Soft Rot Fungi Research Articles

Modelling the Material Resistance of Wood—Part 1: Utilizing Durability Test Data Based on Different Reference Wood Species

To evaluate the performance of new wood-based products, reference wood species with known performances are included in laboratory and field trials. However, different wood species vary in their durability performance, and there will also be a within-species variation. The primary aim of this paper was to compare the material resistance against decay fungi and moisture performance of three European reference wood species, i.e., Scots pine sapwood (Pinus sylvestris), Norway spruce (Picea abies), and European beech (Fagus sylvatica). Wood material was collected from 43 locations all over Europe and exposed to brown rot (Rhodonia placenta), white rot (Trametes versicolor) or soft rot fungi. In addition, five different moisture performance characteristics were analyzed. The main results were the two factors accounting for the wetting ability (kwa) and the inherent protective properties of wood (kinh), factors for conversion between Norway spruce vs. Scots pine sapwood or European beech for the three decay types and four moisture tests, and material resistance dose (DRd) per wood species. The data illustrate that the differences between the three European reference wood species were minor, both with regard to decay and moisture performance. The results also highlight the importance of defined boundaries for density and annual ring width when comparing materials within and between experiments. It was concluded that with the factors obtained, existing, and future test data, where only one or two of the mentioned reference species were used, can be transferred to models and prediction tools that use another of the reference species.

Growth behavior of wood-destroying fungi in chemically modified wood: wood degradation and translocation of nitrogen compounds

Abstract Chemical wood modification has been used to modify wood and improve its decay resistance. However, the mode of protective action is still not fully understood. Occasionally, outdoor products made from chemically modified timber (CMT) show internal decay while their outer shell remains intact. Hence, it was hypothesized that wood decay fungi may grow through CMT without losing their capability to degrade non-modified wood. This study aimed at developing a laboratory test set-up to investigate (1) whether decay fungi grow through CMT and (2) retain their ability to degrade non-modified wood. Acetylated and 1,3-dimethylol-4,5-dihydroxyethyleneurea (DMDHEU) treated wood were used in decay tests with modified ‘mantle specimens’ and untreated ‘core dowels’. It became evident that white rot (Trametes versicolor), brown rot (Coniophora puteana) and soft rot fungi can grow through CMT without losing their ability to degrade untreated wood. Consequently, full volume impregnation of wood with the modifying agent is required to achieve complete protection of wooden products. In decay tests with DMDHEU treated specimens, significant amounts of apparently non-fixated DMDHEU were translocated from modified mantle specimens to untreated wood cores. A diffusion-driven transport of nitrogen and DMDHEU seemed to be responsible for mass translocation during decay testing.

Assessment of Wooden Foundation Piles after 125 Years of Service

Buildings on piles have been constructed in Ljubljana since the Bronze Age. The piles were made of different types of wood. In the present study, piles that were erected about 125 years ago were investigated. Investors tend to renovate a building; therefore, the piles were analysed to assess the structural condition of the building. The building showed no signs of damage. To gain access to the piles, a 2 m thick layer of soil was removed. On-site, the following analyses were carried out: drilling resistance with a resistograph and a screw withdrawal test. Part of the piles was isolated and light microscopy, scanning electron microscopy, infrared spectroscopy, dynamic vapour sorption, density analysis, and chemical analysis were performed. Microscopic analysis revealed that the piles were made from the wood of Scots pine (Pinus sylvestris). The results indicate that the wood was severely degraded, mainly by soft-rot fungi and bacteria, resulting in a significant deterioration of its mechanical properties.

