Isolation of fungal cellobiohydrolase I genes from sporocarps and forest soils by PCR

Enhanced humification of full-scale apple wood and cow manure by promoting lignocellulose degradation via biomass pretreatments

Agroforestry waste and cow manure pollute the environment, of which, agroforestry waste is difficult to degrade. Compost is an effective way to dispose agroforestry waste; however, the low degradation efficiency of lignocellulose in agroforestry waste affects the process of composting humification. This study investigated lignocellulose degradation and composting humification in full-size apple wood and cow manure composting processes by applying different pretreatments (acidic, alkaline, and high-temperature) to apple wood. Simultaneously, physicochemical characterization and metagenome sequencing were combined to analyze the function of carbohydrate-active enzymes database (CAZy). Therefore, microbial communities and functions were linked during the composting process and the lignocellulose degradation mechanism was elaborated. The results showed that the addition of apple wood increased the compost humus (HS) yield, and pretreatment of apple wood enhanced the lignocellulose degradation during composting processes. In addition, pretreatment improved the physicochemical properties, such as temperature, pH, electric conductivity (EC), ammonium nitrogen (NH4+), and nitrate nitrogen (NO3-) in the compost, of which, acid treated apple wood compost (AcAWC) achieved the highest temperature of 58.4 °C, effectively promoting nitrification with NO3- ultimately reaching 0.127 g/kg. In all composts, microbial networks constructed a high proportion of positively correlated connections, and microorganisms promoted the composting process through cooperation. The proportions of glycosyltransferase (GT) and glycoside hydrolase (GH) promoted the separation and degradation of lignocellulose during composting to form HS. Notably, the adverse effects of the alkali-treated apple wood compost on bacteria were greater. AcAWC showed significant correlations between bacterial and fungal communities and both lignin and hemicellulose, and had more biomarkers associated with lignocellulose degradation and humification. The lignin degradation rate was 24.57 % and the HS yield increased by 27.49 %. Therefore, AcAWC has been confirmed to enhance lignocellulose degradation and promote compost humification by altering the properties of the apple wood and establishing a richer microbial community.

Fine root decomposition in forest ecosystems: an ecological perspective

Fine root decomposition is a physio-biochemical activity that is critical to the global carbon cycle (C) in forest ecosystems. It is crucial to investigate the mechanisms and factors that control fine root decomposition in forest ecosystems to understand their system-level carbon balance. This process can be influenced by several abiotic (e.g., mean annual temperature, mean annual precipitation, site elevation, stand age, salinity, soil pH) and biotic (e.g., microorganism, substrate quality) variables. Comparing decomposition rates within sites reveals positive impacts of nitrogen and phosphorus concentrations and negative effects of lignin concentration. Nevertheless, estimating the actual fine root breakdown is difficult due to inadequate methods, anthropogenic activities, and the impact of climate change. Herein, we propose that how fine root substrate and soil physiochemical characteristics interact with soil microorganisms to influence fine root decomposition. This review summarized the elements that influence this process, as well as the research methods used to investigate it. There is also need to study the influence of annual and seasonal changes affecting fine root decomposition. This cumulative evidence will provide information on temporal and spatial dynamics of forest ecosystems, and will determine how logging and reforestation affect fine root decomposition.

Organic amendments with high proportion of heterocyclic compounds promote soil microbiome shift and microbial use efficiency of straw-C

