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Two yeast strains were isolated from rotting wood samples collected on Qingyuan Mountain, Fujian Province, PR China. Phylogenetic analysis, based on the concatenated sequences of the internal transcribed spacer (ITS) region and the D1/D2 domain of the large subunit rRNA gene, revealed that these two strains represent a novel species of the genus Cyberlindnera . The proposed name for this new species is Cyberlindnera qingyuanensis f.a., sp. nov. (holotype: GDMCC 2.300; ex-type: PYCC 9925) although the formation of ascospores was not observed. The novel species differs from its close relative Cyberlindnera galapagoensis by 7.7% sequence divergence (37 substitutions and seven indels) in the D1/D2 domain and 9.7% sequence divergence (42 substitutions and 34 indels) in the ITS region, respectively. Additionally, Cyb. qingyuanensis differs from its close relative Cyb. galapagoensis by its ability to grow in cellobiose, l-rhamnose, ribitol, galactitol, and dl-lactate, its growth at 37 °C, and its inability to ferment raffinose. The Mycobank number is MB 854693.

A Gram-positive, aerobic, rod-shaped mesophilic bacterium was isolated from birch wood, referred to as the AB strain. Allergological tests suggest that this strain may cause allergic alveolitis in sawmill workers. Employing a polyphasic taxonomic approach, the AB strain's 16S rRNA gene sequence showed high similarity to Microbacterium barkeri and M. oryzae, with 97.25% and 96.91%, respectively, a finding supported by rpoB and gyrB sequence analysis. Further genome sequence comparison with the closely related M. barkeri type strain indicated a digital DNA-DNA hybridization value of 25.5% and an average nucleotide identity of 82.52%. The AB strain's cell wall peptidoglycan contains ornithine, and its polar lipids comprise diphosphatidylglycerol, phosphatidylglycerol, and unidentified glycolipids. Its major fatty acids include anteiso C15:0, anteiso C17:0, and iso C16:0, while MK-10 is its predominant respiratory quinone. Comprehensive analysis through 16S rRNA, whole-genome sequencing, phenotyping, chemotaxonomy, and MALDI-TOF MS profiling indicates that the AB strain represents a new species within the Microbacterium genus. It has been proposed to name this species Microbacterium betulae sp. nov., with AB T (PCM 3040 T  = CEST 30706 T ) designated as the type strain., (© 2024 The Author(s). Environmental Microbiology Reports published by John Wiley & Sons Ltd.)

Fungi are key decomposers of deadwood, but the impact of anthropogenic changes in nutrients and temperature on fungal community and its consequences for wood microbial respiration are not well understood. Here, we examined how nitrogen and phosphorus additions (field experiment) and warming (laboratory experiment) together influence fungal composition and microbial respiration from decomposing wood of angiosperms and gymnosperms in a subtropical forest. Nutrient additions significantly increased wood microbial respiration via fungal composition, but effects varied with nutrient types and taxonomic groups. Specifically, phosphorus addition significantly increased wood microbial respiration (65%) through decreased acid phosphatase activity and increased abundance of fast-decaying fungi (e.g., white rot), while nitrogen addition marginally increased it (30%). Phosphorus addition caused a greater increase in microbial respiration in gymnosperms than in angiosperms (83.3% vs. 46.9%), which was associated with an increase in Basidiomycota:Ascomycota operational taxonomic unit abundance in gymnosperms but a decrease in angiosperms. The temperature dependencies of microbial respiration were remarkably constant across nutrient levels, consistent with metabolic scaling theory hypotheses. This is because there was no significant interaction between temperature and wood phosphorus availability or fungal composition, or the interaction among the three factors. Our results highlight the key role of tree identity in regulating nutrient response of wood microbial respiration through controlling fungal composition. Given that the range of angiosperm species may expand under climate warming and forest management, our data suggest that expansion will decrease nutrient effects on forest carbon cycling in forests previously dominated by gymnosperm species., (© 2024 The Ecological Society of America.)

Background: Gut microbiota have several advantages in influencing the host nutrition, metabolism, immunity and growth. However, the understanding of the gut microbiota in key edible wood-boring beetle larvae remain largely undefined. In the present study, the characteristics of the gut microbiota of two edible wood-boring species (Titocerus jaspideus and Passalus punctiger) from two indigenous forested areas were investigated., Results: Over 50% of Amplicon Sequence Variants (ASVs) constituted of Firmicutes in T. jaspideus. The dominant phyla in both beetle species were Bacteroidota (4.20-19.79%) and Proteobacteria (15.10-23.90%). Lactococcus lactis was the most abundant and core prokaryote in the guts of T. jaspideus. The fungi identified in the gut of both insects belong to the phylum Obazoa (66%) and Ascomycota (> 15%). Scheffersomyeces sp. was the core eukaryote recorded. The diversity of gut microbiota in both insect species did not vary significantly. Most of the prokaryotic genes expressed were predominantly associated with biosynthesis and metabolism., Conclusion: Our findings demonstrated that Lactococcus lactis and Scheffersomyeces are core gut microbes of wood boring beetle larvae with desirable probiotic properties and promising use in food product fermentation for improved growth performance, gut barrier health, intestinal flora balance and immune protection for human and animals. Further studies to highlight the latest medical-based applications of L. lactis as live-delivery vector for the administration of therapeutics against both communicable and non-communicable diseases are warranted., (© 2024. The Author(s).)

Wetwood of living trees is a habitat of methanogenic archaea, but the ubiquity of methanogenic archaea in the trunk of various trees has not been revealed. The present study analysed methanogenic archaeal communities inside coniferous and broadleaved trees in a cold temperate mountain forest by culture-dependent or independent techniques. Heartwood and sapwood segments were obtained from the trunk of seven tree species, Cryptomeria japonica, Quercus crispula, Fraxinus mandshurica, Acer pictum, Aesculus turbinata, Magnolia obovata, and Populus tremula. Amplicon sequencing analysis of 16S rRNA genes showed that Methanobacteriaceae predominated the archaeal communities and Methanomassiliicoccaceae also inhabited some trees. Real-time PCR analysis detected methanogenic archaeal mcrA genes from all the tree species, with a maximum of 10 7  copies g -1 dry wood. Digital PCR analysis also detected mcrA genes derived from Methanobacterium spp. and Methanobrevibacter spp. from several samples, with a maximum of 10 5 and 10 4  copies g -1 dry wood. The enumeration by the most probable number method demonstrated the inhabitation of viable methanogenic archaea inside the trees; 10 6  cells g -1 dry wood was enumerated from a heartwood sample of C. japonica. Methanogenic archaea related to Methanobacterium beijingense were cultivated from a heartwood sample of Q. crispula and F. mandshurica. The present study demonstrated that the inside of various trees is a common habitat for methanogenic archaeal communities and a potential source of methane in forest ecosystems., (© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Wood-rotting fungi play an important role in the global carbon cycle because they are the only known organisms that digest wood, the largest carbon stock in nature. In the present study, we used linear discriminant analysis and random forest (RF) machine learning algorithms to predict white- or brown-rot decay modes from the numbers of genes encoding Carbohydrate-Active enZymes with over 98% accuracy. Unlike other algorithms, RF identified specific genes involved in cellulose and lignin degradation, including auxiliary activities (AAs) family 9 lytic polysaccharide monooxygenases, glycoside hydrolase family 7 cellobiohydrolases, and AA family 2 peroxidases, as critical factors. This study sheds light on the complex interplay between genetic information and decay modes and underscores the potential of RF for comparative genomics studies of wood-rotting fungi., Importance: Wood-rotting fungi are categorized as either white- or brown-rot modes based on the coloration of decomposed wood. The process of classification can be influenced by human biases. The random forest machine learning algorithm effectively distinguishes between white- and brown-rot fungi based on the presence of Carbohydrate-Active enZyme genes. These findings not only aid in the classification of wood-rotting fungi but also facilitate the identification of the enzymes responsible for degrading woody biomass., Competing Interests: The authors declare no conflict of interest.