Fungal succession in decomposing woody debris across a tropical forest disturbance gradient

Fungi decompose woody debris, an important carbon pool in forests. Fungal community structure is expected to vary according to the wood species, habitats and extent of abiotic disturbance, which have consequences for carbon cycling in tropical forests. Here we examined the effects of fungal diversity and composition on woody debris decomposition rates and sought potential mechanisms to explain an observed lack of difference in decomposition rates across a disturbance gradient in a tropical montane rainforest in Xishuangbanna, SW China. We measured wood specific gravity (WSG) loss from 280 logs of Litsea cubeba and Castanopsis mekongensis over 3 years and monitored fungal communities from 418 samples using next-generation sequencing after 0, 18 and 36 months field exposure. Wood species and termite presence determined changes in fungal diversity through time. Overall there was a peak in fungal diversity at 18 mo, suggesting an initial period of colonization followed by a period of increasingly competitive interactions leading to decreased diversity. Litsea logs, which had relatively low initial WSG and thinner bark, harbored higher fungal diversity. Shared fungal OTUs between wood species peaked at 18 mo (~50%). However, fungal diversity was not a significant predictor of WSG loss. An effect of habitat on fungal community composition suggests that functional replacement explains the similar decay rates across the disturbance gradient. In addition, the proportions of saprotroph and white-rot fungi increased through time regardless of wood species. Termite presence reduced WSG loss, but the effect was mediated via the abundance of soft rot fungi. Our results suggest that changes in functional traits, rather than fungal species diversity, may better explain variation in WSG loss. Future studies should investigate roles of fungal functional traits and rot types, particularly those of Ascomycete fungi, whose roles in wood decay are still poorly characterized.

Hallmarks of Basidiomycete Soft- and White-Rot in Wood-Decay -Omics Data of Two Armillaria Species.

Wood-decaying Basidiomycetes are among the most efficient degraders of plant cell walls, making them key players in forest ecosystems, global carbon cycle, and in bio-based industries. Recent insights from -omics data revealed a high functional diversity of wood-decay strategies, especially among the traditional white-rot and brown-rot dichotomy. We examined the mechanistic bases of wood-decay in the conifer-specialists Armillaria ostoyae and Armillaria cepistipes using transcriptomic and proteomic approaches. Armillaria spp. (Fungi, Basidiomycota) include devastating pathogens of temperate forests and saprotrophs that decay wood. They have been discussed as white-rot species, though their response to wood deviates from typical white-rotters. While we observed an upregulation of a diverse suite of plant cell wall degrading enzymes, unlike white-rotters, they possess and express an atypical wood-decay repertoire in which pectinases and expansins are enriched, whereas lignin-decaying enzymes (LDEs) are generally downregulated. This combination of wood decay genes resembles the soft-rot of Ascomycota and appears widespread among Basidiomycota that produce a superficial white rot-like decay. These observations are consistent with ancestral soft-rot decay machinery conserved across asco- and Basidiomycota, a gain of efficient lignin-degrading ability in white-rot fungi and repeated, complete, or partial losses of LDE encoding gene repertoires in brown- and secondarily soft-rot fungi.

Natural durability of the Iranian domestic bamboo (Phyllostachys vivax) against fungal decay and its chemical protection with propiconazole

Bamboo culms are unique building materials for various kinds of structures. A wider acceptance of bamboo for structural uses, however, is often hindered by its propensity to biological degradation. The preservation of bamboo structures against biological hazards is an important requirement for utilizing this valuable lignocellulose resource. In this research, first, the chemical composition of bamboo tissue and its extractives, natural durability and the process of bamboo decay were investigated using two species of white rot fungi, i.e. Trametes versicolor and Xylaria polymorpha, two brown rot fungi, i.e. Coniophora puteana and Oligoporus placenta, and the soft rot fungus, Xylaria longipes. The samples were subjected to 4, 8, 12, and 16 weeks of exposure to fungi according to EN 113, and their weight loss (WL) and moisture content (MC) were studied. Secondly, aqueous suspension of 1% propiconazole was used as a fungicide to protect bamboo against different rotting fungi. The bamboo species Phyllostachys vivax was highly vulnerable to soft and white rots but showed a relatively higher durability against brown-rot fungi. However, it was not durable enough to be used without preservation and its biological resistance improved after treatment. Surprisingly, WL of bamboos decreased after leaching procedure, which could be related to the extraction of non-structural carbohydrates during leaching with water. A light microscopic study showed that different fungi preferably degrade different cells; white and soft rots mostly invaded ground parenchyma, while in brown rots, deterioration of phloem cells was more severe. In brief, bamboo needs to be treated before indoor and outdoor applications, and propiconazole as a cheap and environmentally friendly preservative can safely protect it against different fungal decay.