Soil microbial use efficiency of straw carbon (C), which is the proportion of straw-C microbes assimilate into new biosynthetic material relative to C lost out of the system as CO₂, is critical in increasing soil organic C (SOC) content, and hence maintaining soil fertility and productivity. However, the effect of chemical structures of the organic amendments (OAs) on the microbial use efficiency of straw-C remains unclear. The effect of the chemical structure of the OAs on microbial use efficiency of straw-C was elucidated by a combination of ¹³C-straw labeling with high-throughput sequencing and pyrolysis-GC/MS. We found a strong positive correlation between the microbial use efficiency of straw-C and the proportion of heterocyclic compounds (Hete_C). The microbial use efficiency of straw-C was highest in soil supplemented with Hete_C-dominant OAs, which significantly shifted microbial community structure toward fungal dominance. Specifically, fungal-to-bacterial ratio, fungal richness, and the relative abundance of Ascomycota were higher in soil with a higher proportion of Hete_C-dominant OAs. Together, our study suggests that OAs with high proportion of Hete_C promote the microbial use efficiency of straw-C by increasing the dominance of fungi in the soil microbial community in agroecosystems.

Investigating the Bacterial and Fungal Communities Involved in Dead Biomass Degradation in Forest Soils

Stable isotope probing (SIP) provides the opportunity to label decomposer microorganisms that build their biomass on a specific substrate. In combination with high-throughput sequencing, SIP allows for the identification of microbial community members involved in a particular decomposition process. Further information can be gained (in SIP experiments) through gene-targeted metagenomics and metatranscriptomics, opening the possibility to describe the pool of genes catalyzing specific decomposition reactions in situ and to identify the diversity of genes that are expressed. When combined with gene descriptions of fungal and/or bacterial isolates from the same environment, specific biochemical reactions involved in decomposition can be linked to individual microbial taxa. Here, we describe the use of these methods to explore the decomposer community of fungi and bacteria in forest litter and soil.

Impact of twenty pesticides on soil carbon microbial functions and community composition

Pesticides are known to affect non-targeted soil microorganisms. Still, studies comparing the effect of multiple pesticides on a wide range of microbial endpoints associated with carbon cycling are scarce. Here, we employed fluorescence enzymatic assay and real-time PCR to evaluate the effect of 20 commercial pesticides, applied at their recommended dose and five times their recommended dose, on soil carbon cycling related enzymatic activities (α-1,4-glucosidase, β-1,4-glucosidase, β-d-cellobiohydrolase and β-xylosidase), and on the absolute abundance of functional genes (cbhl and chiA), in three different South Australian agricultural soils. The effects on cellulolytic and chitinolytic microorganisms, and the total microbial community composition were determined using shotgun metagenomic sequencing in selected pesticide-treated and untreated samples. The application of insecticides significantly increased the cbhl and chiA genes absolute abundance in the acidic soil. At the community level, insecticide fipronil had the greatest stimulating effect on cellulolytic and chitinolytic microorganisms, followed by fungicide metalaxyl-M and insecticide imidacloprid. A shift towards a fungal dominated microbial community was observed in metalaxyl-M treated soil. Overall, our results suggest that the application of pesticides might affect the soil carbon cycle and may disrupt the formation of soil organic matter and structure stabilisation.

Grazing greatly reduces the temporal stability of soil cellulolytic fungal community in a steppe on the Tibetan Plateau

Excessive livestock grazing degrades grasslands ecosystem stability and sustainability by reducing soil organic matter and plant productivity. However, the effects of grazing on soil cellulolytic fungi, an important indicator of the degradation process for soil organic matter, remain less well understood. Using T-RFLP and sequencing methods, we investigated the effects of grazing on the temporal changes of cellulolytic fungal abundance and community structure in dry steppe soils during the growing months from May to September, on the Tibetan Plateau using T-RFLP and sequencing methods. The results demonstrated that the abundance of soil cellulolytic fungi under grazing treatment changed significantly from month to month, and was positively correlated with dissolved organic carbon (DOC) and soil temperature, but negatively correlated with soil pH. Contrastingly, cellulolytic fungal abundance did not change within the fencing treatment (ungrazed conditions). Cellulolytic fungal community structure changed significantly in the growing months in grazed soils, but did not change in fenced soils. Grazing played a key role in determining the community structure of soil cellulolytic fungi by explaining 8.1% of the variation, while pH and DOC explained 4.1% and 4.0%, respectively. Phylogenetically, the cellulolytic fungi were primarily affiliated with Ascomycota (69.65% in relative abundance) and Basidiomycota (30.35%). Therefore, grazing substantially reduced the stability of soil cellulolytic fungal abundance and community structure, as compared with the fencing treatment. Our finding provides a new insight into the responses of organic matter-decomposing microbes for grassland managements.

