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Correction: A review on architecture with fungal biomaterials: the desired and the feasible. 更正:真菌生物材料建筑的综述:期望和可行。
Q1 Agricultural and Biological Sciences Pub Date : 2022-07-12 DOI: 10.1186/s40694-022-00142-x
Dimitra Almpani-Lekka, Sven Pfeiffer, Christian Schmidts, Seung-Il Seo
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引用次数: 0
Exploring fungal RiPPs from the perspective of chemical ecology. 从化学生态学的角度探讨真菌ripp。
Q1 Agricultural and Biological Sciences Pub Date : 2022-06-25 DOI: 10.1186/s40694-022-00144-9
R E Ford, G D Foster, A M Bailey

Since the initial detection, in 2007, of fungal ribosomally synthesised and post-translationally modified peptides (RiPPs), this group of natural products has undergone rapid expansion, with four separate classes now recognised: amatoxins/phallotoxins, borosins, dikaritins, and epichloëcyclins. Largely due to their historically anthropocentric employment in medicine and agriculture, novel fungal proteins and peptides are seldom investigated in relation to the fungus itself. Therefore, although the benefits these compounds confer to humans are often realised, their evolutionary advantage to the fungus, the reason for their continued production, is often obscure or ignored. This review sets out to summarise current knowledge on how these small peptide-derived products influence their producing species and surrounding biotic environment.

自2007年首次检测到真菌核糖体合成和翻译后修饰肽(RiPPs)以来,这组天然产物经历了快速扩展,目前已识别出四种不同的类别:amatoxins/phallotoxins, borosins, dikaritins和epichloëcyclins。很大程度上由于它们在医学和农业中以人类为中心的历史应用,新的真菌蛋白质和肽很少被研究与真菌本身有关。因此,虽然这些化合物给人类带来的好处经常被认识到,但它们对真菌的进化优势,它们继续生产的原因,往往是模糊的或被忽视的。这篇综述概述了目前关于这些小肽衍生产品如何影响其生产物种和周围生物环境的知识。
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引用次数: 1
Subcellular localization of fungal specialized metabolites. 真菌特殊代谢物的亚细胞定位。
Q1 Agricultural and Biological Sciences Pub Date : 2022-05-25 DOI: 10.1186/s40694-022-00140-z
Elizabeth Skellam

Fungal specialized metabolites play an important role in the environment and have impacted human health and survival significantly. These specialized metabolites are often the end product of a series of sequential and collaborating biosynthetic enzymes that reside within different subcellular compartments. A wide variety of methods have been developed to understand fungal specialized metabolite biosynthesis in terms of the chemical conversions and the biosynthetic enzymes required, however there are far fewer studies elucidating the compartmentalization of the same enzymes. This review illustrates the biosynthesis of specialized metabolites where the localization of all, or some, of the biosynthetic enzymes have been determined and describes the methods used to identify the sub-cellular localization.

真菌的特殊代谢物在环境中发挥着重要作用,并对人类的健康和生存产生了重大影响。这些特化代谢物通常是不同亚细胞区室中一系列有序和协作生物合成酶的最终产物。目前已开发出多种方法,从化学转换和所需生物合成酶的角度来了解真菌特化代谢物的生物合成,但阐明相同酶的区室划分的研究却少得多。本综述说明了特化代谢物的生物合成,其中所有或部分生物合成酶的定位已经确定,并介绍了用于确定亚细胞定位的方法。
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引用次数: 0
Press water from the mechanical drying of Douglas-fir wood chips has multiple beneficial effects on lignocellulolytic fungi. 道格拉斯冷杉木屑机械干燥产生的压水对木质纤维素分解真菌有多种有益作用
Q1 Agricultural and Biological Sciences Pub Date : 2022-05-23 DOI: 10.1186/s40694-022-00141-y
Manfred J Reppke, Rebecca Gerstner, Elisabeth Windeisen-Holzhauser, Klaus Richter, J Philipp Benz

