Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 868
Filter
Add more filters

Publication year range
1.
Nature ; 631(8022): 796-800, 2024 Jul.
Article in English | MEDLINE | ID: mdl-39048683

ABSTRACT

Methane is an important greenhouse gas1, but the role of trees in the methane budget remains uncertain2. Although it has been shown that wetland and some upland trees can emit soil-derived methane at the stem base3,4, it has also been suggested that upland trees can serve as a net sink for atmospheric methane5,6. 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.


Subject(s)
Atmosphere , Forests , Methane , Trees , Wood , Atmosphere/chemistry , Methane/metabolism , Methane/analysis , Taiga , Trees/chemistry , Trees/metabolism , Trees/microbiology , Tropical Climate , Wood/chemistry , Wood/metabolism , Wood/microbiology , Greenhouse Gases/analysis , Greenhouse Gases/metabolism , Carbon Isotopes , Forestry , Global Warming/prevention & control , Global Warming/statistics & numerical data , Greenhouse Effect/prevention & control , Greenhouse Effect/statistics & numerical data
2.
EMBO Rep ; 24(5): e57255, 2023 05 04.
Article in English | MEDLINE | ID: mdl-37017146

ABSTRACT

The observation that soil-dwelling fungi seem to exchange information via electrical impulses has raised new interest about their interactions with plants and their ecological significance.


Subject(s)
Fungi , Wood , Wood/microbiology , Fungi/genetics , Plants , Soil
3.
Yeast ; 41(7): 437-447, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38850070

ABSTRACT

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.


Subject(s)
Coleoptera , Phylogeny , Rainforest , Saccharomycetales , Wood , Xylose , Animals , Wood/microbiology , Coleoptera/microbiology , Brazil , Saccharomycetales/genetics , Saccharomycetales/classification , Saccharomycetales/isolation & purification , Saccharomycetales/metabolism , Xylose/metabolism , Fermentation , DNA, Fungal/genetics , Sequence Analysis, DNA
4.
Appl Environ Microbiol ; 90(7): e0048224, 2024 Jul 24.
Article in English | MEDLINE | ID: mdl-38832775

ABSTRACT

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.


Subject(s)
Machine Learning , Wood , Wood/microbiology , Algorithms , Fungal Proteins/genetics , Fungal Proteins/metabolism , Lignin/metabolism , Carbohydrate Metabolism , Fungi/genetics , Fungi/enzymology , Fungi/classification , Cellulose/metabolism , Random Forest
5.
Appl Environ Microbiol ; 90(3): e0193123, 2024 Mar 20.
Article in English | MEDLINE | ID: mdl-38376171

ABSTRACT

White-rot fungi employ secreted carbohydrate-active enzymes (CAZymes) along with reactive oxygen species (ROS), like hydrogen peroxide (H2O2), to degrade lignocellulose in wood. H2O2 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 (MetO2) 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 H218O2 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 (H2O2) on secreted proteins remains unclear. This study aims at evaluating the effect of H2O2 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 H2O2. 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.


Subject(s)
Basidiomycota , Hydrogen Peroxide , Polyporaceae , Catalase/metabolism , Hydrogen Peroxide/metabolism , Wood/microbiology , Reactive Oxygen Species/metabolism , Fungal Proteins/metabolism , Lignin/metabolism , Basidiomycota/metabolism , Oxidation-Reduction , Cellulose 1,4-beta-Cellobiosidase/metabolism , Carbohydrates , Methionine/metabolism , Sulfones/metabolism
6.
BMC Microbiol ; 24(1): 282, 2024 Jul 30.
Article in English | MEDLINE | ID: mdl-39080520

ABSTRACT

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.


Subject(s)
Coleoptera , Gastrointestinal Microbiome , Lactococcus lactis , Larva , Symbiosis , Animals , Lactococcus lactis/genetics , Coleoptera/microbiology , Larva/microbiology , Wood/microbiology , RNA, Ribosomal, 16S/genetics , Phylogeny , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification
7.
New Phytol ; 242(6): 2775-2786, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38567688

ABSTRACT

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 (R2 = 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 (R2 = 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.


Subject(s)
Ecosystem , Tracheophyta , Tracheophyta/microbiology , Fungi/physiology , Wood/microbiology , Species Specificity , Lignin/metabolism , Geography , Trees/microbiology
8.
Glob Chang Biol ; 30(3): e17212, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38450825

ABSTRACT

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.