Production of Innovative Essential Oil-Based Emulsion Coatings for Fungal Growth Control on Postharvest Fruits

This work assessed the antimicrobial potential of natural essential oils (EOs) from cinnamon (CEO), zataria (ZEO), and satureja (SEO), applied natively or as coatings against Penicillium expansum and Botrytis cinerea during both in vitro and in vivo (on apple fruits) experiments. The induced inhibitory effect towards fungal growth, as a function of both EO type and concentration (75–1200 μL/L), was preliminarily investigated to select the most suitable EO for producing bacterial cellulose nanocrystals (BCNCs)/fish gelatin (GelA)-based emulsions. CEO and ZEO exhibited the best performances against P. expansum and B. cinerea, respectively. None of the pristine EOs completely inhibited the fungal growth and “disease severity”, properly quantified via size measurements of lesions formed on fruit surfaces. As compared to pristine CEO, coating emulsions with variable CEO concentration (75–2400 µL/L) curbed lesion spreading on apples, owing to the controlled CEO release during a 21-day temporal window. The strongest effect was displayed by BCNCs/GelA-CEO emulsions at the highest CEO concentration, upon which lesions on fruit skins were barely detectable. This work demonstrated the capability of EOs embedded in BCNCs/GelA-based nanocapsules to efficiently slow down microbial spoilage on postharvest fruits, thus offering viable opportunities for developing innovative antimicrobial packaging systems.

Nitrapyrin Addition Mitigated CO2 Emission from a Calcareous Soil Was Closely Associated with Its Effect on Decreasing Cellulolytic Fungal Community Diversity

Application of nitrification inhibitors (NIs) has been widely used to inhibit nitrification and reduce N₂O emissions. However, the impacts of NI addition on soil carbon transformation and carbon-degrading microbial communities have not been well explored. Here, a microcosm experiment was carried out, and four treatments were designed: (i) unfertilized control, (ii) urea alone, (iii) urea plus cattle manure, and (iv) urea plus cattle manure with nitrapyrin. The influence of nitrapyrin on soil CO₂ emissions, carbon-degrading extracellular enzyme activities, and the abundance and diversity of the cbhI community was investigated. Compared to the treatment of urea plus cattle manure, nitrapyrin significantly decreased cumulative CO₂ emissions by 51.8%. Moreover, cbhI community gene copies and their α-diversities (P < 0.05) were also significantly reduced by nitrapyrin application. A partial least squares path model showed that CO₂ emission was positively associated with cbhI community α-diversity but negatively associated with nitrapyrin addition. We conclude that the mitigation of soil CO₂ emissions by nitrapyrin can be ascribed to its effects on decreasing of cellulose-degrading gene community diversity. Our findings provide new insights into the side-effects of nitrapyrin on abating CO₂ emission.

Land-Use Change Enhanced SOC Mineralization but Did Not Significantly Affect Its Storage in the Surface Layer

