Antagonistic fungal interactions influence carbon dioxide evolution from decomposing wood

Fungal species vary in the rate and way in which they decay wood. Thus, understanding fungal community dynamics within dead wood is crucial to understanding decomposition and carbon cycling. Mycelia compete for wood territory, by employing antagonistic mechanisms involving changes in morphology, and production of volatile and diffusible chemicals. This is metabolically costly, and may affect the rate of use of the resource. The metabolic rate during pairwise interactions between wood decay ascomycetes and basidiomycetes was determined by measuring CO₂ production. CO₂ evolution altered over time, but changes were combination-specific. In only two combinations – when the dominant competitor overgrew the opponent's territory as mycelia cords – did CO₂ evolution increase over the course of the whole interaction. In most interactions, CO₂ evolution increased only after complete replacement of one competitor, suggesting utilisation of the predecessor mycelium or differences in decay ability due to alteration of the resource by the predecessor. There was no relationship between rate of CO₂ evolution and combative ability nor outcome of interaction.     

Fungal succession and decomposition of <Emphasis Type="Italic">Camellia japonica</Emphasis> leaf litter

Decomposition processes of Camellia japonica leaf litter were investigated over an 18-month period with reference to the role of fungal succession in the decomposition of lignin and holocellulose. Decomposition and fungal succession were studied in bleached and nonbleached portions of litter, which were precolonized by ligninolytic and cellulolytic fungi, respectively. Coccomyces nipponicum and Lophodermium sp. (Rhytismataceae), which can attack lignin selectively, caused mass loss of lignin and were responsible for bleaching during the first 4 months (stage I), whereas cellulolytic fungi caused mass loss of holocellulose in adjacent nonbleached portions. Soluble carbohydrates and polyphenols also decreased rapidly during this stage. Pestalotiopsis guepini, coelomycete sp.1, and the Nigrospora state of Khuskia oryzae caused mass loss of holocellulose between 4 and 14 months (stage II) and Xylaria sp. caused mass loss of both lignin and holocellulose from 14–18 months (stage III). In stages II and III, decomposition was more rapid in bleached portions than in nonbleached portions probably due to the prior delignification of lignified holocellulose in bleached portions. Frequencies of these fungi showed different responses among species to the pattern of changes in lignin and holocellulose contents during decomposition. Total hyphal length increased in both portions over the study period, but mycelia of basidiomycetes accounted for about 2% of total hyphal length, suggesting that their role in fungal succession and decomposition was low. Lignin and nitrogen contents were consistently lower and holocellulose content was higher in bleached portions than in nonbleached portions during decomposition. The succession of ligninolytic and cellulolytic fungi was a major driving factor that promoted decomposition and precolonization by ligninolytic fungi enhanced decomposition.     

Impact of Norway spruce pre-degradation stages induced by Gloeophyllum trabeum on fungal and bacterial communities

In forest ecosystems, fungi are the key actors in wood decay. They have the capability to degrade lignified substrates and the woody biomass of coniferous forests, with brown rot fungi being common colonizers. Brown rots are typically involved in the earliest phase of lignocellulose breakdown, which therefore influences colonization by other microorganisms. However, few studies have focused on the impact of introducing decayed wood into forest environments to gauge successional colonization by natural bacterial and fungal communities following partial decay. This study aimed to address this issue by investigating the bacterial and fungal colonization of Norway spruce (Picea abies) wood, after intermediate and advanced laboratory-based, pre-decay, by the brown rot fungus Gloeophyllum trabeum. Using Illumina metabarcoding, the in situ colonization of the wood blocks was monitored 70 days after the blocks were placed on the forest floor and covered with litter. We observed significant changes in the bacterial and fungal communities associated with the pre-decayed stage. Further, the wood substrate condition acted as a gatekeeper by reducing richness for both microbial communities and diversity of fungal communities. Our data also suggest that the growth of some fungal and bacterial species was driven by similar environmental conditions.     