Subject(s)
Fungi , Temperature , Wood , Climate Change , Fungi/physiology , Microbiota , Soil , Wood/microbiology
9.
Article in English | MEDLINE | ID: mdl-38415711

ABSTRACT

A yeast strain (CGMCC 2.6937T) 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 2.6937T group is most closely related to Saturnispora dispora and Saturnispora zaruensis. However, strain CGMCC 2.6937T 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 2.6937T group represents an undescribed species in the genus Saturnispora, for which the name Saturnispora sinensis sp. nov. is proposed. The holotype strain is CGMCC 2.6937T.


Subject(s)
Ascomycota , Phylogeny , Soil Microbiology , Wood , Ascomycota/classification , Ascomycota/genetics , Base Composition , Sequence Analysis, DNA , Wood/microbiology , Mycological Typing Techniques
10.
Microb Ecol ; 87(1): 66, 2024 May 03.
Article in English | MEDLINE | ID: mdl-38700528

ABSTRACT

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.


Subject(s)
Forests , Fungi , Mycobiome , Wood , Wood/microbiology , Fungi/genetics , Fungi/classification , Fungi/isolation & purification , Tropical Climate , Phylogeny , High-Throughput Nucleotide Sequencing , Biodiversity
11.
Antonie Van Leeuwenhoek ; 117(1): 22, 2024 Jan 13.
Article in English | MEDLINE | ID: mdl-38217778

ABSTRACT

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.


Subject(s)
Saccharomycetales , Phylogeny , Netherlands , Yeasts , DNA, Fungal , Sequence Analysis, DNA , Mycological Typing Techniques , Wood/microbiology
12.
Antonie Van Leeuwenhoek ; 117(1): 107, 2024 Jul 26.
Article in English | MEDLINE | ID: mdl-39060562

ABSTRACT

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 107 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 105 and 104 copies g-1 dry wood. The enumeration by the most probable number method demonstrated the inhabitation of viable methanogenic archaea inside the trees; 106 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.


Subject(s)
Forests , Methane , Phylogeny , RNA, Ribosomal, 16S , RNA, Ribosomal, 16S/genetics , Methane/metabolism , Trees/microbiology , Archaea/classification , Archaea/genetics , Archaea/metabolism , Archaea/isolation & purification , Wood/microbiology , DNA, Archaeal/genetics
13.
Food Microbiol ; 123: 104586, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39038892

ABSTRACT

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/cm2) versus untreated wood (3.72 ± 0.67 log CFU/cm2). 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/cm2 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.


Subject(s)
Bacterial Adhesion , Hydrophobic and Hydrophilic Interactions , Listeria monocytogenes , Salmonella enterica , Silanes , Wood , Wood/microbiology , Wood/chemistry , Listeria monocytogenes/drug effects , Listeria monocytogenes/growth & development , Listeria monocytogenes/physiology , Bacterial Adhesion/drug effects , Salmonella enterica/drug effects , Salmonella enterica/growth & development , Humans , Silanes/pharmacology , Silanes/chemistry , Food Microbiology , Food Contamination/prevention & control , Food Contamination/analysis , Food Packaging/methods , Colony Count, Microbial , Quercus/microbiology , Quercus/chemistry , Pinus/microbiology
14.
World J Microbiol Biotechnol ; 40(7): 207, 2024 May 20.
Article in English | MEDLINE | ID: mdl-38767733

ABSTRACT

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.


Subject(s)
Cellulose , Fungi , Lignin , Wood , Lignin/metabolism , Fungi/metabolism , Wood/microbiology , Cellulose/metabolism , Biotechnology/methods
15.
Environ Microbiol ; 25(11): 2351-2367, 2023 11.
Article in English | MEDLINE | ID: mdl-37403552

ABSTRACT

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.


Subject(s)
Fungi , Microbiota , Fungi/genetics , Forests , Wood/microbiology , Microbiota/genetics , Bacteria/genetics , Cellulose
16.
Environ Microbiol ; 25(9): 1696-1712, 2023 09.
Article in English | MEDLINE | ID: mdl-37105180

ABSTRACT

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 (NO3 - ) removal rates, and attenuated production of nitrous oxide (N2 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 NO3 - removal and attenuated N2 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 N2 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.