To achieve carbon (C) neutrality and mitigate climate change, it is crucial to understand how converting natural forests to agricultural plantations influences soil organic C (SOC) mineralization. In this study, we investigated the impact of converting evergreen broadleaf forests (EBF) to extensively managed Moso bamboo (Phyllostachys edulis (Carriere) J. Houzeau) plantations (MBP) in subtropical China on SOC mineralization rate; the concentrations of labile SOC fractions such as dissolved organic C (DOC), microbial biomass C (MBC), and readily oxidizable C (ROC); the activities of C-degrading enzymes (cellobiohydrolase and phenol oxidase); and the abundance of C-degrading enzyme-encoding genes (cbhI and lcc). Three paired soil samples were taken from the surface layer (0–20 cm) of adjacent EBF-MBP sites in Anji County, Zhejiang province. Results showed that converting EBF to MBP significantly increased the SOC mineralization rate as well as soil pH, MBC, cellobiohydrolase, and phenol oxidase activities, and cbhI gene abundance, but did not change other soil properties described above. In addition, structural equation modelling (SEM) showed that the conversion increased SOC mineralization rate through increasing soil pH, cbhI gene abundance, MBC, and cellobiohydrolase and phenol oxidase activities. Our novel finding that converting EBF to extensively managed MBP enhanced SOC mineralization via increasing the activities of C-degrading enzymes suggests that C-degrading enzymes were a key factor regulating SOC mineralization in the extensively managed subtropical bamboo plantations.

Effect of Fenton pretreatment and bacterial inoculation on cellulose-degrading genes and fungal communities during rice straw composting

The aims of this article were to study the effect of Fenton pretreatment and bacterial inoculation on cellulose-degrading genes and fungal communities during rice straw composting. The rice straw was pretreated by Fenton reactions and functional bacterial agents were then inoculated during the cooling phase of composting. Three treatment groups were carried out, the control (CK), Fenton pretreatment (FeW) and Fenton pretreatment and bacterial inoculation (FeWI). The results indicated that Fenton pretreatment and bacterial inoculation changed the fungal communities composition and increased fungal diversity, leading to changes in the cellulose-degrading genes. In addition, a network analysis showed that in the FeWI treatment, the fungi from modules 1, 5 and 8 were core hosts of the cellulose-degrading genes driving the cellulosic degradation. Moreover, Fenton pretreatment and bacterial inoculation changed the core module fungal communities and strengthened the correlation between the core fungi and the cellulose-degrading genes, thereby promoting cellulosic degradation. Based on redundancy and structural equation model analyses, the NH₄⁺-N, TOC, pH and Shannon index were important factors influencing the variations in the cellulose-degrading genes. This study provides a foundation for cellulosic degradation during cellulosic waste composting.

Lignocellulose biomass bioconversion during composting: Mechanism of action of lignocellulase, pretreatment methods and future perspectives

Composting is a biodegradation and transformation process that converts lignocellulosic biomass into value-added products, such as humic substances (HSs). However, the recalcitrant nature of lignocellulose hinders the utilization of cellulose and hemicellulose, decreasing the bioconversion efficiency of lignocellulose. Pretreatment is an essential step to disrupt the structure of lignocellulosic biomass. Many pretreatment methods for composting may cause microbial inactivation and death. Thus, the pretreatment methods suitable for composting can promote the degradation and transformation of lignocellulosic biomass. Therefore, this review summarizes the pretreatment methods suitable for composting. Microbial consortium pretreatment, Fenton pretreatment and surfactant-assisted pretreatment for composting may improve the bioconversion process. Microbial consortium pretreatment is a cost-effective pretreatment method to enhance HSs yields during composting. On the other hand, the efficiency of enzyme production during composting is very important for the degradation of lignocellulose, whose action mechanism is unknown. Therefore, this review describes the mechanism of action of lignocellulase, the predominant microbes producing lignocellulase and their related genes. Finally, optimizing pretreatment conditions and increasing enzymatic hydrolysis to improve the quality of composts by controlling suitable microenvironmental factors and core target microbial activities as a research focus in the bioconversion of lignocellulose during composting in the future.