Initial decay of woody fragments in soil is influenced by size, vertical position, nitrogen availability and soil origin

Fast-growing bacteria and fungi are expected to cause the initial stage of decomposition of woody fragments in and on soils, i.e. the respiration of sugars, organic acids, pectin and easily accessible cellulose and hemi-cellulose. However, little is known about the factors regulating initial wood decomposition. We examined the effect of wood fragment size, vertical position, nitrogen addition and soil origin on initial wood decay and on the relative importance of fungi and bacteria therein. Two fractions of birch wood were used in microcosm experiments, namely wood blocks (dimensions: 3 × 0.5 × 0.5 cm) and sawdust (dimensions: 0.5–2 mm). The woody fragments were enclosed in nylon bags and placed on top of- or buried in an abandoned arable soil and in a heathland soil. After 15, 25 and 40 weeks of incubation, fungal biomass was quantified (as ergosterol and chitin content) and bacterial numbers were determined. The results indicated that initial wood decay was mostly caused by fungi; bacteria were only contributing in sawdust in/on abandoned arable soil. Larger fragment size, burial of fragments and nitrogen addition positively influenced fungal biomass and activity. Fungal biomass and decay activities were much lower in woody fragments incubated in/on heathland soil than in those incubated in/on abandoned arable soil, indicating that soil origin is also an important factor determining initial wood decay.     

Phyllosphere fungi on living and decomposing leaves of giant dogwood

Phyllosphere fungi on living leaves and their succession on decomposing leaves were studied on giant dogwood (Swida controversa). A total of 12 and 34 fungal species were isolated from the interior and surface, respectively, of living leaves, and 15 frequent species were considered as phyllosphere fungi. Six of these 15 species were also frequent on decomposing litter. Characteristic successional trends were observed in the 6 phyllosphere fungi during decomposition. The sum of frequencies of endophytes decreased as decomposition progressed, and no endophytes were isolated from the litter at the 11th month of decomposition. The sum of frequencies of epiphytes increased as decomposition progressed. Endophytes and epiphytes showed different responses to litter mass loss and concentrations of nitrogen, lignin, and total carbohydrates during the decomposition process. These results suggested that epiphytes may survive on decomposing leaves as primary decomposers on the ground, thereby excluding endophytes by competition for available energy sources, and that epiphytes may have a greater contribution to decomposition than endophytes in dogwood leaves.     

Initial fungal colonizer affects mass loss and fungal community development in Picea abies logs 6 yr after inoculation

Picea abies logs were inoculated with Resinicium bicolor, Fomitopsis pinicola or left un-inoculated and placed in an old-growth boreal forest. Mass loss and fungal community data were collected after 6 yr to test whether simplification of the fungal community via inoculation affects mass loss and fungal community development. Three techniques were used to survey communities: (1) observation of fruiting structures; (2) culturing on media; and (3) cloning and sequencing of ITS rDNA. Fruit body surveys detected the smallest number of species (18, 3.8 per log), DNA-based methods detected the most species (72, 31.7 per log), and culturing detected an intermediate number (23, 7.2 per log). Initial colonizer affected community development and inoculation with F. pinicola led to significantly greater mass loss. Relationships among fungal community composition, community richness and mass loss are complex and further work is needed to determine whether simplification of fungal communities affects carbon sequestration in forests.     

Fungal wood decomposer activities influence community structures of myxomycetes and bryophytes on coarse woody debris

Dead wood is an important habitat for forest organisms, and wood decay fungi are the principal agents determining the dead wood properties that influence the communities of organisms inhabiting dead wood. In this study, we investigated the effects of wood decomposer fungi on the communities of myxomycetes and bryophytes inhabiting decayed logs. On 196 pine logs, 72 species of fungi, 34 species and seven varieties of myxomycetes, and 16 species of bryophytes were identified. Although white rot was the dominant decay type in sapwood and heartwood, brown and soft rots were also prevalent, particularly in sapwood. Moreover, white rot and soft rot were positively and brown rot negatively correlated with wood pH. Ordination analyses clearly showed a succession of cryptogam species during log decomposition and showed significant correlations of communities with the pH, water content, and decay type of wood. These analyses indicate that fungal wood decomposer activities strongly influence the cryptogam communities on dead wood.     

Fungal resistance of rubber wood modified by fatty acid chlorides

Decay resistance of Rubber wood (Hevea brasiliensis) esterified with three fatty acid chlorides (hexanoyl chloride (C6), decanoyl chloride (C10) and tetra-decanoyl chloride (C14)) was evaluated. Unmodified and modified wood samples were exposed to a brown rot (Polyporus meliae) and a white rot (Coriolus versicolor) fungus for 12 weeks. Unmodified rubber wood was severely decayed by P. meliae and C. versicolor, which was indicated by significant weight loss. The rate of decay by brown rot was higher than white rot. Modified wood samples exhibited very good resistant to brown and white-rot fungi. The degree of protection increased with increase in degree of modification. P. meliae, a brown rot fungus, removed structural carbohydrate component in unmodified wood selectively whereas, C. vesicolor showed preference to lignin. The FTIR spectra of modified wood exposed to fungi show no significant changes in relative peak intensities of lignin/carbohydrates indicating effectiveness of chemically modified wood in restricting chemical degradation. Chemical modification occurred more efficiently at carbohydrate portion of the wood. Therefore, it is more effective in retarding decay due to P. meliae.     