Background: The mechanical drying of wood chips is an innovative method that improves the heating value of sawmill by-products in an energy-efficient continuous process. The liquid that comes out of the wood chips as press water (PW), however, contains a variety of undissolved as well as dissolved organic substances. The disposal of the PW as wastewater would generate additional costs due to its high organic load, offsetting the benefits in energy costs associated with the enhanced heating value of the wood chips. Our research explored if the organic load in PW could be utilized as a substrate by cellulolytic filamentous fungi. Hence, using the industrially relevant Ascomycete Trichoderma reesei RUT-C30 as well as several Basidiomycete wood-rotting fungi, we examined the potential of press water obtained from Douglas-fir wood chips to be used in the growth and enzyme production media.

Results: The addition of PW supernatant to liquid cultures of T. reesei RUT-C30 resulted in a significant enhancement of the endoglucanase and endoxylanase activities with a substantially shortened lag-phase. A partial replacement of Ca2+, Mg2+, K+, as well as a complete replacement of Fe2+, Mn2+, Zn2+ by supplementing PW of the liquid media was achieved without negative effects on enzyme production. Concentrations of PW above 50% showed no adverse effects regarding the achievable endoglucanase activity but affected the endoxylanase activity to some extent. Exploring the enhancing potential of several individual PW components after chemical analysis revealed that the observed lag-phase reduction of T. reesei RUT-C30 was not caused by the dissolved sugars and ions, nor the wood particles in the PW sediment, suggesting that other, so far non-identified, compounds are responsible. However, also the growth rate of several basidiomycetes was significantly enhanced by the supplementation of raw PW to the agar medium. Moreover, their cultivation in liquid cultures reduced the turbidity of the PW substantially.

Conclusions: PW was identified as a suitable media supplement for lignocellulolytic fungi, including the cellulase and xylanase producer T. reesei RUT-C30 and several wood-degrading basidiomycetes. The possibility to replace several minerals, trace elements and an equal volume of fresh water in liquid media with PW and the ability of fungal mycelia to filter out the suspended solids is a promising way to combine biological wastewater treatment with value-adding biotechnological applications.

背景:木片机械干燥是一种创新方法,可在节能的连续过程中提高锯木厂副产品的热值。然而,从木片中流出的压榨水(PW)含有各种未溶解和已溶解的有机物质。将压榨水作为废水处理会因有机物含量高而产生额外成本,抵消了因木片热值提高而带来的能源成本效益。我们的研究探讨了废水中的有机负荷能否被纤维素丝状真菌用作底物。因此,我们利用与工业相关的子囊菌Trichoderma reesei RUT-C30以及几种基生木腐真菌,研究了从花旗松木屑中获得的压榨水用于生长和酶生产培养基的潜力:结果:将压榨水上清液加入雷氏木霉 RUT-C30 的液体培养物中,可显著提高内切葡聚糖酶和内切木糖酶的活性,并大大缩短滞后期。通过补充液体培养基中的 PW 来部分替代 Ca2+、Mg2+、K+,以及完全替代 Fe2+、Mn2+、Zn2+,不会对酶的生产产生负面影响。PW浓度超过50%对可达到的内切葡聚糖酶活性没有不利影响,但在一定程度上影响了内切木聚糖酶活性。经过化学分析后,对废水中几种单独成分的增强潜力进行了探索,结果表明,观察到的 T. reesei RUT-C30 滞后期减少现象不是由溶解的糖和离子造成的,也不是由废水沉淀物中的木质颗粒造成的,而是由其他迄今尚未确定的化合物造成的。不过,在琼脂培养基中添加未加工的废水也能显著提高几种基枝菌的生长速度。此外,它们在液体培养物中的培养大大降低了废水的浑浊度:结论:研究发现,废水是木质纤维素分解真菌(包括纤维素酶和木聚糖酶生产者 T. reesei RUT-C30 和几种木材降解基枝菌)的合适培养基补充物。用 PW 替代液体培养基中的几种矿物质、微量元素和等量淡水的可能性,以及真菌菌丝体过滤悬浮固体的能力,是将生物废水处理与增值生物技术应用相结合的一种很有前景的方法。
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引用次数: 0
Recent advances in the chemo-biological characterization of decalin natural products and unraveling of the workings of Diels-Alderases. 十氢化萘天然产物的化学生物学特性和diels - alderase作用机制的最新进展
Q1 Agricultural and Biological Sciences Pub Date : 2022-04-29 DOI: 10.1186/s40694-022-00139-6
Kenji Watanabe, Michio Sato, Hiroyuki Osada