Antifungal features and properties of chitosan/sandalwood oil Pickering emulsion coating stabilized by appropriate cellulose nanofiber dosage for fresh fruit application

A novel composite edible coating film was developed from 0.8% chitosan (CS) and 0.5% sandalwood oil (SEO). Cellulose nanofibers (CNFs) were used as a stabilizer agent of oil-in-water Pickering emulsion. We found four typical groups of CNF level-dependent emulsion stabilization, including (1) unstable emulsion in the absence of CNFs; (2) unstable emulsion (0.006-0.21% CNFs); (3) stable emulsion (0.24-0.31% CNFs); and (4) regular emulsion with the addition of surfactant. Confocal laser scanning microscopy was performed to reveal the characteristics of droplet diameter and morphology. Antifungal tests against Botrytis cinerea and Penicillium digitatum, between emulsion coating stabilized with CNFs (CS-SEOpick) and CS or CS-SEO was tested. The effective concentration of CNFs (0.24%) may improve the performance of CS coating and maintain CS-SEO antifungal activity synergistically confirmed with a series of assays (in vitro, in vivo, and membrane integrity changes). The incorporation of CNFs contributed to improve the functional properties of CS and SEO-loaded CS including light transmission at UV and visible light wavelengths and tensile strength. Atomic force microscopy and scanning electron microscopy were employed to characterize the biocompatibility of each coating film formulation. Emulsion-CNF stabilized coating may have potential applications for active coating for fresh fruit commodities.

Linking enhanced soil nitrogen mineralization to increased fungal decomposition capacity with Moso bamboo invasion of broadleaf forests

Plant invasion can markedly alter soil fungal communities and nitrogen (N) availability; however, the linkage between the fungal decomposition capacity and N mineralization during plant invasion remains largely unknown. Here, we examined the relationship between net mineralization rates and relevant functional genes, as well as fungal species composition and function following Moso bamboo (Phyllostachys edulis) invasion of evergreen broadleaf forests, by studying broadleaf forests (non-invaded), mixed bamboo-broadleaf forests (moderately invaded) and bamboo forests (heavily invaded). Fungal species composition and functional genes involved in organic matter decomposition (laccase and cellobiohydrolase), N mineralization (alkaline peptidases) and nitrification (ammonia monooxygenase) were determined via high-throughput sequencing and real-time PCR. Both net ammonification and nitrification rates were generally increased with bamboo invasion into the broadleaf forest, where the net ammonification rate, on average, was 10.8 times higher than the nitrification rate across the three forest types. The fungal species composition and ecological guilds were altered with bamboo invasion, as demonstrated by the increased proportion of saprotrophs but decreased proportion of symbiotrophs in the bamboo forest. The increased net ammonification rate in bamboo forest was positively correlated with both fungal species composition and functional groups, and the fungal lcc gene (for lignin breakdown) abundance explained 67% of the variation of the net ammonification rate. In addition, the gene abundance of ammonia-oxidizing bacteria (AOB) explained 62% of the variation of net nitrification rate across the three forest types. The increased soil ammonification and nitrification rates following bamboo invasion of broadleaf forests suggest that the bamboo-invasion associated increase in soil N supply provided a positive feedback that facilitated bamboo invasion into broadleaf forests.

Predominant secretion of cellobiohydrolases and endo-β-1,4-glucanases in nutrient-limited medium by Aspergillus spp. isolated from subtropical field

Biological degradation of cellulose from dead plants in nature and plant biomass from agricultural and food-industry waste is important for sustainable carbon recirculation. This study aimed at searching diverse cellulose-degrading systems of wild filamentous fungi and obtaining fungal lines useful for cellooligosaccharide production from agro-industrial wastes. Fungal lines with cellulolytic activity were screened and isolated from stacked rice straw and soil in subtropical fields. Among 13 isolated lines, in liquid culture with a nutrition-limited cellulose-containing medium, four lines of Aspergillus spp. secreted 50–60 kDa proteins as markedly dominant components and gave clear activity bands of possible endo-β-1,4-glucanase in zymography. Mass spectroscopy (MS) analysis of the dominant components identified three endo-β-1,4-glucanases (GH5, GH7 and GH12) and two cellobiohydrolases (GH6 and GH7). Cellulose degradation by the secreted proteins was analysed by LC-MS-based measurement of derivatized reducing sugars. The enzymes from the four Aspergillus spp. produced cellobiose from crystalline cellulose and cellotriose at a low level compared with cellobiose. Moreover, though smaller than that from crystalline cellulose, the enzymes of two representative lines degraded powdered rice straw and produced cellobiose. These fungal lines and enzymes would be effective for production of cellooligosaccharides as cellulose degradation-intermediates with added value other than glucose.

