Fungal Decomposers Research Articles

Comparing lignocellulose physiochemistry after decomposition by brown rot fungi with distinct evolutionary origins.

Among wood-degrading fungi, lineages holding taxa that selectively metabolize carbohydrates without significant lignin removal (brown rot) are polyphyletic, having evolved multiple times from lignin-removing white rot fungi. Given the qualitative nature of the 'brown rot' classifier, we aimed to quantify and compare the temporal sequence of carbohydrate removal among brown rot clades. Lignocellulose deconstruction was compared among fungi using distinct plant substrates (angiosperm, conifer, grass). Specifically, aspen, pine and corn stalk were harvested over a 16-week time series from microcosms containing Gloeophyllum trabeum, Fomitopsis pinicola, Ossicaulis lignatilis, Fistulina hepatica, Serpula lacrymans, Wolfiporia cocos or Dacryopinax sp. After quantifying plant mass loss, a thorough compositional analysis was complemented by a saccharification test to determine wood cell wall accessibility. Mass loss and accessibility varied depending on fungal decomposer and substrate, and trajectories of loss for hemicellulosic components and cellulose differed among plant tissue types. At any given stage of decomposition, however, lignocellulose accessibility and the fraction remaining of carbohydrates and lignin within a plant tissue type were generally the same, regardless of fungal isolate. This suggests that the sequence of plant component removal at this typical scale of characterization is shared among these brown rot lineages, despite their diverse genomes and secretomes.

Elevated temperature may intensify the positive effects of nutrients on microbial decomposition in streams

Summary Climate change scenarios predict an increase in global temperature and alterations in precipitation regimes, which may change nutrient concentrations in waterbodies. In forested streams, decomposition of allochthonous organic matter is a key ecosystem process that is affected by the quality of plant litter entering the streams and several environmental factors, including nutrient concentrations, whose interactive effects are difficult to predict. We examined the concomitant effects of increased temperature, concentration of inorganic nutrients in stream water and litter quality on leaf decomposition and activity of microbial decomposers. Leaves of alder (Alnus glutinosa) and oak (Quercus robur), representative of high and low initial N content, respectively, were immersed in a stream (NW Portugal) to allow microbial colonisation and then were exposed in microcosms to increasing concentrations of N‐NO3 (0.09–5 mg L−1; six levels) and P‐PO4 (0.003–0.3 mg L−1; three levels) alone or in all possible combinations. One set of microcosms was kept at 12 °C, a temperature typically found in Iberian streams in autumn, and the other set at 18 °C to simulate a warming scenario. Nitrogen immobilisation was higher in alder than in oak leaves, and increased with temperature and N concentration in stream water for both leaf species. Leaf decomposition, fungal biomass accrual and reproduction were not affected by P concentration, but overall microbial activity increased asymptotically (Michaelis–Menten kinetics) with N concentration. Increased temperature led to an increase in maximum activity of fungal decomposers and to a decrease in N concentration needed to achieve it, especially in alder leaves. Under the predicted warming scenario, leaf decomposition may become faster in streams with lower nutrient levels, especially those receiving high‐quality leaf litter.

The role of endophytic fungal individuals and communities in the decomposition of Pinus massoniana needle litter.

The role of fungal endophytes (FEs) as “pioneer” decomposers has recently been recognized; however, the extent to which FEs contribute to litter loss is less well understood. The genetic and enzymatic bases of FE-mediated decomposition have also rarely been addressed. The effects of populations and individuals (with an emphasis on two dominant Lophodermium taxa) of FEs on needle-litter decomposition were assessed for Pinus massoniana, a ubiquitous pine in southern China. Data from in vivo (microcosm) experiments indicated that the percentage of litter-mass loss triggered by FEs was linearly correlated with incubation time and approached 60% after seven months. In vitro decomposition tests also confirmed that endophytic Lophodermium isolates caused 14–22% mass loss within two months. Qualitative analysis of exoenzymes (cellulase and laccase, important for lignocellulose degradation) revealed that almost all of the Lophodermium isolates showed moderate or strong positive reactions. Furthermore, partial sequences of β-glucosidase (glycoside hydrolase family 3, GH3), laccase, and cellobiohydrolase (GH7) genes were amplified from Lophodermium isolates as “functional markers” to evaluate their potential for lignocellulolytic activity. Three different genes were detected, suggesting a flexible and delicate decomposition system rich in FEs. Our work highlights the possibility that the saprophytism and endophytism of FEs may be prerequisites to initiating rapid decomposition and thus may be key in Fes’ contribution to litter decomposition, at least in the early stage. Potential indicators of the presence of core fungal decomposers are also briefly discussed.