Inflammatory thresholds and the species-specific effects of colonising bacteria in stable chronic obstructive pulmonary disease

Background

There has been increasing interest in the use of newer, culture-independent techniques to study the airway microbiome of COPD patients. We investigated the relationships between the three common potentially pathogenic microorganisms (PPMs) Haemophilus influenzae, Streptococcus pneumoniae and Moraxella catarrhalis, as detected by quantitative PCR (qPCR), and inflammation and health status in stable patients in the London COPD cohort.

Methods

We prospectively collected sputum, serum and plasma samples for analysis of airway bacterial presence and load, and airway and systemic inflammation from 99 stable COPD patients between January 2011 and October 2012. Health status was measured with St George’s Respiratory Questionnaire and COPD Assessment Test.

Results

Airway inflammation and plasma fibrinogen, but not C-reactive protein, were greater in samples with PPM detection (p < 0.001, p = 0.049 and p = 0.261, respectively). Increasing total bacterial load was associated with increasing airway (p < 0.01) but not systemic inflammation (p > 0.05). Samples with high total bacterial loads had significantly higher airway inflammation than both samples without PPM detection and those with lower loads. Haemophilus influenzae presence was associated with significantly higher levels of airway but not systemic inflammation for all given pathogen loads (p < 0.05), and was significantly greater than with other PPMs. No association was observed between inflammation and health status (p > 0.05).

Conclusions

Airway and systemic inflammation, as measured by fibrinogen, is greater in stable COPD patients with PPMs detected using the culture-independent qPCR technique. The airway, but not systemic inflammatory response, appears to have a total pathogen-load threshold and appears attributable to Haemophilus influenzae. However, discordance between inflammation and health status was observed.

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-014-0114-1) contains supplementary material, which is available to authorized users.     

Fungal control of nitrous oxide production in semiarid grassland

Fungi are capable of both nitrification and denitrification and dominate the microbial biomass in many soils. Recent work suggests that fungal rather than bacterial pathways dominate N transformation in desert soils. We evaluated this hypothesis by comparing the contributions of bacteria and fungi to N₂O production at control and N fertilized sites within a semiarid grassland in central New Mexico (USA). Soil samples were taken from the rhizosphere of blue grama (B. gracilus) and the microbiotic crusts that grow in open areas between the bunch grasses. Soils incubated at 30% or 70% water holding capacity, were exposed to one of three biocide treatments (control, cycloheximide or streptomycin). After 48 h, N₂O and CO₂ production were quantified along with the activities of several extracellular enzymes. N₂O production from N fertilized soils was higher than that of control soils (165 vs. 41 pmol h⁻¹ g⁻¹), was higher for crust soil than for rhizosphere soil (108 vs. 97 pmol h⁻¹ g⁻¹), and increased with soil water content (146 vs. 60 pmol h⁻¹ g⁻¹). On average, fungicide (cycloheximide) addition reduced N₂O production by 85% while increasing CO₂ production by 69%; bactericide (streptomycin) reduced N₂O by 53% with mixed effects on CO₂ production. N₂O production was significantly correlated with C and N mineralization potential as measured by assays for glycosidic and proteolytic enzymes, and with extractable nitrate and ammonium. Our data indicate that fungal nitrifier denitrification and bacterial autotrophic nitrification dominate N transformation in this ecosystem and that N₂O production is highly sensitive to soil cover, N deposition and moisture.     

A quantitative study of the morphological development and bacterial colonisation of the gut of the tammar wallaby Macropus eugenii eugenii and brushtail possum Trichosurus vulpecula during in-pouch development