Using Wood Rot Phenotypes to Illuminate the "Gray" Among Decomposer Fungi.

Wood-decomposing fungi use distinct strategies to deconstruct wood that can significantly vary carbon release rates and fates. White and brown rot-type fungi attack lignin as a prerequisite to access carbohydrates (white rot) or selectively remove carbohydrates (brown rot). Soft rot fungi use less well-studied mechanisms to deconstruct wood (e.g., cavitation and erosion). These fungi often co-exist in nature, creating a balance in carbon turnover that could presumably “tip” in a changing climate. There is no simple genetic marker, however, to distinguish fungi by rot types, and traditional black and white distinctions (brown and white, in this case) cannot explain a spectrum of “gray” carbon loss possibilities. In this study, we tested 39 wood-degrading fungal strains along this spectrum of rot types. We tracked wood mass loss and chemical changes in aspen blocks in early- to mid-decay stages, including three signatures of fungal nutritional mode measured from wood rather than from fungus: dilute alkali solubility, water-soluble monosaccharides, and lignin loss (%) relative to density loss (%) (L/D). Results were then plotted relative to rot types and correlated with gene counts, combining new data with past results in some cases. Results yielded a novel distinction in soluble monosaccharide patterns for brown rot fungi, and reliable distinctions between white and brown rot fungi, although soft rot fungi were not as clearly distinguished as suggested in past studies. Gene contents (carbohydrate-active enzymes and peroxidases) also clearly distinguished brown and white rot fungi, but did not offer reliable correlation with lignin vs. carbohydrate selectivity. These results support the use of wood residue chemistry to link fungal genes (with known or unknown function) with emergent patterns of decomposition. Wood signatures, particularly L/D, not only confirm the rot type of dominant fungi, but they offer a more nuanced, continuous variable to which we can correlate genomic, transcriptomic, and secretomic evidence rather than limit it to functional categories as distinct “bins.”

Three-Dimensional Exploration of Soft-Rot Decayed Conifer and Angiosperm Wood by X-Ray Micro-Computed Tomography

X-ray micro-computed tomography (XμCT) was used to explore the decomposed structure of conifer and angiosperm wood after colonization by soft-rot fungi. The visualization of degradation features of soft-rot decay was challenging to achieve through XμCT. Difficulties in visualization emerged due to a decreased grayscale contrast (i.e. X-ray density) of the degraded wood. Nevertheless, we were able to image fungal-induced cell deformations in earlywood and cavities in the thick wall of latewood cells in three-dimensions (3D). Unlike the organic wood material, the higher X-ray density of inorganic deposits, identified as mainly calcium-based particles by energy-dispersive spectroscopy, allowed a facilitated 3D survey. The visualization of inorganic particles in 3D revealed a localized distribution in certain cells in conifer and angiosperm found mostly in earlywood.

Perlakuan Biologis Dengan Memanfaatkan Fungi Untuk Meningkatkan Kualitas Pakan Ternak Asal Limbah Pertanian.

ABSTRACTAn improvement in animal feeding is one of the important and basic conditions for the better management of farming of animals. It was recognized that poor quality of the feed is mainly responsible for the poor animal performance. For most farming practices, feed is an expensive component in livestock farming. Alternative feed can be obtained from agricultural by-products with huge amount around the world. The main factors limiting the utilization of agricultural by-products like paddy straw, wheat straw and corn stover are their low digestibility, low protein content and some time low palatability. However, the nutritive value of the agricultural by-products can be enhanced through their biological treatment and hence play an important role to meet nutrient requirements of the animals. Thus, an alternative approach is biological treatment especially fungi to increase digestibility of agricultural by-products. The use of white rot fungi, brown rot fungi and soft rot fungi that metabolize lignocelluloses is a potential biological treatment to improve the nutritional value of agricultural by-products. This paper aims to discuss the role of fungi in increasing the nutritional value of agricultural by-products like paddy straw, wheat straw and corn stover.Keywords: Agricultural by-products, Biological treatment, fungi, Lignocelluloses

Functional analysis of chimeric TrCel6A enzymes with different carbohydrate binding modules.