In this study, 327 presumptive lactic acid bacteria (LAB) were isolated from goats' milk acid curds produced at a Sicilian dairy farm with the aim to identify potential starter cultures for traditional cheeses. All isolates were first processed by randomly amplified polymorphic DNA (RAPD)-PCR analysis. This approach identified 63 distinct strains which were evaluated for their acidifying capacity. Only 15 strains specifically stood out for their acidification capacity and were identified through 16S rRNA gene sequencing as Lactococcus lactis (11 strains) Enterococcus faecalis (three strains), and Ligilactobacillus animalis (one strain). Notably, all 15 LAB isolates produced bacteriocin-like inhibitory substances and anti-biofilm compounds, against both planktonic and biofilm forms of Listeria monocytogenes, Salmonella Enteritidis, Escherichia coli, and Staphylococcus aureus, albeit at varying levels. Among these 15 LAB, En. faecalis RGM25 and Lc. lactis RGM55, susceptible to five antibiotics tested, were put in contact with wooden vat prototypes, because all equipment used in traditional cheese production in Sicily are made of wood. Scanning electron microscopy and bacterial plate counts of the wooden vat prototypes showed the development of biofilms at levels of approximately 6.0 log CFU/cm 2 . Overall, this study contributes to establishing a custom-made LAB starter cultures with bio-preservatives properties for Sicilian cheese productions., Competing Interests: Declaration of competing interest The authors declare that there is no conflict of interest for this research., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

While the succession of terrestrial plant communities is well studied, less is known about succession on dead wood, especially how it is affected by environmental factors. While temperate forests face increasing canopy mortality, which causes considerable changes in microclimates, it remains unclear how canopy openness affects fungal succession. Here, we used a large real-world experiment to study the effect of closed and opened canopy on treatment-based alpha and beta fungal fruiting diversity. We found increasing diversity in early and decreasing diversity at later stages of succession under both canopies, with a stronger decrease under open canopies. However, the slopes of the diversity versus time relationships did not differ significantly between canopy treatments. The community dissimilarity remained mainly stable between canopies at ca. 25% of species exclusively associated with either canopy treatment. Species exclusive in either canopy treatment showed very low number of occupied objects compared to species occurring in both treatments. Our study showed that canopy loss subtly affected fungal fruiting succession on dead wood, suggesting that most species in the local species pool are specialized or can tolerate variable conditions. Our study indicates that the fruiting of the fungal community on dead wood is resilient against the predicted increase in canopy loss in temperate forests., (© 2024. The Author(s).)

Ascomycetes, basidiomycetes and deuteromycetes can degrade wood, but less attention has been paid to basidiomycetes involved in Esca, a major Grapevine Trunk Disease. Using a wood sawdust microcosm system, we compared the wood degradation of three grapevine cultivars inoculated with Fomitiporia mediterranea M. Fisch, a basidiomycete responsible for white-rot development and involved in Esca disease. The grapevine cultivar Ugni blanc was more susceptible to wood degradation caused by F. mediterranea than the cultivars Cabernet Sauvignon and Merlot. Solid-state Nuclear Magnetic Resonance (NMR) spectroscopy showed that F. mediterranea preferentially degrades lignin and hemicellulose over cellulose (preferential, successive or sequential white-rot). In addition, co-inoculation of sawdust with two cellulolytic and xylanolytic bacterial strains of Paenibacillus (Nakamura) Ash (Paenibacillus sp. (S231-2) and P. amylolyticus (S293)), enhanced F. mediterranea ability to degrade Ugni blanc. The NMR data further showed that the increase in Ugni blanc sawdust degradation products was greater when bacteria and fungi were inoculated together. We also demonstrated that these two bacterial strains could degrade the wood components of Ugni blanc sawdust. Genome analysis of these bacterial strains revealed numerous genes predicted to be involved in cellulose, hemicellulose, and lignin degradation, as well as several other genes related to bacteria-fungi interactions and endophytism inside the plant. The occurrence of this type of bacteria-fungus interaction could explain, at least in part, why necrosis develops extensively in certain grapevine varieties such as Ugni blanc., (© 2024. The Author(s).)

The electrical potential of the mycelia of a cord-forming wood decay fungus, Pholiota brunnescens, was monitored for over 100 days on a plain agar plate during the colonization onto a wood bait. Causality analyses of the electrical potential at different locations of the mycelium revealed a clear and stable causal relationship with the directional flow of the electrical potential from the hyphae at the bait location to other parts of the mycelium. However, this causality disappeared after 60 days of incubation, coinciding with the onset of slow electrical oscillation at the bait location, which occurred over one week per oscillation cycle. We speculated that the hyphae that initially colonized the bait may act as a temporary activity center, which generates electrical signals to other parts of the mycelium, thereby facilitating the colonization of the entire mycelial body to the bait. The week-long electrical oscillation represents the longest oscillation period ever recorded in fungi and warrants further investigation to elucidate its function and stability in response to environmental stimuli., (© 2024. The Author(s).)

Methane is an important greenhouse gas 1 , but the role of trees in the methane budget remains uncertain 2 . Although it has been shown that wetland and some upland trees can emit soil-derived methane at the stem base 3,4 , it has also been suggested that upland trees can serve as a net sink for atmospheric methane 5,6 . Here we examine in situ woody surface methane exchange of upland tropical, temperate and boreal forest trees. We find that methane uptake on woody surfaces, in particular at and above about 2 m above the forest floor, can dominate the net ecosystem contribution of trees, resulting in a net tree methane sink. Stable carbon isotope measurement of methane in woody surface chamber air and process-level investigations on extracted wood cores are consistent with methanotrophy, suggesting a microbially mediated drawdown of methane on and in tree woody surfaces and tissues. By applying terrestrial laser scanning-derived allometry to quantify global forest tree woody surface area, a preliminary first estimate suggests that trees may contribute 24.6-49.9 Tg of atmospheric methane uptake globally. Our findings indicate that the climate benefits of tropical and temperate forest protection and reforestation may be greater than previously assumed., (© 2024. The Author(s).)

Four yeast isolates were obtained from rotting wood and galleries of passalid beetles collected in different sites of the Brazilian Amazonian Rainforest in Brazil. This yeast produces unconjugated allantoid asci each with a single elongated ascospore with curved ends. Sequence analysis of the internal transcribed spacer-5.8 S region and the D1/D2 domains of the large subunit ribosomal RNA (rRNA) gene showed that the isolates represent a novel species of the genus Spathaspora. The novel species is phylogenetically related to a subclade containing Spathaspora arborariae and Spathaspora suhii. Phylogenomic analysis based on 1884 single-copy orthologs for a set of Spathaspora species whose whole genome sequences are available confirmed that the novel species represented by strain UFMG-CM-Y285 is phylogenetically close to Sp. arborariae. The name Spathaspora marinasilvae sp. nov. is proposed to accommodate the novel species. The holotype of Sp. marinasilvae is CBS 13467  T (MycoBank 852799). The novel species was able to accumulate xylitol and produce ethanol from  d-xylose, a trait of biotechnological interest common to several species of the genus Spathaspora., (© 2024 John Wiley & Sons Ltd.)