The Diels-Alder (DA) reaction refers to a [4 + 2] cycloaddition reaction that falls under the category of pericyclic reactions. It is a reaction that allows regio- and stereo-selective construction of two carbon-carbon bonds simultaneously in a concerted manner to generate a six-membered ring structure through a six-electron cyclic transition state. The DA reaction is one of the most widely applied reactions in organic synthesis, yet its role in biological systems has been debated intensely over the last four decades. A survey of secondary metabolites produced by microorganisms suggests strongly that many of the compounds possess features that are likely formed through DA reactions, and most of them are considered to be catalyzed by enzymes that are commonly referred to as Diels-Alderases (DAases). In recent years, especially over the past 10 years or so, we have seen an accumulation of a substantial body of work that substantiates the argument that DAases indeed exist and play a critical role in the biosynthesis of complex metabolites. This review will cover the DAases involved in the biosynthesis of decalin moieties, which are found in many of the medicinally important natural products, especially those produced by fungi. In particular, we will focus on a subset of secondary metabolites referred to as pyrrolidine-2-one-bearing decalin compounds and discuss the decalin ring stereochemistry and the biological activities of those compounds. We will also look into the genes and enzymes that drive the biosynthetic construction of those complex natural products, and highlight the recent progress made on the structural and mechanistic understanding of DAases, especially regarding how those enzymes exert stereochemical control over the [4 + 2] cycloaddition reactions they catalyze.

Diels-Alder(DA)反应是指一种[4 + 2]环化反应,属于过环反应的范畴。它是一种通过六电子环状过渡态,同时以协同方式构建两个碳-碳键,从而生成六元环结构的反应,具有区域和立体选择性。DA 反应是有机合成中应用最广泛的反应之一,但在过去的四十年中,它在生物系统中的作用一直备受争议。对微生物产生的次级代谢产物的调查强烈表明,许多化合物都具有可能是通过 DA 反应形成的特征,其中大多数被认为是由通常称为 Diels-Alderases (DAases)的酶催化的。近年来,特别是在过去 10 年左右的时间里,我们看到大量研究成果证实了 DAases 确实存在,并且在复杂代谢物的生物合成过程中发挥着关键作用。本综述将介绍参与蜕皮激素生物合成的 DA 酶,它们存在于许多具有重要药用价值的天然产品中,尤其是由真菌生产的产品。我们将特别关注次生代谢物的一个子集,即含有吡咯烷-2-酮的蜕皮素化合物,并讨论这些化合物的蜕皮素环立体化学和生物活性。我们还将研究驱动这些复杂天然产物生物合成构建的基因和酶,并重点介绍对萘烷酶的结构和机理认识的最新进展,特别是这些酶如何对其催化的[4 + 2]环化反应进行立体化学控制。
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引用次数: 0
Connecting materials sciences with fungal biology: a sea of possibilities. 将材料科学与真菌生物学联系起来:无限可能。
Q1 Agricultural and Biological Sciences Pub Date : 2022-03-01 DOI: 10.1186/s40694-022-00137-8
Vera Meyer

The Special Issue "Connecting materials science with fungal biology" celebrates recent breakthroughs in the fabrication of fungal-based materials, all of which have been made possible by the interdisciplinary and transdisciplinary collaboration of fungal biologists and biotechnologists with artists, designers, materials scientists, and architects. It features conceptual considerations and latest developments of these joint research efforts and the paradigm shift that is involved. The aim of this collection of twelve papers is to highlight the infinite possibilities for the development of innovative fungal-based materials which can be realized through integrating the knowledge and methods from different disciplines.