Stream-dwelling fungal decomposer communities along a gradient of eutrophication unraveled by 454 pyrosequencing

Microbial decomposers, especially a fungal group called aquatic hyphomycetes, play a critical role in processing plant litter in freshwaters by increasing its palatability to invertebrate shredders. Traditionally, communities of aquatic hyphomycetes have been assessed through the identification of spores, which misses non-sporulating taxa. Among new technologies, 454 pyrosequencing stands out as most promising for large-scale species identification. However, very few attempts have been made to validate its effectiveness for assessing the diversity of stream-dwelling fungal communities. We attempted to gain greater insight into the diversity of aquatic fungal communities in streams exposed to various degrees of eutrophication by using the 454 pyrosequencing technology. A total of 173,889 ITS2 pyrosequencing reads with hits for fungi were obtained from the 5 investigated streams. The majority of operational taxonomic units (OTUs) belonged to Ascomycota and the identification to the genus level was achieved for 169 OTUs. Of the total, 135,257 reads (ca. 78 %) showed close affinities to aquatic hyphomycete species. Pyrosequencing showed declining fungal diversity in the most eutrophic streams, which was congruent with a reduced diversity found through spore identification. Dominance patterns revealed by connecting representative OTUs to ITS sequences from aquatic hyphomycetes were similar to those determined by traditional spore identification techniques. However, 454 pyrosequencing provided a more comprehensive view of fungal diversity; it captured almost twice as many taxa as spore counts. This study validates the effectiveness of 454 pyrosequencing for surveying the diversity of stream-dwelling fungal decomposer communities. Its application may accelerate the use of these communities for monitoring the integrity of freshwaters.

Stable isotope variation during fungal colonisation of leaf detritus in aquatic environments

Measuring C and N stable isotopes at natural abundance can provide information on the role of fungi associated with litter decay in the nutrient cycle of freshwater ecosystems. However, uncertainty regarding isotopic fractionation by decomposer fungi during uptake or metabolic turnover is a serious limitation, weakening the description of taxon-specific ecological differences in nutrient transfer in aquatic detritus-based systems. We performed two laboratory experiments to assess C and N isotopic changes during leaf litter colonization by: (1) mixed fungal communities on three different leaf litter species, and (2) four different fungal strains growing on the same leaf litter. Our approach served to decouple the isotopic effects of different fungal taxa from those arising from structural changes occurring in leaf litter during decomposition. N isotopic changes were directly related to fungal biomass accrual on litter, whereas carbon isotopic changes were mainly dependent on the remaining lignin fraction. Isotopic mixing model equations enabled us to calculate strain-specific isotopic fractionation, indicating that fungi were enriched in 15N by 3.6–5.9‰ with respect to bulk N litter.

Nitrogen and carbon reallocation in fungal mycelia during decomposition of boreal forest litter.

Boreal forests are characterized by spatially heterogeneous soils with low N availability. The decomposition of coniferous litter in these systems is primarily performed by basidiomycete fungi, which often form large mycelia with a well-developed capacity to reallocate resources spatially- an advantageous trait in heterogeneous environments. In axenic microcosm systems we tested whether fungi increase their biomass production by reallocating N between Pinus sylvestris (Scots pine) needles at different stages of decomposition. We estimated fungal biomass production by analysing the accumulation of the fungal cell wall compound chitin. Monospecific systems were compared with systems with interspecific interactions. We found that the fungi reallocated assimilated N and mycelial growth away from well-degraded litter towards fresh litter components. This redistribution was accompanied by reduced decomposition of older litter. Interconnection of substrates increased over-all fungal C use efficiency (i.e. the allocation of assimilated C to biomass rather than respiration), presumably by enabling fungal translocation of growth-limiting N to litter with higher C quality. Fungal connection between different substrates also restricted N-mineralization and production of dissolved organic N, suggesting that litter saprotrophs in boreal forest ecosystems primarily act to redistribute rather than release N. This spatial integration of different resource qualities was hindered by interspecific interactions, in which litters of contrasting quality were colonised by two different basidiomycete species. The experiments provide a detailed picture of how resource reallocation in two decomposer fungi leads to a more efficient utilisation of spatially separated resources under N-limitation. From an ecosystem point of view, such economic fungal behaviour could potentially contribute to organic matter accumulation in the litter layers of boreal forests.

