes the oxygenation of polyunsaturated fatty acids (PUFAs) with a high preference towards the C18-PUFA linoleic acid (C18:2 (ω-6)). In contrast, longer PUFAs, generally not present in the fungal cell such as eicosatrienoic acid (C20:3(ω-3)) and docosatrienoic acid (C22:3 (ω-3)), are converted with drastically lower activities. With site-directed mutagenesis, we were able to create two variants with enhanced activities towards longer chain PUFAs. The W330L variant showed a ~ 20 % increased specific activity towards C20:3(ω-3), while a ~ 2.5-fold increased activity against C22:3 (ω-3) was accomplished by the V581 variant.
    Language English
    Publishing date 2021-03-04
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2621432-5
    ISSN 2191-0855
    ISSN 2191-0855
    DOI 10.1186/s13568-021-01195-8
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  9. Article ; Online: Fatty acids derived from oviposition systems guide female black soldier flies (Hermetia illucens) toward egg deposition sites.

    Klüber, Patrick / Arous, Emna / Jerschow, Jeanny / Fraatz, Marco / Bakonyi, Daniel / Rühl, Martin / Zorn, Holger

    Insect science

    2023  

    Abstract: The black soldier fly, Hermetia illucens, comes with big promises for industrial purposes since its larvae feed polyphagously on a broad spectrum of organic substrates. However, research focusing on adult flies is scarce, which is inconsistent with their ...

    Abstract The black soldier fly, Hermetia illucens, comes with big promises for industrial purposes since its larvae feed polyphagously on a broad spectrum of organic substrates. However, research focusing on adult flies is scarce, which is inconsistent with their reproductive relevance within the rearing cycle. In particular, directed oviposition is a challenge in artificial systems. Currently, decomposing organic matter is commonly used as oviposition substrate, which has extensive potential for improvement in view of the lack of standardization and the risk of microbial contamination. Here, we identified three fatty acids and one fatty acid methyl ester derived from the surface of old oviposition sites and targeted to elucidate their effect on preference behavior and oviposition site selection using Y-olfactometry and prepared oviposition sites, respectively. Exposure to tetradecanoic acid attracted gravid females and stimulated oviposition most strongly, while decanoic acid demonstrated a repulsive effect. Females kept in mixed-sex populations were attracted by tetradecanoic acid, resulting in a higher egg mass found in the compound box (3.0-11.4 fold), a ≥ 2.3 fold reduction of nonspecifically deposited eggs, and the highest total egg mass. Conversely, decanoic and dodecanoic acid caused females to lay a greater proportion of eggs nonspecifically outside both boxes. Our data suggest that fatty acids, especially tetradecanoic acid, are important cues for oviposition site selection in black soldier flies. In order to achieve a directed oviposition behavior, the role of further short- and long-chain fatty acids as attractants should be examined.
    Language English
    Publishing date 2023-10-12
    Publishing country Australia
    Document type Journal Article
    ZDB-ID 2179775-4
    ISSN 1744-7917 ; 1672-9609
    ISSN (online) 1744-7917
    ISSN 1672-9609
    DOI 10.1111/1744-7917.13287
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  10. Article: Isolation of Bacterial and Fungal Microbiota Associated with

    Klüber, Patrick / Müller, Stephanie / Schmidt, Jonas / Zorn, Holger / Rühl, Martin

    Microorganisms

    2022  Volume 10, Issue 2

    Abstract: Larvae of the black soldier fly (BSF) ...

    Abstract Larvae of the black soldier fly (BSF)
    Language English
    Publishing date 2022-01-29
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms10020319
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