特刊 "将材料科学与真菌生物学联系起来 "庆祝了最近在制造真菌基材料方面取得的突破,所有这些都是真菌生物学家和生物技术专家与艺术家、设计师、材料科学家和建筑师的跨学科和跨领域合作的成果。这本论文集介绍了这些联合研究工作的概念性考虑和最新进展,以及其中涉及的范式转变。这本由十二篇论文组成的论文集旨在强调通过整合不同学科的知识和方法,开发基于真菌的创新材料的无限可能性。
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引用次数: 0
Establishment of the basidiomycete Fomes fomentarius for the production of composite materials. 建立了用于复合材料生产的担子菌。
Q1 Agricultural and Biological Sciences Pub Date : 2022-02-24 DOI: 10.1186/s40694-022-00133-y
Carsten Pohl, Bertram Schmidt, Tamara Nunez Guitar, Sophie Klemm, Hans-Jörg Gusovius, Stefan Platzk, Harald Kruggel-Emden, Andre Klunker, Christina Völlmecke, Claudia Fleck, Vera Meyer

Background: Filamentous fungi of the phylum Basidiomycota are considered as an attractive source for the biotechnological production of composite materials. The ability of many basidiomycetes to accept residual lignocellulosic plant biomass from agriculture and forestry such as straw, shives and sawdust as substrates and to bind and glue together these otherwise loose but reinforcing substrate particles into their mycelial network, makes them ideal candidates to produce biological composites to replace petroleum-based synthetic plastics and foams in the near future.

Results: Here, we describe for the first time the application potential of the tinder fungus Fomes fomentarius for lab-scale production of mycelium composites. We used fine, medium and coarse particle fractions of hemp shives and rapeseed straw to produce a set of diverse composite materials and show that the mechanical materials properties are dependent on the nature and particle size of the substrates. Compression tests and scanning electron microscopy were used to characterize composite material properties and to model their compression behaviour by numerical simulations. Their properties were compared amongst each other and with the benchmark expanded polystyrene (EPS), a petroleum-based foam used for thermal isolation in the construction industry. Our analyses uncovered that EPS shows an elastic modulus of 2.37 ± 0.17 MPa which is 4-times higher compared to the F. fomentarius composite materials whereas the compressive strength of 0.09 ± 0.003 MPa is in the range of the fungal composite material. However, when comparing the ability to take up compressive forces at higher strain values, the fungal composites performed better than EPS. Hemp-shive based composites were able to resist a compressive force of 0.2 MPa at 50% compression, rapeseed composites 0.3 MPa but EPS only 0.15 MPa.

Conclusion: The data obtained in this study suggest that F. fomentarius constitutes a promising cell factory for the future production of fungal composite materials with similar mechanical behaviour as synthetic foams such as EPS. Future work will focus on designing materials characteristics through optimizing substrate properties, cultivation conditions and by modulating growth and cell wall composition of F. fomentarius, i.e. factors that contribute on the meso- and microscale level to the composite behaviour.