The glycoside hydrolase (GH) family 6 is an important group of enzymes that constitute an essential part of industrial enzyme cocktails used to convert lignocellulose into fermentable sugars. In nature, enzymes from this family often have a carbohydrate binding module (CBM) from the CBM family 1. These modules are known to promote adsorption to the cellulose surface and influence enzymatic activity. Here, we have investigated the functional diversity of CBMs found within the GH6 family. This was done by constructing five chimeric enzymes based on the model enzyme, TrCel6A, from the soft-rot fungus Trichoderma reesei. The natural CBM of this enzyme was exchanged with CBMs from other GH6 enzymes originating from different cellulose degrading fungi. The chimeric enzymes were expressed in the same host and investigated in adsorption and quasi-steady-state kinetic experiments. Our results quantified functional differences of these phylogenetically distant binding modules. Thus, the partitioning coefficient for substrate binding varied 4-fold, while the maximal turnover (kcat) showed a 2-fold difference. The wild-type enzyme showed the highest cellulose affinity on all tested substrates and the highest catalytic turnover. The CBM from Serendipita indica strongly promoted the enzyme's ability to form productive complexes with sites on the substrate surface but showed lower turnover of the complex. We conclude that the CBM plays an important role for the functional differences between GH6 wild-type enzymes.

Susceptibility of Populus x euramericana ‘I-214’ of Spanish origin to xylophagous attacks: durability tests for its possible inclusion in European standard

Aim of study: to assess the natural durability of Populus x euramericana ‘I-214’ against xylophagous fungi and termites, and to carry out a macro-microscopic analysis of the alterations caused by each xylophagous agent in order to get the necessary information for its possible inclusion in existing European standards.Area of study: A 20-years-old commercial plantation Populus x euramericana‘I-214’ located in Quintanilla de Sollamas (42° 36′ 00″N - 05° 49′ 00″ W), Spanish community of Castile-LeonMaterial and methods: material sampling and selection was carried out following EN 350:2017 for commercial sawn timber. Poplar resistance to xylophagous basidiomycete, soft rot fungi and subterranean termites was determined according to CEN/TS 15083-1:2005, CEN/TS 15083-2:2005 and EN 117:2012, respectively. The durability and use classes were estimated according to EN 350:2016 and EN 335:2013, respectively. The anatomical studies were carried out with Optical and Scanning Electron Microscope. Material characterization was carried out by reference to Anagnost (1998) and Schwarze (2007).Main results: ‘I-214’ poplar wood proved to be “Not-durable” to the action of basidiomycetes, soft rot fungi and termites, use classes 1-2, and showed macro-microscopic evidence of these types of decay.Research highlights: the information obtained in this study would allow the inclusion of clone I-214 in the standard EN 350 and its explicit classification within it.Keywords: wood-decay fungi; termites; EN 350.Abbreviations used: TM: test material; RM: reference material; RH: relative humidity; ML: mass loss; mi: initial dry mass; mf: final dry mass; DC: durability class; OM: Optical Microscope; SEM: Scanning Electron Microscope; TS: transverse section samples; LS: longitudinal section samples; CI: robust confidence intervals; F: fibre; V: vessel; h: hole; t: erosion trough; R: radial parenchyma cell; ep: erosion pitting; Fc: fungal colonization; fr: fracture; c: cavity; b: bore hole; m: mycelium.

Unveiling of Concealed Processes for the Degradation of Pharmaceutical Compounds by Neopestalotiopsis sp.