We compared the rates of change of various morphological parameters of the stomach, small intestine, caecum and colon of tammar wallabies and brushtail possums with body mass during in-pouch development. These were correlated with changes in the numbers of bacterial species in the various gut segments. In the pouch-young of both species, the wet tissue masses of all gut segments increased with body mass in a positively allometric manner (i.e. with a body mass exponent > 1), suggesting that the mass of each component was disproportionately low at birth, but increased disproportionately rapidly postnatally. However, the lengths of the wallaby stomach and small intestine scaled isometrically with respect to body mass (i.e. with a body mass exponent around 0.33), which may indicate that the shape of these components changes to the adult form during early neonatal development. Conversely, the length of the caecum and colon of both wallabies and possums scaled in a positively allometric manner with respect to body mass, showing area to volume compensation. This may indicate a more general pattern of disproportionately rapid postnatal enlargement in areas that are distal to the principal sites of neonatal digestion (i.e. the stomach). The numbers of bacterial species present in the various gastrointestinal segments of both species were low in animals aged 100 days or less but there was a significant increase in microbial diversity in the caecum of brushtail possums aged over 100 days. The possum caecum also showed the greatest rate of increase in wet tissue mass relative to body mass. It is postulated that caecal development may act as a nidus for establishment of communities of commensal microflora in the developing marsupial.     

Fungal diversity and deterioration in mummified woods from the ad Astra Ice Cap region in the Canadian High Arctic

Non-permineralized or mummified ancient wood found within proglacial soil near the ad Astra Ice Cap (81°N, 76°W), Ellesmere Island, Canada was investigated to ascertain the identification of the trees, current morphological and chemical characteristics of the woods and the fungi within them. These woods, identified as Betula, Larix, Picea and Pinus, were found with varying states of physical and chemical degradation. Modern microbial decomposition caused by soft rot fungi was evident and rDNA sequencing of fungi obtained from the samples revealed several species including Cadophora sp., Exophiala sp., Phialocephala sp., as well as others. Analytical ¹³C-labeled tetramethylammonium hydroxide thermochemolysis showed the lignin from the ancient wood was in a high degree of preservation with minor side chain alteration and little to no demethylation or ring hydroxylation. The exposure of these ancient woods to the young soils, where woody debris is not usually prevalent, provides carbon and nutrients into the polar environment that are captured and utilized by unique decay fungi at this Arctic site.     

Secondary metabolites and nutrients explain fungal community composition in aspen wood

Fungi are the main decomposers of litter and wood, driving carbon and nutrient cycles. Despite a large number of studies, fungal community composition is remarkably difficult to predict. In the present study, we explore the importance of secondary metabolites and nutrient content in wood and bark as determinants of fungal community composition. We used aspen (Populus tremula) logs of similar size, from one location, and measured concentrations of carbon, nitrogen and secondary metabolites in bark and wood sampled shortly after felling. Fungal DNA was extracted from logs directly after felling and after two seasons of decomposition, and the fungal communities were assessed using DNA-metabarcoding. Concentrations of metabolites varied considerably between individual trees, and we also observed significant differences within single trees. Plant metabolites and nitrogen concentrations significantly affected fungal community composition. For the overall fungal communities and for wood saprotrophic fungi, the explanatory power of wood and bark metabolites was highest in logs decomposed over two seasons. In recently felled trees however, concentration of metabolites had a stronger effect on plant pathogens and endophytes. We conclude that secondary metabolites represent an overlooked, but important niche dimension for fungal communities in both functional sapwood and dead wood.     

Recovery and succession in a multi-species tropical seagrass meadow following experimental disturbance: the role of sexual and asexual reproduction

Recolonisation and succession in a multi-species tropical seagrass meadow was examined by creating gaps (50×50 cm) in the meadow and manipulating the supply of sexual and asexual propagules. Measurements of leaf shoot density and estimates of above-ground biomass were conducted monthly to measure recovery of gaps between September 1995 and November 1997. Measurements of the seeds stored in the sediment (seed bank) and horizontal rhizome growth of colonising species were also conducted to determine their role in the recovery process.Asexual colonisation through horizontal rhizome growth from the surrounding meadow was the main mechanism for colonisation of gaps created in the meadow. The seed bank played no role in recolonisation of cleared plots. Total shoot density and above-ground biomass (all species pooled) of cleared plots recovered asexually to the level of the undisturbed controls in 10 and 7 months, respectively. There was some sexual recruitment into cleared plots where asexual colonisation was prevented but seagrass abundance (shoot density and biomass) did not reach the level of unmanipulated controls. Seagrass species did not appear to form seed banks despite some species being capable of producing long-lived seeds.The species composition of cleared plots remained different to the undisturbed controls throughout the 26-month experiment. Syringodium isoetifolium was a rapid asexual coloniser of disturbed plots and remained at higher abundances than in the control treatments for the duration of the study. S. isoetifolium had the fastest horizontal rhizome growth of species asexually colonising cleared plots (6.9 mm day⁻¹). Halophila ovalis was the most successful sexual coloniser but was displaced by asexually colonising species. H. ovalis was the only species observed to produce fruits during the study.Small disturbances in the meadow led to long-term (>2 years) changes in community composition. This study demonstrated that succession in tropical seagrass communities was not a deterministic process. Variations in recovery observed for different tropical seagrass communities highlighted the importance of understanding life history characteristics of species within individual communities to effectively predict their response to disturbance. A reproductive strategy involving clonal growth and production of long-lived, locally dispersed seeds is suggested which may provide an evolutionary advantage to plants growing in tropical environments subject to temporally unpredictable major disturbances such as cyclones.     