Characterization of Cellobiohydrolases from Schizophyllum commune KMJ820

A novel cellobiohydrolase (CBH)-generating fungi have been isolated and categorized as Schizophyllum commune KMJ820 based on morphology and rDNA gene sequence. Cellulose powder was used as carbon source, the total enzyme activity was 11.51 U/ml is noted; which is among the highest amounts of CBH-generating microbes studied. CBH have been purified to homogenize, with pursual of serial chromatography using S. commune supernatants and two different CBHs were found; CBH 1 and 2. The filtered CBHs showed greater activity (V max = 51.4 and 20.8 U/mg) in contrast to CBHs from earlier studies. The MW (molecular weights) of S. commune CBH 1 and 2 were verified to be approximately 50 kDa and 150 kDa, respectively, by size exclusion chromatography. Even though CBHs have been evaluated from other sources, but S. commune CBH is prominent in comparison to other CBHs by its high enzyme activity.

Metabolomic, functional, and ecologic responses of the common freshwater fungus Neonectria lugdunensis to mine drainage stress

Metal contamination of watersheds is a global problem. Here, we conducted litter decomposition studies with Neonectria lugdunensis, a cosmopolitan aquatic fungus. Fungal isolates from four reference (non-impacted) and six metal-contaminated streams (due to mine drainage) were exposed to mine drainage and reference stream waters in Central Portugal. Impact of mine drainage waters on N. lugdunensis hyphae was investigated by performing metabolomic profiling of 200 lipids and 25 amino acids (AA) with ultra-high performance liquid chromatography-mass spectrometry. In parallel, functional response of N. lugdunensis isolates was assessed through expression profiles of a functional gene, cellobiohydrolase I (CbhI). Ecological performance via leaf mass loss was also determined. Exposure to mine drainage waters altered the concentration of numerous AA and lipids. Most strikingly, a gradual increase in the concentration of the triacylglycerols (TAG) with shorter acyl chains and lesser unsaturation was observed after the exposure to mine drainage waters. In addition, the changes in the concentration of numerous TAG, lysophosphatidylcholines, and AA were more significant in the isolates from the metal-contaminated streams after exposure to mine drainage water. CbhI gene of the isolates from reference streams was down-regulated by metal stress, while those from metal-contaminated streams remained unaffected. Finally, leaf mass loss was influenced by both exposure to mine drainage waters and the origin of isolates. Overall, our study demonstrates unique functional signatures displayed by fungi under metal stress and the relevant role that fungal AA and lipids play to cope with metal toxicity.

Thermostable endoglucanase gene derived by amplification from the genomic DNA of a cellulose-enriched mixed culture from mudspring water of Mt. Makiling, Laguna, Philippines

Culture-independent molecular-based approaches can be used to identify genes of interest from environmental sources that have desirable properties such as thermo activity. For this study, a putative thermo stable endoglucanase gene was identified from a mixed culture resulting from the inoculation of Brock-CMcellulose (1%) broth with mudspring water from Mt. Makiling, Laguna, Philippines that had been incubated at 90 °C. Genomic DNA was extracted from the cellulose-enriched mixed culture and endo1949 forward and reverse primers were used to amplify the endoglucanase gene, which was cloned into pCR-script plasmid vector. Blastn alignment of the sequenced insert revealed 99.69% similarity to the glycosyl hydrolase, sso1354 (CelA1; Q97YG7) from Saccharolobus solfataricus. The endoglucanase gene (GenBank accession number MK984682) was determined to be 1,021 nucleotide bases in length, corresponding to 333 amino acids with a molecular mass of ~ 37 kDa. The endoglucanase gene was inserted into a pET21 vector and transformed in E. coli BL21 for expression. Partially purified recombinant Mt. Makiling endoglucanase (MM-Engl) showed a specific activity of 187.61 U/mg and demonstrated heat stability up to 80 °C. The thermo-acid stable endoglucanase can be used in a supplementary hydrolysis step to further hydrolyze the lignocellulosic materials that were previously treated under high temperature-dilute acid conditions, thereby enhancing the release of more glucose sugars for bioethanol production.