Priming in the microbial landscape: periphytic algal stimulation of litter-associated microbial decomposers.

Microbial communities associated with submerged detritus in aquatic ecosystems often comprise a diverse mixture of autotrophic and heterotrophic microbes, including algae, bacteria, protozoa, and fungi. Recent studies have documented increased rates of plant litter mass loss when periphytic algae are present. We conducted laboratory and field experiments to assess potential metabolic interactions between natural autotrophic and heterotrophic microbial communities inhabiting submerged decaying plant litter of Typha angustifolia and Schoenoplectus acutus. In the field, submerged plant litter was either exposed to natural sunlight or placed under experimental canopies that manipulated light availability and growth of periphytic algae. Litter was collected and returned to the laboratory, where algal photosynthesis was manipulated (light/dark incubation), while rates of bacterial and fungal growth and productivity were simultaneously quantified. Bacteria and fungi were rapidly stimulated by exposure to light, thus establishing the potential for algal priming of microbial heterotrophic decay activities. Experimental incubations of decaying litter with 14C- and 13C-bicarbonate established that inorganic C fixed by algal photosynthesis was rapidly transferred to and assimilated by heterotrophic microbial decomposers. Periphytic algal stimulation of microbial heterotrophs, especially fungal decomposers, is an important and largely unrecognized interaction within the detrital microbial landscape, which may transform our current conceptual understanding of microbial secondary production and organic matter decomposition in aquatic ecosystems.

Quantitative PCR for measuring biomass of decomposer fungi in planta

The biomass of brown and white rot fungi were estimated using ergosterol and quantitative PCR (qPCR). Each biomass estimate was compared with biomass measured gravimetrically from liquid cultures, as well as from three wood substrata at two decay stages. Fungal morphological changes in two different substrata, agar and pine, were measured using a chitin-specific fluorophore and confocal microscopy. In liquid culture, the two fungal isolates had significantly different biomass conversion factors for both methods. In wood colonized for 3 wks, qPCR yielded a lower estimate than did ergosterol, while at week 8 it yielded a higher estimate. Changes in average fungal cell dimensions partially explained differences between the two methods. Overall, our results suggest that a constant conversion factor cannot be assumed as default for either method. Instead, it demonstrates the importance of standardizing wood species, decay class, fungus-specific conversion factor, and DNA extraction protocol in order to properly estimate fungal biomass in woody substrata.

Interactive effects of aluminium and phosphorus on microbial leaf litter processing in acidified streams: A microcosm approach

Decline in pH, elevated aluminium (Al) concentrations, and base cations depletion often covary in acidified headwater streams. These parameters are considered as the main factors reducing microbial activities involved in detritus processing, but their individual and interactive effects are still unclear. In addition to its direct toxicity, Al can also reduce the bioavailability of phosphorus (P) in ecosystems through the formation of stable chemical complexes. A three week microcosm experiment was carried out in acid conditions to assess the interactive effects of Al (three levels: 0, 200, and 1000 μg L−1) and P (25, 100, and 1000 μg L−1) on alder leaf litter processing by an aquatic hyphomycete consortium. Our results showed that Al alone reduced fungal growth and altered fungal decomposer activities. High P levels, probably through an alleviation of Al-induced P limitation and a reduction of Al toxic forms, suppressed the negative effects of Al on detritus decomposition.