Evaluation of mold,decay and termite resistance of pine wood treated with zinc- and copper-based nanocompounds

In this work, the resistance of black pine wood (Pinus nigra L.) vacuum-treated with zinc oxide, zinc borate and copper oxide nanoparticles against mold and decay fungi and the subterranean termites was evaluated. Some of the nanocompounds tested were forced with acrylic emulsions to avoid leaching. Results showed that mold fungi were slightly inhibited by nanozinc borate, while the other nanometal preparations did not inhibit mold fungi. Mass loss from fungal attack by Trametes versicolor was significantly inhibited by the zinc-based preparations, while the brown-rot fungus, Tyromyces palustris was not inhibited by the nanometal treatments. Notably, nanozinc borate plus acrylic emulsion imparted very high resistance in pine wood to the white-rot fungus, T. versicolor with a mass loss of 1.8%. Following leaching, all pine specimens treated with nanozinc borate, with or without acrylic emulsion, strongly inhibited termite feeding, i.e. mass losses varying at 5.2–5.4%. In contrast, the copper-based treatments were much less effective against the subterranean termites, Coptotermes formosanus. In general, nanozinc borate possessed favorable properties, that is, inhibition of termite feeding and decay by T. versicolor.     

Carbon and nitrogen acquisition strategies by wood decay fungi influence their isotopic signatures in Picea abies forests

We examined whether sporocarp carbon and nitrogen isotope ratios (δ¹³C and δ¹⁵N values) reflected different functional strategies in 15 species of wood decay fungi. In Finnish Picea abies forests, we compared sporocarp δ¹³C and δ¹⁵N against log diameter, proximity to ground, and three wood decay types, specifically brown rot, nonselective white rot, and selective white rot (targeting hemicellulose and lignin preferentially). In regression analysis (adjusted r² = 0.576), species accounted for 31% of variability in δ¹³C, with factors influencing wood δ¹³C accounting for the remainder. Brown rot fungi and three white rot fungi that selectively attacked hemicellulose (Heterobasidion parviporum, Phellopilus nigrolimitatus, and Trichaptum abietinum) were higher in δ¹³C than nonselective white rot fungi. This was attributed to greater assimilation of ¹³C-enriched pentoses from hemicellulose by these fungi. The pathogenic white rot fungus Heterobasidion parviporum had higher δ¹⁵N with proximity to ground and increasing log diameter. This suggested that ¹⁵N-enriched soil N contributed to decomposing logs and that Heterobasidion growing from a bigger resource base had increased access to soil N. These isotopic patterns accordingly reflected both functional diversity of wood decay fungi and site-specific factors.     

Proteome analysis of fungal and bacterial involvement in leaf litter decomposition

Fungi and bacteria are key players in the decomposition of leaf litter, but their individual contributions to the process and their interactions are still poorly known. We combined semi‐quantitative proteome analyses (1‐D PAGE‐LC‐MS/MS) with qualitative and quantitative analyses of extracellular degradative enzyme activities to unravel the respective roles of a fungus and a bacterium during litter decomposition. Two model organisms, a mesophilic Gram‐negative bacterium (Pectobacterium carotovorum) and an ascomycete (Aspergillus nidulans), were grown in both, pure culture and co‐culture on minimal medium containing either glucose or beech leaf litter as sole carbon source. P. carotovorum grew best in co‐culture with the fungus, whereas growth of A. nidulans was significantly reduced when the bacterium was present. This observation suggests that P. carotovorum has only limited capabilities to degrade leaf litter and profits from the degradation products of A. nidulans at the expense of fungal growth. In accordance with this interpretation, our proteome analysis revealed that most of the extracellular biodegradative enzymes (i.e. proteases, pectinases, and cellulases) in the cultures with beech litter were expressed by the fungus, the bacterium producing only low levels of pectinases.