Wood Ducks (Aix sponsa) are secondary cavity nesters that use natural cavities and artificial nest boxes, the latter of which has been attributed to the recovery of populations across the southeastern US. Continual use of these boxes results in a buildup of bacteria, parasites, and other pathogens. To avoid the accumulation of these deleterious organisms, best management practices include the occasional removal of old nesting material (i.e., wood shavings) and replacement with fresh wood shavings. No studies have been performed on the effects of shaving material on nest box selection, nest success, and bacterial growth. We monitored 142 and 111 nest boxes in Florida and Georgia, USA, respectively, and filled a random sample with aspen or cedar shavings. We then swabbed the surface of 144 and 150 eggs during 2020 and 2021, respectively, to screen for culturable bacteria. We detected no effect of shaving type on nest box selection, nest success, or egg surface bacterial growth. We found 3-8 bacterial colony types (1-123 colony-forming units [CFU]/box) and 1-8 bacterial colony types (3-382 CFU/box) among the Georgia and Florida samples, respectively. We detected no effect from shaving type on Wood Duck reproduction or bacterial growth in the sampled nest boxes. We concluded that both shaving types are suitable nesting materials for box-nesting Wood Duck populations and the continued use of either would be a reasonable decision for managers., (© Wildlife Disease Association 2024.)

Wood is reportedly more difficult to maintain in hygienic condition versus other food contact materials, yet its use in produce packing and retail warrants efforts to reduce the risk of microbial pathogen contamination and attachment. This study characterized antifouling capabilities of fluorinated silanes applied to wood used in fresh edible produce handling to render the wood superhydrophobic and less supportive of bacterial pathogen attachment. Pine and oak cubic coupon surfaces were treated with 1% (w/w) silane or left untreated. Treated and untreated coupons were inoculated with Salmonella enterica or Listeria monocytogenes and held to facilitate pathogen attachment for 1, 4, or 8 h. Silane treatment of wood produced significant reductions in the proportions of strongly attaching cells for both pathogens versus loosely attaching cells (P < 0.01). Salmonella attachment demonstrated a dependency on wood treatment; silane-treated wood supported a lower fraction of strongly adhering cells (1.87 ± 1.24 log CFU/cm 2 ) versus untreated wood (3.72 ± 0.67 log CFU/cm 2 ). L. monocytogenes demonstrated significant declines in strongly attaching cells during extended exposure to silane-treated wood, from 7.59 ± 0.14 to 5.27 ± 0.68 log CFU/cm 2 over 8 h post-inoculation. Microscopic analysis demonstrated silane treatment increased the surface roughness of both woods, leading to superhydrophobic conditions on wood surfaces, consequently decreasing strong attachment of pathogenic bacteria., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Agarwood is a resinous heartwood of Aquilaria sinensis that is formed in response to mechanical wounding. In the present study pre-treatment of Aquilaria sinensis was carried out, and then the dominant fungi were isolated and purified from the surface and electroshock holes of trees. The isolated Trichoderma sp. and Neurospora sp. were then screened for resistance against benzyl acetone and then inoculated into healthy Aquilaria sinensis trees. After six months, the agarwood was collected for analysis. The chemical composition of incense was analyzed using gas chromatography-mass spectroscopy, and 82 chemical constituents were identified. Agarwood products formed by using Trichoderma sp. and Neurospora sp. consisted of 50.22% and 48.71% ether extracts, respectively, which surpassed the 10% threshold specified by the Chinese Pharmacopoeia. Similarly, relative aromatic contents in the two agarwood products were 30.1% and 32.86%, while proportions of sesquiterpene constituents were 10.21% and 11.19%, respectively. These two agarwood-specific chemical constituents accounted for a large proportion of the total chemical composition, which showed that the generated agarwood was of good quality. The results of the study revealed that both Trichoderma sp. and Neurospora sp. were able to effectively induce agarwood production in Aquilaria sinensis trees in 6 months. This study expands the library of fungi that promote the production of agarwood from Aquilaria sinensis trees., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Liu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Fungal trunk diseases (FTDs) have been a significant threat to the global stone fruit industry. FTDs are caused by a consortium of wood-decaying fungi. These fungi colonize woody tissues, causing cankers, dieback, and other decline-related symptoms in host plants. In this study, a detailed screening of the fungal microbiota associated with the decline of stone fruit trees in the Czech Republic was performed. The wood fragments of plum and apricot trees showing symptoms of FTDs were subjected to fungal isolation. The partial internal transcribed spacer region, partial beta-tubulin, and translation elongation factor 1-α genes were amplified from genomic DNA extracted from fungal cultures. All isolates were classified, and the taxonomic placement of pathogenic strains was illustrated in phylogenetic trees. The most abundant pathogenic genus was Dactylonectria (31%), followed by Biscogniauxia (13%), Thelonectria (10%), Eutypa (9%), Dothiorella (7%), Diplodia (6%), and Diaporthe (6%). The most frequent endophytic genus was Aposphaeria (17%). The pathogenicity of six fungal species ( Cadophora daguensis , Collophorina africana , Cytospora sorbicola , Dothiorella sarmentorum , Eutypa lata , and E. petrakii var. petrakii ) to four Prunus spp. was evaluated, and Koch's postulates were fulfilled. All tested isolates caused lesions on at least one Prunus sp. The most aggressive species was E. lata , which caused the largest lesions on all four tested Prunus spp., followed by E. petrakii var. petrakii and D. sarmentorum . Japanese plum ( Prunus salicina ) and almond ( P. amygdalus ) were the most susceptible hosts, while apricot ( P. armeniaca ) was the least susceptible host in the pathogenicity trial., Competing Interests: The author(s) declare no conflict of interest.

Unlike 'white rot' (WR) wood-decomposing fungi that remove lignin to access cellulosic sugars, 'brown rot' (BR) fungi selectively extract sugars and leave lignin behind. The relative frequency and distribution of these fungal types (decay modes) have not been thoroughly assessed at a global scale; thus, the fate of one-third of Earth's aboveground carbon, wood lignin, remains unclear. Using c. 1.5 million fungal sporocarp and c. 30 million tree records from publicly accessible databases, we mapped and compared decay mode and tree type (conifer vs angiosperm) distributions. Additionally, we mined fungal record metadata to assess substrate specificity per decay mode. The global average for BR fungi proportion (BR/(BR + WR records)) was 13% and geographic variation was positively correlated (R 2  = 0.45) with conifer trees proportion (conifer/(conifer + angiosperm records)). Most BR species (61%) were conifer, rather than angiosperm (22%), specialists. The reverse was true for WR (conifer: 19%; angiosperm: 62%). Global BR proportion patterns were predicted with greater accuracy using the relative distributions of individual tree species (R 2  = 0.82), rather than tree type. Fungal decay mode distributions can be explained by tree type and, more importantly, tree species distributions, which our data suggest is due to strong substrate specificities., (© 2024 The Authors New Phytologist © 2024 New Phytologist Foundation.)