Contrasting Effects of Elevated Temperature and Invertebrate Grazing Regulate Multispecies Interactions between Decomposer Fungi

Predicting the influence of biotic and abiotic factors on species interactions and ecosystem processes is among the primary aims of community ecologists. The composition of saprotrophic fungal communities is a consequence of competitive mycelial interactions, and a major determinant of woodland decomposition and nutrient cycling rates. Elevation of atmospheric temperature is predicted to drive changes in fungal community development. Top-down regulation of mycelial growth is an important determinant of, and moderator of temperature-driven changes to, two-species interaction outcomes. This study explores the interactive effects of a 4 °C temperature increase and soil invertebrate (collembola or woodlice) grazing on multispecies interactions between cord-forming basidiomycete fungi emerging from colonised beech (Fagus sylvatica) wood blocks. The fungal dominance hierarchy at ambient temperature (16 °C; Phanerochaete velutina > Resinicium bicolor > Hypholoma fasciculare) was altered by elevated temperature (20 °C; R. bicolor > P. velutina > H. fasciculare) in ungrazed systems. Warming promoted the competitive ability of the fungal species (R. bicolor) that was preferentially grazed by all invertebrate species. As a consequence, grazing prevented the effect of temperature on fungal community development and maintained a multispecies assemblage. Decomposition of fungal-colonised wood was stimulated by warming, with implications for increased CO2 efflux from woodland soil. Analogous to aboveground plant communities, increasing complexity of biotic and abiotic interactions appears to be important in buffering climate change effects on soil decomposers.

Effects of Fungal Inocula and Habitat Conditions on Alder and Eucalyptus Leaf Litter Decomposition in Streams of Northern Spain

We investigated how fungal decomposer (aquatic hyphomycetes) communities colonizing alder and eucalyptus leaf litter respond to changes in habitat characteristics (transplantation experiment). We examined the breakdown of leaf materials and the associated fungal communities at two contrasting sites, a headwater stream (H) and a midreach (M). Agroforestry increased from headwater to midreach. One month after the start of experiments at both sites, some leaf samples from the midreach site were transplanted to the headwater site (M-H treatment). Although both sites showed similar dissolved inorganic nutrient concentrations, eucalyptus leaves initially incubated at the midreach site (M, M-H) increased their breakdown rate compared to those incubated along the experiment at the headwater site (H). Alder breakdown rate was not enhanced, suggesting that their consumption was not limited by nutrient availability. Sporulation rates clearly differed between leaf types (alder > eucalyptus) and streams (H > M), but no transplantation effect was detected. When comparing conidial assemblages after transplantation, an inoculum effect (persistence of early colonizing species) was clear in both leaf species. Substrate preference and shifts in the relative importance of some fungal species along the process were also observed. Overall, our results support the determining role of the initial conditioning phase on the whole litter breakdown process, highlighting the importance of intrinsic leaf characteristics and those of the incubation habitat.

Decomposer communities in human‐impacted streams: species dominance rather than richness affects leaf decomposition

SummaryThere is compelling evidence that anthropogenic disturbance can decrease biodiversity and impair ecological functioning. A major challenge to biodiversity–ecosystem function research is to disentangle the effects of biodiversity loss on ecosystem functions from the direct effects of human disturbance.We studied the influence of human disturbance (acidification and eutrophication) and a natural stressor (lowpHdue to bedrock geology) on leaf‐shredding macroinvertebrates, fungal decomposers and leaf decomposition rates in boreal streams. We used pyrosequencing techniques to determine fungal richness and assemblage structure.Decomposition rates were higher in anthropogenically disturbed than in circumneutral reference or naturally acidic sites, but did not differ between the latter two groups. Macroinvertebrate richness was higher in circumneutral than in human‐impacted or naturally acidic sites, and shredder evenness was highest in circumneutral sites. Fungal evenness was also lower in human‐disturbed than in reference sites, whereas fungal richness did not vary among site groups.Decomposition rate in fine‐mesh bags was related positively to current velocity and fungal dominance, while in coarse‐mesh bags, it was related positively to total phosphorus. In anthropogenically disturbed streams, the effects of lowpHwere overridden by eutrophication, and increased decomposition rates resulted from disturbance‐induced increase in species dominance rather than richness. Furthermore, decomposition rates were positively correlated with abundances of dominant taxa, suggesting that ecosystem processes may be driven by a few key species.Synthesis and applications. Our results suggest that leaf decomposition rates are insensitive to natural background variation, supporting the use of decomposition assays, preferably accompanied by molecular analysis of fungal assemblages, to assess stream ecosystem health. Instead of focusing solely on diversity, however, more emphasis should be placed at changes in dominance patterns, particularly if management aims are to improve stream ecosystem functioning.