Subject(s)
Bacteria , Fungi , Wood , Bioreactors , Wood/microbiology , Carbon , Denitrification , Oxidation-Reduction , Fungi/classification , Fungi/genetics , Fungi/isolation & purification , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification , Archaea/classification , Archaea/genetics , Archaea/isolation & purification
17.
Appl Environ Microbiol ; 89(12): e0140623, 2023 12 21.
Article in English | MEDLINE | ID: mdl-38014962

ABSTRACT

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.


Subject(s)
Ascomycota , Basidiomycota , Microbiota , Wood/microbiology , Forests
18.
Arch Microbiol ; 205(5): 194, 2023 Apr 15.
Article in English | MEDLINE | ID: mdl-37061655

ABSTRACT

In esca disease affecting grapevines, Phaeomoniella chlamydospora and Phaeoacremonium minimum colonize the woody parts of the trunks and arms, where they obtain nutrition from xylem sap and, potentially, from residues resulting from the enzymatic breakdown of lignified cell walls, particularly osidic residues. We quantified the secretion of lignin peroxidase, manganese peroxidase and laccase by these fungi in woody tissues of selectively infected cuttings using immunolabeling and transmission electron microscopy. Our results indicated that the detection of these enzymes was generally higher in tissues infected with Phaeoacremonium minimum. These data were confirmed through immunodetection of enzymes secreted by hyphae of fungi grown in vitro. Additionally, we observed that the supply of various carbohydrates (mono, di, tri and tetrasaccharides and polymers) differentially influenced fungal growth and polypeptide secretion. Since some secreted polypeptides display detrimental effects on grapevine cells, these results raise the question of whether the carbohydrate environment could be a factor affecting the aggressiveness of these pathogens.


Subject(s)
Vitis , Wood , Wood/microbiology , Plant Diseases/microbiology , Vitis/microbiology , Carbohydrates
19.
J Anim Ecol ; 92(5): 965-978, 2023 05.
Article in English | MEDLINE | ID: mdl-36377902

ABSTRACT

The patterns of successional change of decomposer communities is unique in that resource availability predictably decreases as decomposition proceeds. Saproxylic (i.e. deadwood-dependent) beetles are a highly diverse and functionally important decomposer group, and their community composition is affected by both deadwood characteristics and other environmental factors. Understanding how communities change with faunal succession through the decomposition process is important as this process influences terrestrial carbon dynamics. Here, we evaluate how beta-diversity of saproxylic beetle communities change with succession, as well as the effects of different major drivers of beta-diversity, such as deadwood tree species, spatial distance between locations, climate and forest structure. We studied spatial beta-diversity (i.e. dissimilarity of species composition between deadwood logs in the same year) of saproxylic beetle communities over 8 years of wood decomposition. Our study included 379 experimental deadwood logs comprising 13 different tree species in 30 forest stands in Germany. We hypothesized that the effects of tree species dissimilarity, measured by phylogenetic distance, and climate on beta-diversity decrease over time, while the effects of spatial distance between logs and forest structure increase. Observed beta-diversity of saproxylic beetle communities increased over time, whereas standardized effects sizes (SES; based on null models) of beta-diversity decreased indicating higher beta-diversity than expected during early years. Beta-diversity increased with increasing phylogenetic distance between tree species and spatial distance among regions, and to a lesser extent with spatial distance within regions and differences in climate and forest structure. Whereas effects of space, climate and forest structure were constant over time, the effect of phylogenetic distance decreased. Our results show that the strength of the different drivers of saproxylic beetle community beta-diversity changes along deadwood succession. Beta-diversity of early decay communities was strongly associated with differences among tree species. Although this effect decreased over time, beta-diversity remained high throughout succession. Possible explanations for this pattern include differences in decomposition rates and fungal communities between logs or the priority effect of early successional communities. Our results suggest that saproxylic beetle diversity can be enhanced by promoting forests with diverse tree communities and structures.


Subject(s)
Coleoptera , Wood , Animals , Wood/chemistry , Wood/microbiology , Phylogeny , Forests , Climate
20.
Microb Ecol ; 86(3): 2109-2119, 2023 Oct.
Article in English | MEDLINE | ID: mdl-37099155

ABSTRACT

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.


Subject(s)
Cellulose , Microbiota , Humans , Cellulose/metabolism , Rivers , Microbiota/genetics , Fungi/genetics , Bacteria/genetics , Wood/microbiology
SELECTION OF CITATIONS
SEARCH DETAIL