Biological pretreatment of wood chips by fungi is a well-known approach prior to mechanical- or chemical pulp production. For this biological approach, a limited number of white-rot fungi with an ability to colonize and selectively degrade lignin are used to pretreat wood chips allowing the remaining cellulose to be processed for further applications. Biopulping is an environmentally friendly technology that can reduce the energy consumption of traditional pulping processes. Fungal pretreatment also reduces the pitch content in the wood chips and improves the pulp quality in terms of brightness, strength, and bleachability. The bleached biopulps are easier to refine compared to pulps produced by conventional methodology. In the last decades, biopulping has been scaled up with pilot trials towards industrial level, with optimization of several intermediate steps and improvement of economic feasibility. Nevertheless, fundamental knowledge on the biochemical mechanisms involved in biopulping is still lacking. Overall, biopulping technology has advanced rapidly during recent decades and pilot mill trials have been implemented. The use of fungi as pretreatment for pulp production is in line with modern circular economy strategies and can be implemented in existing production plants. In this review, we discuss some recent advances in biopulping technology, which can improve mechanical-, chemical-, and organosolv pulping processes along with their mechanisms., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Despite the importance of wood-inhabiting fungi on nutrient cycling and ecosystem functions, their ecology, especially related to their community assembly, is still highly unexplored. In this study, we analyzed the wood-inhabiting fungal richness, community composition, and phylogenetics using PacBio sequencing. Opposite to what has been expected that deterministic processes especially environmental filtering through wood-physicochemical properties controls the community assembly of wood-inhabiting fungal communities, here we showed that both deterministic and stochastic processes can highly contribute to the community assembly processes of wood-inhabiting fungi in this tropical forest. We demonstrated that the dynamics of stochastic and deterministic processes varied with wood decomposition stages. The initial stage was mainly governed by a deterministic process (homogenous selection), whereas the early and later decomposition stages were governed by the stochastic processes (ecological drift). Deterministic processes were highly contributed by wood physicochemical properties (especially macronutrients and hemicellulose) rather than soil physicochemical factors. We elucidated that fine-scale fungal-fungal interactions, especially the network topology, modularity, and keystone taxa of wood-inhabiting fungal communities, strongly differed in an initial and decomposing deadwood. This current study contributes to a better understanding of the ecological processes of wood-inhabiting fungi in tropical regions where the knowledge of wood-inhabiting fungi is highly limited., (© 2024. The Author(s).)

The prevalence and potential functions of common mycorrhizal networks, or the 'wood-wide web', resulting from the simultaneous interaction of mycorrhizal fungi and roots of different neighbouring plants have been increasingly capturing the interest of science and society, sometimes leading to hyperbole and misinterpretation. Several recent reviews conclude that popular claims regarding the widespread nature of these networks in forests and their role in the transfer of resources and information between plants lack evidence. Here we argue that mycoheterotrophic plants associated with ectomycorrhizal or arbuscular mycorrhizal fungi require resource transfer through common mycorrhizal networks and thus are natural evidence for the occurrence and function of these networks, offering a largely overlooked window into this methodologically challenging underground phenomenon. The wide evolutionary and geographic distribution of mycoheterotrophs and their interactions with a broad phylogenetic range of mycorrhizal fungi indicate that common mycorrhizal networks are prevalent, particularly in forests, and result in net carbon transfer among diverse plants through shared mycorrhizal fungi. On the basis of the available scientific evidence, we propose a continuum of carbon transfer options within common mycorrhizal networks, and we discuss how knowledge on the biology of mycoheterotrophic plants can be instrumental for the study of mycorrhizal-mediated transfers between plants., (© 2024. Springer Nature Limited.)

Consuming wood as a primary food source poses many challenges for animals. Rich in non-assimilable carbohydrates, wood digestion requires a high degree of anatomical and physiological specialization by both the host and its microbiome. However, wood comsumption (xylivory) as a dietary strategy to obtain energy has been recorded in a small number of animals including beaver, porcupine, and moose and wood typically accounts for a small fraction of the overall diet in these organisms, or, is limited to the nutrient-rich tissues of the bark and vascular cambium. The paucity of wood-feeding organisms is due to the recalcitrant and nutrient-poor nature of the substrate. Our current understanding of wood feeding is limited to a small number of marine and terrestrial invertebrate systems. In this chapter we focus on the Neotropical catfish, Panaque nigrolineatus, which ingests large quantities of wood as part of its diet. The microbiome of P. nigrolineatus has been shown to include bacterial and fungal communities participating in both lignocellulose degradation and nitrogen fixation that are taxonomically distinct from all other wood-feeding organisms, although the functional capacity of these communities is consistent with those observed in other wood-feeders. This environmentally recruited microbiome allows the gastrointestinal tract microbiome a high degree of flexibility and resilience ideally suited to rapid changes in dietary strategy. [ABSTRACT FROM AUTHOR]

In the last few years, trunk surgery has gained increasing attention as a method to reduce foliar symptoms typical of some of the Esca complex diseases. The technique relies on the mechanical removal of decayed wood by a chainsaw. A study on a 14-year-old Cabernet Sauvignon vineyard was carried out to validate the efficacy of trunk surgery and explore possible explanations behind it. Three levels of treatment were applied to three of the most characteristic symptoms associated with some diseases of the Esca complex, such as leaf stripe symptoms (LS), wilted shoots (WS) and apoplexy (APP). The most promising results were obtained by complete trunk surgery, where the larger decay removal allowed lower symptom re-expression. According to the wood types analyzed (decay, medium and sound wood), different changes in microbiota were observed. Alpha-diversity generally decreased for bacteria and increased for fungi. More specifically, main changes were observed for Fomitiporia mediterranea abundance that decreased considerably after trunk surgery. A possible explanation for LS symptom reduction after trunk surgery could be the microbiota shifting caused by the technique itself affecting a microbic-shared biochemical pathway involved in symptom expression. [ABSTRACT FROM AUTHOR]

Although sodium arsenite was widely used in Europe until its ban in 2003, its effects on microorganisms is not clearly understood. To improve our understanding of sodium arsenite curative effect on GTDs, grapevines displaying esca-foliar symptoms from different French regions (Alsace, Champagne, Languedoc) were treated or not with sodium arsenite, and analyzed for their wood microbiota. Using metabarcoding, we identified the fungal and bacterial taxa composition of microbiota colonizing woody trunk tissues. Large differences in fungal microbiota composition between treated and untreated grapevines were observed while no major impacts were observed on bacteria microbiota. The main fungal species detected in untreated necrotic woody tissues was Fomitiporia mediterranea (63–94%), a fungal pathogen associated with esca. The relative abundance of this fungal species significantly decreased after sodium arsenite treatment in the three vineyards, in particular in white-rot necrotic tissues and their borders (−90%). F. mediterranea was the most sensitive to sodium arsenite among fungi from grapevine woody tissues. These results strongly suggest that the effect of sodium arsenite on GTDs is due to its ability to efficiently and almost specifically eliminate F. mediterranea from white-rot necrotic tissues, allowing saprobic fungi to colonize the tissues previously occupied by this pathogenic fungus. [ABSTRACT FROM AUTHOR]

In a time with decreasing biodiversity, especially among insects, a detailed understanding about specific resource utilization strategies is crucial. The physiological and behavioural responses to host switches in phytophagous insects are poorly understood. Earlier studies indicate that a host plant switch might be associated with distinctive molecular and physiological responses in different lineages. Expanding the assessment of such associations across Lepidoptera will reveal if there are general patterns in adaptive responses, or if each switch event is more of a unique character. We investigated host plant preference, fitness consequences, effects on expression profiles and gut microbiome composition in two common wood white (Leptidea sinapis) populations with different host plant preferences from the extremes of the species distribution area (Sweden and Catalonia). Our results show that female Catalonian wood whites lack preference for either host plant (Lotus corniculatus or L. dorycnium), while Swedish females laid significantly more eggs on L. corniculatus. Individuals from both populations reared on L. dorycnium had longer developmental times and smaller body size as adults. This indicates that both environmental and genetic factors determine the choice to use a specific host plant. Gene expression analysis revealed a more pronounced response to host plant in the Catalonian compared to the Swedish population. In addition, host plant treatment resulted in a significant shift in microbiome community structure in the Catalonian population. Together, this suggests that population specific plasticity associated with local conditions underlies host plant utilisation in wood whites. [ABSTRACT FROM AUTHOR]