A thready affair: linking fungal diversity and community dynamics to terrestrial decomposition processes

Filamentous fungi are critical to the decomposition of terrestrial organic matter and, consequently, in the global carbon cycle. In particular, their contribution to degradation of recalcitrant lignocellulose complexes has been widely studied. In this review, we focus on the functioning of terrestrial fungal decomposers and examine the factors that affect their activities and community dynamics. In relation to this, impacts of global warming and increased N deposition are discussed. We also address the contribution of fungal decomposer studies to the development of general community ecological concepts such as diversity-functioning relationships, succession, priority effects and home-field advantage. Finally, we indicate several research directions that will lead to a more complete understanding of the ecological roles of terrestrial decomposer fungi such as their importance in turnover of rhizodeposits, the consequences of interactions with other organisms and niche differentiation.

Benthic algae stimulate leaf litter decomposition in detritus‐based headwater streams: a case of aquatic priming effect?

In detritus-based ecosystems, autochthonous primary production contributes very little to the detritus pool. Yet primary producers may still influence the functioning of these ecosystems through complex interactions with decomposers and detritivores. Recent studies have suggested that, in aquatic systems, small amounts of labile carbon (C) (e.g., producer exudates), could increase the mineralization of more recalcitrant organic-matter pools (e.g., leaf litter). This process, called priming effect, should be exacerbated under low-nutrient conditions and may alter the nature of interactions among microbial groups, from competition under low-nutrient conditions to indirect mutualism under high-nutrient conditions. Theoretical models further predict that primary producers may be competitively excluded when allochthonous C sources enter an ecosystem. In this study, the effects of a benthic diatom on aquatic hyphomycetes, bacteria, and leaf litter decomposition were investigated under two nutrient levels in a factorial microcosm experiment simulating detritus-based, headwater stream ecosystems. Contrary to theoretical expectations, diatoms and decomposers were able to coexist under both nutrient conditions. Under low-nutrient conditions, diatoms increased leaf litter decomposition rate by 20% compared to treatments where they were absent. No effect was observed under high-nutrient conditions. The increase in leaf litter mineralization rate induced a positive feedback on diatom densities. We attribute these results to the priming effect of labile C exudates from primary producers. The presence of diatoms in combination with fungal decomposers also promoted decomposer diversity and, under low-nutrient conditions, led to a significant decrease in leaf litter C:P ratio that could improve secondary production. Results from our microcosm experiment suggest new mechanisms by which primary producers may influence organic matter dynamics even in ecosystems where autochthonous primary production is low.

Preconditioning of leaves by solar radiation and anoxia affects microbial colonisation and rate of leaf mass loss in an intermittent stream

Summary Seasonal flow intermittence in streams often coincides with early leaf abscission of riparian vegetation due to water stress. When accumulated on dry stream beds or in remaining pools, leaves are exposed to solar radiation or fermentation processes, respectively. However, very little information exists on how these preconditioning processes could affect leaf decomposition when stream flow has recovered. We simulated natural preconditioning of leaves by irradiation with UV‐VIS fluorescent lamps and incubation under anoxic conditions. Mass loss rates of preconditioned leaf litter from deciduous trees (Alnus glutinosa, Fraxinus excelsior, Populus tremula and Quercus petreae) were quantified in a temporary stream during base flow conditions. Coarse and fine mesh litter bags were used to study the effect of benthic macroinvertebrates and microorganisms on leaf mass loss. Preconditioning reduced the concentration of macronutrients such as P, K and Mg and increased the relative cellulose content of the leaves. Preconditioning changed the fungal community structure (analysed by DGGE) depending on leaf species and sampling date. Preconditioning in anoxic conditions also suppressed fungal decomposer biomass (measured as ergosterol) by 42% resulting in 33% lower mass loss rates in fine mesh bags. In contrast, mass loss rates were not affected by preconditioning when macroinvertebrate decomposers had access to the leaf litter. In streams exhibiting seasonal flow intermittence, preconditioning will influence organic carbon dynamics towards lower rates of microbially mediated turnover and towards poorer quality of downstream‐transported material.