The presence of pharmaceutical products has raised emerging biorisks in aquatic environments. Fungi have been considered in sustainable approaches for the degradation of pharmaceutical compounds from aquatic environments. Soft rot fungi of the Ascomycota phylum are the most widely distributed among fungi, but their ability to biodegrade pharmaceuticals has not been studied as much as that of white rot fungi of the Basidiomycota phylum. Herein, we evaluated the capacity of the soft rot fungus Neopestalotiopsis sp. B2B to degrade pharmaceuticals under treatment of woody and nonwoody lignocellulosic biomasses. Nonwoody rice straw induced laccase activity fivefold compared with that in YSM medium containing polysaccharide. But B2B preferentially degraded polysaccharide over lignin regions in woody sources, leading to high concentrations of sugar. Hence, intermediate products from saccharification may inhibit laccase activity and thereby halt the biodegradation of pharmaceutical compounds. These results provide fundamental insights into the unique characteristics of pharmaceutical degradation by soft rot fungus Neopestalotiopsis sp. in the presence of preferred substrates during delignification.

Effect of different organic waste on cellulose-degrading enzymes secreted by Petriella setifera in the presence of cellobiose and glucose

Cellulose degradation is less known in the Ascomycota phylum, but it is important to recognize it because this process influences the most important biochemical cycle: the carbon cycle. Cellulose degradation is carried out by a complex enzyme: cellulase. Petriella setifera has recently been recognized as a producer of cellulolytic enzymes. In this work, it was shown, that the activity of cellulose-degrading enzymes, carbon source utilization and the gene expression of P. setifera were not determined by pre-culturing in different lignocellulosic wastes. Moreover, it was found that the presence of glucose and cellobiose could inhibit the activity and the expression of the cellobiohydrolase enzyme. β-glucosidase exhibits a higher activity in all of the analysed wastes and this behaviour can be explained as a mechanism for P. setifera to overcome cellobiose-glucose inhibition through the transglycosylation reaction. The significance of our research is to enable researchers to understand more thoroughly the cellulose degradation caused by soft rot fungus which belongs to the Ascomycota phylum. Our research is contributing to the understanding of cellulase activity and gene expression inhibition through the availability of a carbon source for P. setifera. Furthermore, it facilitates the acquisition of more information concerning the fungus P. setifera.Graphic abstract

Influence of Environmental Growth Factors on the Biomass and Pigment Production of Chlorociboria aeruginascens.

The soft rot fungus Chlorociboria aeruginascens produces a blue–green pigment xylindein, which is of considerable interest for various applications such as in the veneer industry or in organic semiconductors. To understand the fungal growth as well as pigment production of C. aeruginascens, several studies were performed, the results of which are presented here. These studies investigated various growth conditions such as temperature, pH value, oxygen level and light intensity. It was observed that the formation of xylindein by C. aeruginascens decoupled from growth. In the primary metabolismus, the uncolored biomass is formed. Pigment production took place within the secondary metabolism, while biomass growth as well as pigment production depended on various growth conditions. It was also found that certain conditions encourage the switch in metabolism, leading to pigment production.

The effect of various substrate on production of cellobiose dehydrogenase enzyme by Trametes versicolor

Cellobiose dehydrogenase is an extracellular flavocytochrome which uses various oligosaccharide substrates as electron donors to reduce phenoxy radicals, radical or quinone compound. The flexible electrons transfer properties from CDH are currently exploited for many biomedical applications including wound dressing hydrogel. CDH could be isolated and characterized from variety of white rot fungi, soft rot fungi, and brown rot fungi. Some studies of CDH production carried out by Trametes versicolor white rot fungi. In order to support the research about wound dressing hydrogel, the optimization of CDH production could be performed. Several substrates have been used in production culture of CDH from T. versicolor including cellulose. Optimization of CDH enzyme production using several substrates shows that the use of toilet paper substrate is the best substrate in the production culture of cellobiose dehydrogenase (CDH) enzyme by Trametes versicolor.

Influence of the Nutrients on the Biomass and Pigment Production of Chlorociboria aeruginascens.