White-rot fungi employ secreted carbohydrate-active enzymes (CAZymes) along with reactive oxygen species (ROS), like hydrogen peroxide (H 2 O 2 ), to degrade lignocellulose in wood. H 2 O 2 serves as a co-substrate for key oxidoreductases during the initial decay phase. While the degradation of lignocellulose by CAZymes is well documented, the impact of ROS on the oxidation of the secreted proteins remains unclear, and the identity of the oxidized proteins is unknown. Methionine (Met) can be oxidized to Met sulfoxide (MetO) or Met sulfone (MetO 2 ) with potential deleterious, antioxidant, or regulatory effects. Other residues, like proline (Pro), can undergo carbonylation. Using the white-rot Pycnoporus cinnabarinus grown on aspen wood, we analyzed the Met content of the secreted proteins and their susceptibility to oxidation combining H 2 18 O 2 with deep shotgun proteomics. Strikingly, their overall Met content was significantly lower (1.4%) compared to intracellular proteins (2.1%), a feature conserved in fungi but not in metazoans or plants. We evidenced that a catalase, widespread in white-rot fungi, protects the secreted proteins from oxidation. Our redox proteomics approach allowed the identification of 49 oxidizable Met and 40 oxidizable Pro residues within few secreted proteins, mostly CAZymes. Interestingly, many of them had several oxidized residues localized in hotspots. Some Met, including those in GH7 cellobiohydrolases, were oxidized up to 47%, with a substantial percentage of sulfone (13%). These Met are conserved in fungal homologs, suggesting important functional roles. Our findings reveal that white-rot fungi safeguard their secreted proteins by minimizing their Met content and by scavenging ROS and pinpoint redox-active residues in CAZymes.IMPORTANCEThe study of lignocellulose degradation by fungi is critical for understanding the ecological and industrial implications of wood decay. While carbohydrate-active enzymes (CAZymes) play a well-established role in lignocellulose degradation, the impact of hydrogen peroxide (H 2 O 2 ) on secreted proteins remains unclear. This study aims at evaluating the effect of H 2 O 2 on secreted proteins, focusing on the oxidation of methionine (Met). Using the model white-rot fungi Pycnoporus cinnabarinus grown on aspen wood, we showed that fungi protect their secreted proteins from oxidation by reducing their Met content and utilizing a secreted catalase to scavenge exogenous H 2 O 2 . The research identified key oxidizable Met within secreted CAZymes. Importantly, some Met, like those of GH7 cellobiohydrolases, undergone substantial oxidation levels suggesting important roles in lignocellulose degradation. These findings highlight the adaptive mechanisms employed by white-rot fungi to safeguard their secreted proteins during wood decay and emphasize the importance of these processes in lignocellulose breakdown., Competing Interests: The authors declare no conflict of interest.

Heterotrophic soil microorganisms are responsible for ~50% of the carbon dioxide released by respiration from the terrestrial biosphere each year. The respiratory response of soil microbial communities to warming, and the control mechanisms, remains uncertain, yet is critical to understanding the future land carbon (C)-climate feedback. Individuals of nine species of fungi decomposing wood were exposed to 90 days of cooling to evaluate the medium-term effect of temperature on respiration. Overall, the effect of temperature on respiration increased in the medium term, with no evidence of compensation. However, the increasing effect of temperature on respiration was lost after correcting for changes in biomass. These results indicate that C loss through respiration of wood-decomposing fungi will increase beyond the direct effects of temperature on respiration, potentially promoting greater C losses from terrestrial ecosystems and a positive feedback to climate change., (© 2024 The Authors. Global Change Biology published by John Wiley & Sons Ltd.)

Enzymatic compounds can be found abundantly and provide numerous advantages in microbial organisms. Xylanases are used in various pharmaceutical, food, livestock, poultry, and paper industries. This study aimed to investigate xylanase-producing yeasts, xylose concentration curve and their enzymatic activity under various factors including carbon and nitrogen sources, temperature, and pH. Enzyme activity was evaluated under different conditions before, during, and after purification. The yeast strains were obtained from the wood product workshop and were subsequently cultivated on YPD (yeast extract peptone dextrose) medium. Additionally, the growth curve of the yeast and its molecular identification were conducted. The optimization and design process of xylan isolated from corn wood involved the use of Taguchi software to test different parameters like carbon and nitrogen sources, temperature, and pH, with the goal of determining the most optimal conditions for enzyme production. In addition, the Taguchi method was utilized to conduct a multifactorial optimization of xylanase enzyme activity. The isolated species were partially purified using ammonium sulfate precipitation and dialysis bag techniques. The results indicated that 3 species (8S, 18S, and 16W) after molecular identification based on 18S rRNA gene sequencing were identified as Candida tropicalis SBN-IAUF-1, Candida tropicalis SBN-IAUF-3, and Pichia kudriavzevii SBN-IAUF-2, respectively. The optimal parameters for wheat carbon source and peptone nitrogen source were found at 50 °C and pH 9.0 through single-factor optimization. By using the Taguchi approach, the best combination for highest activity was rice-derived carbon source and peptone nitrogen source at 50 °C and pH 6.0. The best conditions for xylanase enzyme production in single-factor optimization of wheat bran were 2135.6 U/mL, peptone 4475.25 U/mL, temperature 50 °C 1868 U/mL, and pH 9.0 2002.4 U/mL. Among the tested yeast, Candida tropicalis strain SBN-IAUF-1 to the access number MZ816946.1 in NCBI was found to be the best xylanase product. The highest ratio of enzyme production at the end of the delayed phase and the beginning of the logarithmic phase was concluded by comparing the growth ratio of 8S, 16W, and 18S yeasts with the level of enzymatic activity. This is the first report on the production of xylan polymer with a relative purity of 80% in Iran. The extracellular xylanases purified from the yeast species of C. tropicalis were introduced as a desirable biocatalyst due to their high enzymatic activity for the degradation of xylan polymers., (© 2023. The Author(s) under exclusive licence to Sociedade Brasileira de Microbiologia.)

A yeast strain (CGMCC 2.6937 T ) belonging to the ascomycetous yeast genus Saturnispora was recently isolated from soil collected in Xinghuacun, Shanxi Province, PR China. The strain produces one or two ellipsoid or spherical ascospores in asci formed by the conjugation between a cell and its bud. Phylogenetic analyses of the internal transcribed spacer (ITS) region and the D1/D2 domain of the large subunit rRNA gene suggest that this strain is conspecific with strains NYNU 14639 isolated from rotten wood collected in Funiu Mountain, Henan province and ES13S05 from soil collected in Nantou County, Taiwan. The CGMCC 2.6937 T group is most closely related to Saturnispora dispora and Saturnispora zaruensis . However, strain CGMCC 2.6937 T differs from S. dispora by 17 (3.2 %, 13 substitutions and four gaps) and 77 (18.8 %, 52 substitutions and 25 gaps) mismatches, and from S. zaruensis by 15 (2.9 %, 12 substitutions and three gaps) and 64 (15.6 %, 44 substitutions and 20 gaps) mismatches, in the D1/D2 domain and ITS region, respectively. The results suggest that the CGMCC 2.6937 T group represents an undescribed species in the genus Saturnispora , for which the name Saturnispora sinensis sp. nov. is proposed. The holotype strain is CGMCC 2.6937 T .