Bottom-up determination of soil collembola diversity and population dynamics in response to interactive climatic factors

Soil invertebrate contributions to decomposition are climate dependent. Understanding the influence of abiotic factors on soil invertebrate population dynamics will strengthen predictions regarding ecosystem functioning under climate change. As well as being important secondary decomposers, mycophagous collembola exert a strong influence on the growth and activity of primary decomposers, particularly fungi. Species-specific grazing preferences for different fungi enable fungal community composition to influence the direct impacts of climate change on collembola populations. We investigate the interactive roles of altered abiotic conditions (warming, wetting and drying) and the identity of the dominant decomposer fungus in determining collembola community dynamics in woodland soil mesocosms. The bottom-up influence of the dominant component of the fungal resource base was an important mediator of the direct climatic impacts on collembola populations. The positive influences of warming and wetting, and the negative influence of drying, on collembola abundance and diversity were much less pronounced in fungal-inoculation treatments, in which populations were reduced compared with uninoculated mesocosms. We conclude that the thick, sclerotised cords of the competitively dominant decomposer fungi reduced the biomass of smaller, more palatable soil fungi, limiting the size of collembola populations and their ability to respond to altered abiotic conditions.

Trophic complexity enhances ecosystem functioning in an aquatic detritus‐based model system

1. Understanding the functional significance of species interactions in ecosystems has become a major challenge as biodiversity declines rapidly worldwide. Ecosystem consequences arising from the loss of diversity either within trophic levels (horizontal diversity) or across trophic levels (vertical diversity) are well documented. However, simultaneous losses of species at different trophic levels may also result in interactive effects, with potentially complex outcomes for ecosystem functioning. 2. Because of logistical constraints, the outcomes of such interactions have been difficult to assess in experiments involving large metazoan species. Here, we take advantage of a detritus-based model system to experimentally assess the consequences of biodiversity change within both horizontal and vertical food-web components on leaf-litter decomposition, a fundamental process in a wide range of ecosystems. 3. Our concurrent manipulation of fungal decomposer diversity (0, 1 or 5 species), detritivore diversity (0, 1 or 3 species), and the presence of predatory fish scent showed that trophic complexity is key to eliciting diversity effects on ecosystem functioning. Specifically, although fungi and detritivores tended to promote decomposition individually, rates were highest in the most complete community where all trophic levels were represented at the highest possible species richness. In part, the effects were trait-mediated, reflected in the contrasting foraging responses of the detritivore species to predator scent. 4. Our results thus highlight the importance of interactive effects of simultaneous species loss within multiple trophic levels on ecosystem functioning. If a common phenomenon, this outcome suggests that functional ecosystem impairment resulting from widespread biodiversity loss could be more severe than inferred from previous experiments confined to varying diversity within single trophic levels.

Soil fungal communities and enzyme activities in a sandy, highly weathered tropical soil treated with biochemically contrasting organic inputs

The regulative effect of long-term application of biochemically contrasting organic inputs such as rice straw (4.7 g N; 6.5 g polyphenols), groundnut stover (22.8 g N; 12.9 g polyphenols) and leaf litter of tamarind (13.6 g N; 31.5 g polyphenols) and dipterocarp (5.7 g N; 64.9 g polyphenols) on fungal decomposers was studied in a tropical sandy soil. Fungal decomposers were assayed by 18S rRNA gene-based community profiling and were combined with measurements of selected enzyme activities. Dipterocarp residue application depressed fungal abundance, but promoted specialized decomposers (e.g., Aspergillus fumigatus and Anguillospora longissima) with increases in polyphenol oxidase activity. The degree of functional redundancy for invertase and B-glucosidase activities was induced after the addition of easily decomposable rice straw and groundnut stover. Higher N availability in the tamarind treatment increased, in contrast to low N rice straw, fungal abundance (i.e., Fusarium oxysporum, Myceliopthora thermophila, and Aspergillus versicolor) and promoted invertase and B-glucosidase activities, while peroxidase activity was depressed. In addition, N availability seemed to regulate not only decomposing soil fungi, but also the abundance of protozoan decomposers whose actual contribution to N turnover in soils is still poorly understood. Prospective research should thus consider apart from studying decomposing fungi also protozoa and bacteria to better understand the microbially mediated degradation of complex organic materials in soils.