Effects of inoculating with lignocellulose-degrading consortium on cellulose-degrading genes and fungal community during co-composting of spent mushroom substrate with swine manure

Composting is used widely for recycling spent mushroom substrate (SMS). This study investigated the effects of inoculating a lignocellulose-degrading consortium at two levels comprising 0% (control: CK) and 10% (T) on the fungal community and cellulose-degrading genes during SMS co-composting with swine manure. Lignocellulose degradation rate in T was 8.77-34.45% higher compared with CK. Inoculation affected the distribution of the fungal community, increased the community diversity, and inhibited pathogens. Network analysis showed that inoculation changed the co-occurrence patterns of the fungal communities and made the co-composting system more stable. The relative abundances of glycoside hydrolase genes GH3E (fungal GH3), GH6, and GH7 were 0.45, 0.09, and 0.39 logs higher in T, respectively, than CK. Partial least-squares path modeling suggested that the variations in cellulose-degrading genes were driven mainly by changes in the fungal community during co-composting. Therefore, the lignocellulose-degrading consortium accelerated the transformation of lignocellulose to facilitate safer composting.

Historical Nitrogen Deposition and Straw Addition Facilitate the Resistance of Soil Multifunctionality to Drying-Wetting Cycles

Climate change is predicted to alter precipitation and drought patterns, which has become a global concern as evidence accumulates that it will affect ecosystem services. Disentangling the ability of soil multifunctionality to withstand this stress (multifunctionality resistance) is a crucial topic for assessing the stability and adaptability of agroecosystems. In this study, we explored the effects of nutrient addition on multifunctionality resistance to drying-wetting cycles and evaluated the importance of microbial functional capacity (characterized by the abundances of genes involved in carbon, nitrogen and phosphorus cycles) for this resistance. The multifunctionality of soils treated with nitrogen (N) and straw showed a higher resistance to drying-wetting cycles than did nonamended soils. Microbial functional capacity displayed a positive linear relationship with multifunctionality resistance. Random forest analysis showed that the abundances of the archeal amoA (associated with nitrification) and nosZ and narG (denitrification) genes were major predictors of multifunctionality resistance in soils without straw addition. In contrast, major predictors of multifunctionality resistance in straw amended soils were the abundances of the GH51 (xylan degradation) and fungcbhIF (cellulose degradation) genes. Structural equation modeling further demonstrated the large direct contribution of carbon (C) and N cycling-related gene abundances to multifunctionality resistance. The modeling further elucidated the positive effects of microbial functional capacity on this resistance, which was mediated potentially by a high soil fungus/bacterium ratio, dissolved organic C content, and low pH. The present work suggests that nutrient management of agroecosystems can buffer negative impacts on ecosystem functioning caused by a climate change-associated increase in drying-wetting cycles via enriching functional capacity of microbial communities.IMPORTANCE Current climate trends indicate an increasing frequency of drying-wetting cycles. Such cycles are severe environmental perturbations and have received an enormous amount of attention. Prediction of ecosystem's stability and adaptability requires a better mechanistic understanding of the responses of microbially mediated C and nutrient cycling processes to external disturbance. Assessment of this stability and adaptability further need to disentangle the relationships between functional capacity of soil microbial communities and the resistance of multifunctionality. Study of the physiological responses and community reorganization of soil microbes in response to stresses requires large investments of resources that vary with the management history of the system. Our study provides evidence that nutrient managements on agroecosystems can be expected to buffer the impacts of progressive climate change on ecosystem functioning by enhancing the functional capacity of soil microbial communities, which can serve as a basis for field studies.