A new species of the yeast genus Blastobotrys was discovered on ancient ship timbers in the Netherlands. The species had developed on the wood of a river barge dating to the Roman period. The growth occurred after the preservative polyethylene glycol (PEG 4000) was washed out of some of the timbers due to an undetected leak in the storage unit. Mycological analysis of various timber samples revealed the presence of Microascus melanosporus (predominant), Microascus paisii, a member of the Acremonium chrysogenum-clade, and a new Blastrobotrys species. The new species produced sporothrix-like conidiophores with clavate blastoconidia (3-7 × 1-3.5 μm) and was found to be osmotolerant, capable of growth on low water activity media like malt yeast 50% glucose agar (MY50G). In this article we formally describe and introduce Blastrobotrys nigripullensis (CBS 17879  T ) based on its morphology, physiology and phylogenetic placement., (© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Deadwood provides habitat for fungi and serves diverse ecological functions in forests. We already have profound knowledge of fungal assembly processes, physiological and enzymatic activities, and resulting physico-chemical changes during deadwood decay. However, in situ detection and identification methods, fungal origins, and a mechanistic understanding of the main lignocellulolytic enzymes are lacking. This study used metaproteomics to detect the main extracellular lignocellulolytic enzymes in 12 tree species in a temperate forest that have decomposed for 8 ½ years. Mainly white-rot (and few brown-rot) Basidiomycota were identified as the main wood decomposers, with Armillaria as the dominant genus; additionally, several soft-rot xylariaceous Ascomycota were identified. The key enzymes involved in lignocellulolysis included manganese peroxidase, peroxide-producing alcohol oxidases, laccase, diverse glycoside hydrolases (cellulase, glucosidase, xylanase), esterases, and lytic polysaccharide monooxygenases. The fungal community and enzyme composition differed among the 12 tree species. Ascomycota species were more prevalent in angiosperm logs than in gymnosperm logs. Regarding lignocellulolysis as a function, the extracellular enzyme toolbox acted simultaneously and was interrelated (e.g. peroxidases and peroxide-producing enzymes were strongly correlated), highly functionally redundant, and present in all logs. In summary, our in situ study provides comprehensive and detailed insight into the enzymatic machinery of wood-inhabiting fungi in temperate tree species. These findings will allow us to relate changes in environmental factors to lignocellulolysis as an ecosystem function in the future., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Grapevine (Vitis vinifera L.) trunk diseases (GTDs) are considered a disease complex including five diseases: esca, Petri disease, black-foot disease, Botryosphaeria dieback, and Eutypa dieback. The main symptom is a general decline in affected plants, which show xylem necrosis and discoloration or sectorial necrosis in the wood. Their diagnosis is tedious due to four main reasons: (i) the wide diversity of internal symptoms that we can find; (ii) the great diversity of fungi that are associated with them; (iii) the high frequency of co-infections in the same plant; and (iv) the different behavior that the fungal species associated with GTDs show in vitro. Here, we describe a detailed protocol to isolate the different fungal trunk pathogens associated with GTDs as well as methods to induce sporulation and formation of fruiting bodies (pycnidia) to make easier their morphological characterization., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Summary: Esca, a major grapevine trunk disease in old grapevines, is associated with the colonization of woody tissues by a broad range of plant pathogenic fungi. To identify which fungal and bacterial species are involved in the onset of this disease, we analysed the microbiota from woody tissues of young (10‐year‐old) grapevines at an early stage of esca. Using meta‐barcoding, 515 fungal and 403 bacterial operational taxonomic units (OTUs) were identified in woody tissues. In situ hybridization showed that these fungi and bacteria co‐inhabited in grapevine woody tissues. In non‐necrotic woody tissues, fungal and bacterial microbiota varied according to organs and seasons but not diseased plant status. Phaeomoniella chlamydospora, involved in the Grapevine trunk disease, was the most abundant species in non‐necrotic tissues from healthy plants, suggesting a possible non‐pathogenic endophytic behaviour. Most diseased plants (70%) displayed cordons, with their central white‐rot necrosis colonized essentially by two plant pathogenic fungi (Fomitiporia mediterranea: 60%–90% and P. chlamydospora: 5%–15%) and by a few bacterial taxa (Sphingomonas spp. and Mycobacterium spp.). The occurrence of a specific association of fungal and bacterial species in cordons from young grapevines expressing esca‐foliar symptoms strongly suggests that that microbiota is involved in the onset of this complex disease. [ABSTRACT FROM AUTHOR]

Neotropical wood‐eating catfishes (family Loricariidae) can occur in diverse assemblages with multiple genera and species feeding on the same woody detritus. As such, they present an intriguing system in which to examine the influence of host species identity on the vertebrate gut microbiome as well as to determine the potential role of gut bacteria in wood digestion. We characterized the gut microbiome of two co‐occurring catfish genera and four species: Panaqolus albomaculatus, Panaqolus gnomus, Panaqolus nocturnus, and Panaque bathyphilus, as well as that of submerged wood on which they feed. The gut bacterial community did not significantly vary across three gut regions (proximal, mid, distal) for any catfish species, although interspecific variation in the gut microbiome was significant, with magnitude of interspecific difference generally reflecting host phylogenetic proximity. Further, the gut microbiome of each species was significantly different to that present on the submerged wood. Inferring the genomic potential of the gut microbiome revealed that the majority of wood digesting pathways were at best equivalent to and more often depleted or nonexistent within the catfish gut compared to the submerged wood, suggesting a minimal role for the gut microbiome in wood digestion. Rather, these fishes are more likely reliant on fiber degradation performed by microbes in the environment, with their gut microbiome determined more by host identity and phylogenetic history. [ABSTRACT FROM AUTHOR]

Waterlogged archaeological wood (WAW) is considered a precious material, first-hand account of past civilizations. Like any organic material, it is subjected to biodegradative action of microorganisms whose activity could be particularly fast and dangerous during the phases of excavation, storage and restoration. The present work aimed to characterize the microorganisms present in WAW during these tricky periods to evaluate the biological risk it is exposed to. The bacterial and fungal communities inhabiting woods coming from two archaeological sites (Pisa and Naples) were investigated through Next-Generation Sequencing (NGS). High-throughput sequencing of extracted DNA fragments was performed using the reversible terminator-based sequencing chemistry with the Illumina MiSeq platform. The analyses revealed that the two archaeological sites showed distinct richness and biodiversity, as expected. In all the WAWs, the bacterial community harbored mainly Proteobacteria, whereas Bacteroidetes was well represented only in Naples communities and taxa belonging to the phyla Chloroflexi only in the Pisa site. Concerning the fungal community, the two sites were dominated by different phyla: Ascomycota for Naples samples and Basidiomycota for Pisa. Interestingly, most of the identified bacterial and fungal taxa have cellulolytic or ligninolytic ability. These results provide new and useful background information concerning the composition of WAW microbiota and the threat it represents for this precious material. [ABSTRACT FROM AUTHOR]

Thermal treatments have the effect of reducing the hygroscopicity and improving the resistance to microbiological attack of wood by the degradation of its chemical constituents. During the treatments, the mass of the wood is reduced, a factor that can affect the quality of the materials according to their use. The objective was to verify the effect of the thermal treatment variables on the thermogravimetric properties and the chemical composition of Eucalyptus grandis. The treatments were carried out in a vacuum oven with three atmosphere conditions - vacuum; N2; vacuum+N2 at temperatures of 140, 180 and 220 °C for 6 hours. It was observed that the mass loss during treatments differed only according to the temperatures used. The extractive content, total lignin and holocellulose presented significant changes only at 220°C in all three atmospheres. In the thermogravimetric analysis, the greatest value of residual mass was found in the treatment that used nitrogen and 220 °C, thus demonstrating that this treatment was more invasive, leading to the conclusion that the vacuum application can help to reduce the degradation of the constituents of the eucalypt wood. Wood, which can lead to the production of thermally treated wood without great losses in the mechanical properties. [ABSTRACT FROM AUTHOR]

Importance: We applied macro- (forest stand and forest management) and micro-scale (bacterial and fungal community) analyses for a better understanding of the Heterobasidion pathosystem and associated wood decay process. The core microbiome, as defined by hierarchy analysis and a consistent model, and environmental factors correlation with the community assembly were found to be novel., Competing Interests: The authors declare no conflict of interest.