Effect of genetic modification of potato starch on decomposition of leaves and tubers and on fungal decomposer communities

As part of a risk evaluation of growing genetically modified crops, we investigated the effects of a genetic modification of starch quality (increased level of amylopectin) in potato tubers (Solanum tuberosum L.) on the decomposition of tissues (tubers and leaves) as well as on the associated fungal functional and phylogenetic diversity. The weight loss of both leaves and tubers in litterbags was analysed after 1, 3 and 6 months of incubation in soils and combined with measurements of fungal extracellular enzyme activities (laccases, Mn-peroxidases and cellulases) as well as molecular analyses of the fungal community (ITS regions and cellobiohydrolase I (cbhI) genes). The study revealed that initial (after one month) decomposition of both tubers and leaves of the parental isoline was significantly faster than that of the genetically modified (GM)-variety. This coincided with differences in fungal community composition. After this initial difference, no significant differences in any of the parameters measured could be detected after 3 and 6 months of decomposition illustrating the transient nature of the initial difference between the cultivars. Thus, it can be concluded that the starch modified tubers are not harmful to the fungal decomposer community and that despite initial differences in decomposition, the final decomposition rate of tissues from the GM-variety was similar to that of tissues from the parental variety. Furthermore, interesting dynamics of fungal phyla and species during decomposition were observed; the basidiomycetal yeasts and ascomycetes were primary colonizers of the potato tissue while basidiomycetes were dominant in the more decomposed and lignin-rich litter.

A better understanding of functional roles of fungi in the decomposition process: using precursor rRNA containing ITS regions as a marker for the active fungal community

Decomposition and biogeochemical cycling are important ecosystem services provided by fungi (Kulhankova et al. 2006; Gange et al. 2007; Trap et al. 2011). Hitherto, different approaches have been used to examine the fungal community and its functional role in the decomposition process. Culture-dependent approaches have limitations because most fungi in environmental samples are likely to be uncultivable or difficult to isolate and such approaches are biased towards fast-growing fungi and affected by media selection (Anderson and Cairney 2004). On the other hand, cultureindependent molecular approaches are used routinely for fungal diversity and community assessment. The main targets of these approaches are the rRNA genes and spacer regions of the RNA operon (rDNA), thus basing diversity and community composition on DNA content. However, some studies show that DNA may have a long life span in the environment (Nielsen et al. 2004; Levy-Booth et al. 2007; Corinaldesi et al. 2008; Pietramellara et al. 2009). DNA can stem from fungal resting structures and spores or even senescent mycelium, all of which would be metabolically inactive at a given sampling time and even permanently. Consequently, fungal community details from DNA carry some memories about the previous community composition, and may poorly reflect the fungi that are active in decomposition processes at the time of sample collection. Additionally, it is possible that dispersed propagules leave their DNA signatures when they are carried there by wind or animals (Stenlid and Gustafsson 2001). The operational taxonomic unit (OTU) richness of decomposer fungal communities revealed by DNA-based community assessment is usually higher than that based on RNA because of the inclusion of dead or inactive fungal DNA (Anderson and Parkin 2007; Rajala et al. 2011). However, there were few cases reported vice versa or no significant differences between OTU richness of the fungal decomposers derived either by DNAor RNA-based approaches (Bastias et al. 2007; Baldrian et al. 2012). These are because some fungal OTUs are only detected using RNA and they compensate the inactive fungi detected by DNA. Nevertheless, we suggest caution that the presence of background communities of dormant or senescent fungi in environmental samples as an artifact is a potentially major hindrance to unbiased interpretation of real functional roles and correlations with enzyme production and environmental parameters. A DNAbased study (Kulhankova et al. 2006; Kubartova et al. 2009) has revealed that a large proportion of ascomycetes produce few oxidative enzymes and so are restricted in their ability to digest complex substances in the late stages of decomposition. Inactive or dead Ascomycota may be remnants of earlier stages of decomposition (Purahong and Hyde 2011; Rajala et al. 2011), which strongly supports the suggestion that there is an inert background fungal community, and that Handling Editor: Ana Rincon