背景:担子菌门的丝状真菌被认为是复合材料生物技术生产的一个有吸引力的来源。许多担子菌能够接受来自农业和林业的残余木质纤维素植物生物量,如秸秆、木屑和锯末作为底物,并将这些松散但增强的底物颗粒结合和粘合在一起,形成它们的菌丝网络,这使它们成为在不久的将来生产生物复合材料以取代石油基合成塑料和泡沫的理想候选者。结果:本文首次描述了火种真菌Fomes fomentarius在实验室规模生产菌丝复合材料方面的应用潜力。我们用麻屑和油菜籽秸秆的细、中、粗颗粒组分制备了一套多样化的复合材料,并表明材料的力学性能取决于基材的性质和颗粒大小。压缩试验和扫描电子显微镜用于表征复合材料的特性,并通过数值模拟模拟其压缩行为。它们的性能相互比较,并与基准膨胀聚苯乙烯(EPS)进行比较,EPS是一种用于建筑行业隔热的石油基泡沫。分析发现,EPS的弹性模量为2.37±0.17 MPa,是真菌复合材料的4倍,而抗压强度为0.09±0.003 MPa,在真菌复合材料的范围内。然而,当比较较高应变值下真菌复合材料承受压缩力的能力时,真菌复合材料的表现优于EPS。在50%压缩时,大麻基复合材料的抗压缩力为0.2 MPa,油菜籽基复合材料的抗压缩力为0.3 MPa, EPS仅为0.15 MPa。结论:本研究获得的数据表明,F. fomentarius是未来生产具有与合成泡沫(如EPS)相似力学性能的真菌复合材料的有希望的细胞工厂。未来的工作将集中在通过优化基质特性、培养条件和调节F. fomentarius的生长和细胞壁组成(即在中观和微观水平上影响复合行为的因素)来设计材料特性。
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引用次数: 11
Risk assessment of fungal materials. 真菌材料的风险评估。
Q1 Agricultural and Biological Sciences Pub Date : 2022-02-24 DOI: 10.1186/s40694-022-00134-x
Jeroen G van den Brandhof, Han A B Wösten

Sustainable fungal materials have a high potential to replace non-sustainable materials such as those used for packaging or as an alternative for leather and textile. The properties of fungal materials depend on the type of fungus and substrate, the growth conditions and post-treatment of the material. So far, fungal materials are mainly made with species from the phylum Basidiomycota, selected for the mechanical and physical properties they provide. However, for mycelium materials to be implemented in society on a large scale, selection of fungal species should also be based on a risk assessment of the potential to be pathogenic, form mycotoxins, attract insects, or become an invasive species. Moreover, production processes should be standardized to ensure reproducibility and safety of the product.

可持续真菌材料很有可能取代非可持续材料,如用于包装或作为皮革和纺织品替代品的材料。真菌材料的性质取决于真菌和基质的类型、生长条件和材料的后处理。到目前为止,真菌材料主要由担子菌门的物种制成,根据它们提供的机械和物理特性进行选择。然而,对于要在社会上大规模使用的菌丝体材料,真菌物种的选择也应基于对致病性、形成真菌毒素、吸引昆虫或成为入侵物种的潜力的风险评估。此外,生产过程应标准化,以确保产品的再现性和安全性。
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引用次数: 0
In silico analyses of maleidride biosynthetic gene clusters. 马来酰胺生物合成基因簇的硅学分析。
Q1 Agricultural and Biological Sciences Pub Date : 2022-02-17 DOI: 10.1186/s40694-022-00132-z
Katherine Williams, Kate M J de Mattos-Shipley, Christine L Willis, Andrew M Bailey

Maleidrides are a family of structurally related fungal natural products, many of which possess diverse, potent bioactivities. Previous identification of several maleidride biosynthetic gene clusters, and subsequent experimental work, has determined the 'core' set of genes required to construct the characteristic medium-sized alicyclic ring with maleic anhydride moieties. Through genome mining, this work has used these core genes to discover ten entirely novel putative maleidride biosynthetic gene clusters, amongst both publicly available genomes, and encoded within the genome of the previously un-sequenced epiheveadride producer Wicklowia aquatica CBS 125634. We have undertaken phylogenetic analyses and comparative bioinformatics on all known and putative maleidride biosynthetic gene clusters to gain further insights regarding these unique biosynthetic pathways.