The emergence of bacterial resistance to antimicrobials poses a significant health threat. To address this issue, exploring the fungal diversity in freshwater environments in the Amazon Forest has potential in the search for new antimicrobials. This study aimed to investigate the production of antibacterial metabolites by aquatic fungi from Amazon lakes, specifically Lake Juá and Lake Maicá (Brazil-PA). The fungal isolates were obtained from wood fragments submerged in these lakes, and the ethyl acetate extracts were evaluated for antibacterial activity against Staphylococcus aureus ATCC 25923, S. aureus (MRSA), ATCC 43300, Escherichia coli ATCC 25922, and E. coli (ESBL) NCTC 13353. Additionally, toxicity of the extracts (EtOAc with antimicrobial activity) against human fibroblasts MRC-5 was investigated. The study identified 40 fungal strains with antimicrobial screening, and the ethyl acetate extracts of Fluviatispora C34, Helicascus C18, Monodictys C15, and Fusarium solani LM6281 exhibited antibacterial activity. F. solani LM6281 showed the lowest minimum inhibitory concentration (MIC) of 50 µg/mL against S. aureus strains and MIC of 100 µg/mL against E. coli strains including ESBL. The cytotoxicity (IC50) of the extract (EtOAc) of F. solani LM6281 was 34.5 µg/mL. Preliminary studies of the TLC culture and RNM-H from the extract (EtOAc) of F. solani suggested the presence of substances from the class of terpenes, quinones, phenolics, and flavonoids. This study highlights the potential of submerged wood fungi in the Amazon region to produce antibacterial substances, thus identifying them as sources of novel bioactive compounds with potential use in the pharmaceutical industry and regional bioeconomy.

This study aimed to evaluate and compare the effects of oil- and air-heat treatments on the durability of Paulownia tomentosa and Pinus koraiensis woods against Fomitopsis palustris and Trametes versicolor. The wood samples were treated in palm oil and air at 180, 200, and 220 °C for 2 h. The weight loss, morphology, crystalline properties, and chemical compounds of untreated and heat-treated wood after fungal attack were investigated. The significant difference in weight loss between oil- and air-heat-treated samples was shown at 220 °C. Heat-treated wood exposed to white-rot fungus showed a lower weight loss than that exposed to brown-rot fungus. The cell components in the untreated- and heat-treated Paulownia tomentosa and Pinus koraiensis at 180 °C were severely damaged due to fungal exposure compared to those at 220 °C. A fungal effect on the relative crystallinity was observed in heat-treated wood at 180 °C, whereas the effect was not observed at 220 °C. Following brown-rot fungus exposure, untreated- and heat-treated wood at 180 °C showed a notable change in the Fourier transform infrared (FTIR) peaks of polysaccharides, whereas no noticeable change in lignin peaks was observed. Heat-treated wood at 220 °C showed no noticeable change in the FTIR spectra owing to brown-rot fungus exposure. Exposure to white-rot fungus did not noticeably change the FTIR spectra of untreated and heat-treated wood., (© 2023. The Author(s).)

Biodiversity drives ecosystem processes, but its influence on deadwood decomposition is poorly understood. To test the effects of insect diversity on wood decomposition, we conducted a mesocosm experiment manipulating the species richness and functional diversity of beetles. We applied a novel approach using computed tomography scanning to quantify decomposition by insects and recorded fungal and bacterial communities. Decomposition rates increased with both species richness and functional diversity of beetles, but the effects of functional diversity were linked to beetle biomass, and to the presence of one large-bodied species in particular. This suggests that mechanisms behind observed biodiversity effects are the selection effect, which is linked to the occurrence probability of large species, and the complementarity effect, which is driven by functional differentiation among species. Additionally, beetles had significant indirect effects on wood decomposition via bacterial diversity, fungal community composition, and fungal biomass. Our experiment shows that wood decomposition is driven by beetle diversity and its interactions with bacteria and fungi. This highlights that both insect and microbial biodiversity are critical to maintaining ecosystem functioning., (© 2023 The Authors. Ecology published by Wiley Periodicals LLC on behalf of The Ecological Society of America.)

One of the most important biological factors that damage wood materials are wood-decay fungi (WDF). Chemical preservatives have traditionally been the most effective method for controlling WDF. However, due to environmental pressures, scientists are working on alternative protection methods. The aim of this study was to investigate the potential of some antagonistic fungi against wood-decay fungi as a biological control agent (BCA). For this purpose, the antagonistic effects of Trichoderma harzianum, Trichoderma viride, Aspergillus niger, and Penicillium brevicompactum fungi were investigated against the Trametes versicolor, Trametes hirsuta, Stereum hirsutum, Coniophora puteana, Neolentinus lepideus, and Postia placenta species of wood-decay Basidiomycetes fungi. In the study, firstly, inhibition rates were determined by comparing dual culture tests on agar medium, and then the performance of BCAs was compared by performing decay tests on wood blocks. As a result of the study, it was determined that the species belonging to the genus Trichoderma showed a very effective performance on WDF, increased the inhibition rate to 76-99%, and reduced the weight loss to 1.9-5.8%. Considering the inhibition rates, it was determined that the most effective rate of the BCAs was on P. placenta and the least on S. hirsutum species. According to the results obtained, it has been determined that some BCAs were very effective biological control agents of rot fungi on agar and wood blocks in vitro. However, in order to more clearly determine the effectiveness of BCAs in practice, this study, which was carried out in the laboratory environment, should be supported by tests performed in contact with the external field and soil., (© 2023. The Author(s), under exclusive licence to Springer Nature B.V.)

We investigated the changes in microbial community diversities and functions in natural downed wood at different decay stages in a natural oak forest in the Italian Alps, through metagenomics analysis and in vitro analysis. Alfa diversity of bacterial communities was affected by the decay stage and log characteristics, while beta diversity was mainly driven by log diameter. Fungal and archaeal beta diversities were affected by the size of the sampled wood (log diameter), although, fungi were prominently driven by wood decay stage. The analysis of genes targeting cell wall degradation revealed higher abundances of cellulose and pectin-degrading enzymes in bacteria, while in fungi the enzymes targeting cellulose and hemicellulose were more abundant. The decay class affected the abundance of single enzymes, revealing a shift in complex hydrocarbons degradation pathways along the decay process. Moreover, we found that the genes related to Coenzyme M biosynthesis to be the most abundant especially at early stages of wood decomposition while the overall methanogenesis did not seem to be influenced by the decay stage. Intra- and inter-kingdom interactions between bacteria and fungi revealed complex pattern of community structure in response to decay stage possibly reflecting both direct and indirect interactions., (© 2023 The Authors. Environmental Microbiology published by Applied Microbiology International and John Wiley & Sons Ltd.)

Importance: Nitrate pollution is a serious problem in agricultural areas in the U.S. Midwest and other parts of the world. Woodchip bioreactor is a promising technology that uses microbial denitrification to remove nitrate from agricultural subsurface drainage, although the reactor's nitrate removal performance is limited under cold conditions. This study showed that the inoculation of cold-adapted denitrifiers (i.e., bioaugmentation) and the addition of labile carbon (i.e., biostimulation) can influence the microbial populations and enhance the reactor's performance under cold conditions. This finding will help establish a strategy to mitigate nitrate pollution., Competing Interests: The authors declare no conflict of interest.