The blue-green pigment xylindein, produced by the soft rot fungus Chlorociboria aeruginascens, is of considerable interest for various applications such as the veneer industry or organic semiconductors. The studies presented were performed in order to understand the fungal growth as well as the pigment production of C. aeruginascens. Therefore, various nutrient compositions were investigated. As a result, observations of the formation of xylindein through C. aeruginascens decoupling from growth were made. In the primary metabolism the uncolored biomass is formed. Various carbohydrates were determined as nutrients for the fungus and as a nitrogen source it was observed that the fungus prefers the complex organic nitrogen source, that being yeast extract. Furthermore, it was discovered that the ratio between carbohydrate and nitrogen sources encourages the switch of the metabolism and therewith the production of the blue-green pigment xylindein.

Properties and fungal biodegradation of the different cellulose derivatives structure included into castor oil-based polyurethane composites

The requirement to protect the environment involves the synthesis of new polymers, blends, and composites with a high content of biodegradable components. This work studies the synthesis and biodegradation of castor oil-based polyurethanes filled with different cellulose derivatives (hydroxyethyl cellulose and hydroxypropyl cellulose). The polyurethane composites present a slight decrease in tensile strength and thermal stability with the increase in cellulose derivatives content. Scanning electron microscopy results showed a good dispersion of the cellulose derivatives within the polyurethane matrix. The degradation of polyurethane–cellulose derivatives by the soft rot fungus Chaetomium globosum was investigated by scanning electron microscopy, Fourier transform infrared spectroscopy, and behavior of mechanical properties. The results showed that the inclusion of cellulose derivatives results in an increase in the rate of degradation. The obtained polyurethane–cellulose derivative composites have preserved their processability and mechanical resistance and exhibited enhanced biodegradability becoming useful eco-friendly polymeric materials.

Correlation between sulfur accumulation and microbial wood degradation on shipwreck timbers

Archaeological shipwreck timber often contains elevated amounts of sulfur and iron rich compounds, accumulated during the long-term exposure in marine environments. This paper investigates if the accumulation of iron and sulfur is correlated and restricted to areas where microbial wood degradation takes place. Examination of microbial degradation in two pine and four oak samples from three historical shipwrecks situated in the Baltic Sea are carried out by light microscopy. Type, degree and amount of wood degradation by fungal and bacterial processes is compared to results on sulfur and iron accumulation studied by X-Ray Fluorescence (XRF) scanning. The highest accumulation of iron and sulfur is found in the surface layers (0–2 cm), where microbial degradation is also most intense. A novel finding is that both decay by erosion bacteria- and soft rot fungi promotes accumulation. Our results also imply that accumulation of inorganic sulfur and iron in archaeological wood involves several different processes which might include solely chemical as well as biogeochemical processes. The processes are different in pine compared to oak and the wood species of the shipwreck timber might therefore have a more important role than previously assumed.

Draft Genome Sequence of Xylaria longipes DSM 107183, a Saprotrophic Ascomycete Colonizing Hardwood.

The saprotrophic soft-rot fungus Xylaria longipes was isolated from deadwood of Acer pseudoplatanus collected in the Bavarian Forest, Germany. The whole genome of this strain (DSM 107183) was sequenced with a total size of 43.2 Mb and a G+C content of 48.5%. The genome comprises 12,638 predicted coding sequences.

Biological resistance of nanoclay-treated plastic composites with different bamboo contents to three types of fungi

The present study investigated the effects of exposure of bamboo–plastic composites to three aggressive fungi species on mass loss values. Polyvinyl chloride was used as the synthetic matrix of the composite. Three mixing combinations were used for bamboo–polymer composites, namely 40/60, 50/50, and 60/40. The injection-molded process was employed to produce the composites. Specimens were prepared according to modified European standard specifications (EN-113) to be exposed to white-, brown-, and soft-rot fungi each month for 4 months. The results indicated that the soft-rot fungus ( Chaetomium globosum) generally caused higher mass losses in all bamboo/plastic combination ratios. Brown- and soft-rot fungi demonstrated different mass losses on different combination ratios. However, the white-rot fungus ( Trametes versicolor) caused nearly the same mass losses on all three combination ratios. Moreover, T. versicolor was highly significant with respect to mass loss and moisture content. It can therefore be concluded that the T. versicolor has a different decay metabolism when compared to the brown- and soft-rot fungus used in this study.