顺丁烯二酸酐是一系列结构相关的真菌天然产物,其中许多具有多种强效生物活性。之前对几个马来酸酐生物合成基因簇的鉴定以及随后的实验工作确定了构建具有马来酸酐分子特征的中型脂环所需的 "核心 "基因。通过基因组挖掘,这项工作利用这些核心基因在公开的基因组中发现了十个全新的马来酸酐生物合成基因簇,并在以前未测序的表海葵生产者 Wicklowia aquatica CBS 125634 的基因组中进行了编码。我们对所有已知和推测的马来酰胺ride 生物合成基因簇进行了系统进化分析和比较生物信息学研究,以进一步了解这些独特的生物合成途径。
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引用次数: 0
The colors of life: an interdisciplinary artist-in-residence project to research fungal pigments as a gateway to empathy and understanding of microbial life. 生命的颜色:一个跨学科的艺术家驻地项目,研究真菌色素作为同情和理解微生物生命的门户。
Q1 Agricultural and Biological Sciences Pub Date : 2022-01-10 DOI: 10.1186/s40694-021-00130-7
Sunanda Sharma, Vera Meyer

Background: Biological pigmentation is one of the most intriguing traits of many fungi. It holds significance to scientists, as a sign of biochemical metabolism and organism-environment interaction, and to artists, as the source of natural colors that capture the beauty of the microbial world. Furthermore, the functional roles and aesthetic appeal of biological pigmentation may be a path to inspiring human empathy for microorganisms, which is key to understanding and preserving microbial biodiversity. A project focused on cross-species empathy was initiated and conducted as part of an artist-in-residence program in 2021. The aim of this residency is to bridge the current divide between science and art through interdisciplinary practice focused on fungi.

Results: The residency resulted in multiple products that are designed for artistic and scientific audiences with the central theme of biological pigmentation in fungi and other microorganisms. The first product is a video artwork that focuses on Aspergillus niger as a model organism that produces melanin pigment in a biosynthetic process similar to that of humans. The growth and morphology of this commonplace organism are displayed through video, photo, animation, and time-lapse footage, inviting the viewer to examine the likenesses and overlaps between humans and fungi. The second product is The Living Color Database, an online compendium of biological colors for scientists, artists, and designers. It links organisms across the tree of life, focusing on fungi, bacteria, and archaea, and the colors they express through biological pigmentation. Each pigment is represented in terms of its chemistry, its related biosynthesis, and its color expressions according to different indices: HEX, RGB, and Pantone. It is available at color.bio.

Conclusions: As fungal biotechnology continues to mature into new application areas, it is as important as ever that there is human empathy for these organisms to promote the preservation and appreciation of fungal biodiversity. The products presented here provide paths for artists, scientists, and designers to understand microorganisms through the lens of color, promoting interspecies empathy through research, teaching, and practice.

背景:生物色素沉着是许多真菌最有趣的特征之一。对科学家来说,它是生化代谢和生物与环境相互作用的标志,对艺术家来说,它是捕捉微生物世界之美的自然色彩的来源。此外,生物色素的功能作用和美学吸引力可能是激发人类对微生物的同理心的途径,这是理解和保护微生物多样性的关键。2021年,作为驻场艺术家项目的一部分,一个专注于跨物种同理心的项目启动并实施。本次驻留的目的是通过专注于真菌的跨学科实践来弥合目前科学与艺术之间的鸿沟。结果:驻留产生了多种产品,为艺术和科学观众设计,中心主题是真菌和其他微生物的生物色素沉着。第一个产品是一个视频艺术作品,重点介绍黑曲霉作为一种模式生物,在类似于人类的生物合成过程中产生黑色素。通过视频、照片、动画和延时镜头展示了这种常见生物的生长和形态,邀请观众检查人类和真菌之间的相似性和重叠。第二个产品是The Living Color Database,这是一个面向科学家、艺术家和设计师的生物颜色在线纲要。它将生命之树上的生物联系起来,重点关注真菌、细菌和古细菌,以及它们通过生物色素沉着表达的颜色。每一种色素都是根据其化学性质、相关的生物合成以及不同的指数(HEX、RGB和Pantone)来表示颜色的。结论:随着真菌生物技术在新的应用领域的不断成熟,人类对这些生物的同情对于促进真菌生物多样性的保护和欣赏同样重要。这里展示的产品为艺术家、科学家和设计师提供了通过颜色来理解微生物的途径,通过研究、教学和实践促进物种间的同理心。
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引用次数: 5
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Fungal Biology and Biotechnology
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