Archaeological wood, also known as wooden cultural relics, refers to ancient wood that has been worked by humans. Further insights into the decomposition mechanism of archaeological wood are needed for its preventive conservation. In this study, we assessed the microbiome diversity and cellulose decomposition processes on a 200-year-old ancient wooden seawall - the Qiantang River of Hangzhou, China. We used high-throughput sequencing (HTS) to deduce the metagenomic functions, particularly the cellulose-decomposing pathway of the microbial communities, through bioinformatical approaches. The predominant cellulose-decomposing microorganisms were then verified with traditional isolation, culture, and identification method. The results showed that the excavation of archaeological wood significantly altered the environment, accelerating the deterioration process of the archaeological wood through the carbohydrate metabolism and the xenobiotic biodegradation and metabolism pathways, under the comprehensive metabolism of complex ecosystem formed by bacteria, archaea, fungi, microfauna, plants, and algae. Bacteroidetes, Proteobacteria, Firmicutes, and Actinobacteria were found to be the predominant source of bacterial cellulose-decomposing enzymes. Accordingly, we suggest relocating the wooden seawall to an indoor environment with controllable conditions to better preserve it. In addition, these results provide further evidence for our viewpoints that HTS techniques, combined with rational bioinformatical data interpretation approaches, can serve as powerful tools for the preventive protection of cultural heritage., (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Summary: While recent reports demonstrate that the direct emission of methane from living tree trunks may be a significant terrestrial emission source, there has been debate whether tree emissions are due to transport from soils or produced in the wood environment itself. Reports of methanogens from wood of trees were prominent in the literature 40 years ago but have not been revisited with molecular ecology approaches.We examined communities associated with Populus deltoides using rRNA gene sequence analyses and how these vary with tree and wood properties.Our data indicate that wood environments are dominated by anaerobic microbiomes. Methanogens are prominent in heartwood (mean 34% relative abundance) compared to sapwood environments (13%), and dominant operational taxonomic units (OTUs) were classified as the Methanobacterium sp. Members of the Firmicutes phylum comprised 39% of total sequences and were in 42% greater abundance in sapwood over heartwood niches. Tree diameter was the strongest predictor of methanogen abundance, but wood moisture content and pH were also significant predictors of taxon abundance and overall community composition.Unlike microbiomes of the soil, rhizosphere and phyllosphere, wood associated communities are shaped by unique environmental conditions and may be prominent and overlooked sources of methane emissions in temperate forest systems. [ABSTRACT FROM AUTHOR]

Highlights • Xylitol is the best reinforcement material for waterlogged wood relics. • The most suitable concentration of xylitol is 40% to 60%. • Adding enough chito-oligosaccharid can improve antimicrobial property of xylitol. Abstract Most unearthed waterlogged wood relics need to be reinforced by dehydration and strengthening, otherwise the dry shrinkage and deformation would severely damage the value of these cultural relics. Till now, a variety of materials, such as trehalose, xylitol, lactitol, glyoxal, and polyethylene glycol, have been reported to be applied in the reinforcement of wood relics, however, the comparison of their effects on wood relics has not been reported yet. In this work, these materials were applied in the reinforcement of waterlogged wood. Firstly, chemically degraded medical tongue depressors and rice paper were prepared and used to simulate wood relics, while aged raw lacquer piece was used to simulate lacquerware relics. Then, samples were dehydrated and reinforced by different reinforcement materials including trehalose, xylitol, chito-oligosaccharide, lactitol, glyoxal, glycerol and polyethylene glycol. Finally, properties including deformation, strength and antimicrobial property were tested successively. From the results, we can conclude that xylitol was the best reinforcement material in the concentration range from 40% (w/v) to 60% (w/v). In some cases, lactitol and trehalose were also proved to be the good reinforcement materials. Besides, adding more than 0.5% (w/v) of chito-oligosaccharide could obviously improve resistance to Gloeophyllum terbium of reinforcement materials such as xylitol. This is the first report on the comparison of different reinforcement materials for the waterlogged wood relics. Our work will give insight into the selection of more effective reinforcement materials for waterlogged wood relics and screening better reinforcement formula with different concentrations. [ABSTRACT FROM AUTHOR]

Deadwood plays an important role in forest ecology; its degradation and, therefore, carbon assimilation is carried out by fungi and bacteria. To quantify the abundance and distribution of microbial taxa inhabiting dead spruce logs fallen over a span of 50 years and the soil beneath, we used taxonomic profiling with NGS sequencing of hypervariable DNA fragments of ITS1 and 16S V3-V4, respectively. The analysis of sequencing data revealed a high level of diversity in microbial communities participating in the degradation of spruce logs. Differences in the relative abundance of microbial taxa between the samples of the wood that died in 1974 and 2014, and of the soil in its immediate vicinity, were visible, especially at the genus level. Based on the Lefse analysis significantly higher numbers of classified bacterial taxa were observed in the wood and soil samples from 2014 (wood: 1974-18 and 2014-28 taxa; soil: 1974-8 and 2014-41 taxa) while the number of classified fungal taxa was significantly higher in the wood and soil samples from 1974 (wood: 1974-17 and 2014-9 taxa; soil: 1974-57 and 2014-28 taxa). Most of the bacterial and fungal amplicon sequence variants (ASVs) unique to wood were found in the samples from 1974, while those unique to soil were detected in the samples from 2014. The ATR-FTIR method supported by CHN analysis revealed physicochemical changes in deadwood induced by the activity of fungal and bacterial organisms.

Denitrifying woodchip bioreactors (WBRs) are increasingly used to manage the release of non-point source nitrogen (N) by stimulating microbial denitrification. Woodchips serve as a renewable organic carbon (C) source, yet the recalcitrance of organic C in lignocellulosic biomass causes many WBRs to be C-limited. Prior studies have observed that oxic-anoxic cycling increased the mobilization of organic C, increased nitrate (NO 3 - ) removal rates, and attenuated production of nitrous oxide (N 2 O). Here, we use multi-omics approaches and amplicon sequencing of fungal 5.8S-ITS2 and prokaryotic 16S rRNA genes to elucidate the microbial drivers for enhanced NO 3 - removal and attenuated N 2 O production under redox-dynamic conditions. Transient oxic periods stimulated the expression of fungal ligninolytic enzymes, increasing the bioavailability of woodchip-derived C and stimulating the expression of denitrification genes. Nitrous oxide reductase (nosZ) genes were primarily clade II, and the ratio of clade II/clade I nosZ transcripts during the oxic-anoxic transition was strongly correlated with the N 2 O yield. Analysis of metagenome-assembled genomes revealed that many of the denitrifying microorganisms also have a genotypic ability to degrade complex polysaccharides like cellulose and hemicellulose, highlighting the adaptation of the WBR microbiome to the ecophysiological niche of the woodchip matrix., (© 2023 Applied Microbiology International and John Wiley & Sons Ltd.)

Wood compounds, especially sterols, are connected with the level of contamination with microscopic fungi. Within this study, tests were conducted on wood dust samples collected at various work stations in a pine and birch timber conversion plant. Their contamination with mycobiota was measured as the concentration of ergosterol (ERG) by ultra performance liquid chromatography (UPLC). Another aim of this study was to assess the effect of contamination with microscopic fungi on the sterol contents in wood dusts. Analyses were conducted on five sterols: desmosterol, cholesterol, lanosterol, stigmasterol, and β-sitosterol using UPLC and their presence was confirmed using gas chromatography/mass spectrometry (GC/MS). The results of chemical analyses showed the greatest contamination with mycobiota in birch wood dust. We also observed varied contents of individual sterols depending on the wood dust type. Their highest concentration was detected in birch dust. The discriminant analysis covering all tested compounds as predictors showed complete separation of all tested wood dust types. The greatest discriminatory power was found for stigmasterol, desmosterol, and ergosterol. [ABSTRACT FROM AUTHOR]