Evaluating the mycostimulation potential of select carbon amendments for the degradation of a model PAH by an ascomycete strain enriched from a superfund site

Although ecological flexibility has been well documented in fungi, it remains unclear how this flexibility can be exploited for pollutant degradation, especially in the Ascomycota phylum. In this work, we assess three mycostimulation amendments for their ability to induce degradation in Trichoderma harzanium, a model fungus previously isolated from a Superfund site contaminated with polycyclic aromatic hydrocarbons. The amendments used in the present study were selected based on the documented ecological roles of ascomycetes. Chitin was selected to simulate the parasitic ecological role while cellulose and wood were selected to mimic bulk soil and wood saprobic conditions, respectively. Each amendment was tested in liquid basal medium in 0.1 and 1% (w/v) suspensions. Both chitin and cellulose amendments were shown to promote anthracene degradation in T. harzanium with the 0.1% chitin amendment resulting in over 90% removal of anthracene. None of the targets monitored for gene expression were found to be upregulated suggesting alternate pathways may be used in T. harzanium. Overall, our data suggest that mycostimulation amendments can be improved by understanding the ecological roles of indigenous fungi. However, further research is needed to better estimate specific amendment requirements for a broader group of target fungi and follow up studies are needed to determine whether the trends observed herein translate to more realistic soil systems.

Fungal community and cellulose-degrading genes in the composting process of Chinese medicinal herbal residues

The fungal community and the population of 16S rRNA, 18S rRNA and cellulose-degrading genes during the 30-day composting process of Chinese medicinal herbal residues were investigated using Illumina MiSeq and quantitative real-time PCR. An obvious succession of fungal communities occurred during the composting process. Unidentified fungi predominated in the raw materials. As composting progressed, Ascomycota became the most dominant phylum, with Aspergillus being the most dominant genus, and Aspergillus fumigatus making up 99.65% of that genus. Because of the inoculation of cellulolytic fungi in the mature stage, the cellulose degradation rate in inoculation groups was faster and the relative abundances of Aspergillus and the glycoside hydrolase family 7 genes were significantly higher than those in the control groups. These indicated that the fungal inoculants facilitated the degradation of cellulose, increased cellulolytic fungi and optimized the community structure.

RNA extraction from decaying wood for (meta)transcriptomic analyses

Wood decomposition is a key step of the terrestrial carbon cycle and is of economic importance. It is essentially a microbiological process performed by fungi and to an unknown extent by bacteria. To gain access to the genes expressed by the diverse microbial communities participating in wood decay, we developed an RNA extraction protocol from this recalcitrant material rich in polysaccharides and phenolic compounds. This protocol was implemented on 22 wood samples representing as many tree species from 11 plant families in the Angiosperms and Gymnosperms. RNA was successfully extracted from all samples and converted into cDNAs from which were amplified both fungal and bacterial protein coding genes, including genes encoding hydrolytic enzymes participating in lignocellulose hydrolysis. This protocol applicable to a wide range of decomposing wood types represents a first step towards a metatranscriptomic analysis of wood degradation under natural conditions.

A new promising phylogenetic marker to study the diversity of fungal communities: The Glycoside Hydrolase 63 gene

In molecular ecology, the development of efficient molecular markers for fungi remains an important research domain. Nuclear ribosomal internal transcribed spacer (ITS) region was proposed as universal DNA barcode marker for fungi, but this marker was criticized for Indel-induced alignment problems and its potential lack of phylogenetic resolution. Our main aim was to develop a new phylogenetic gene and a putative functional marker, from single-copy gene, to describe fungal diversity. Thus, we developed a series of primers to amplify a polymorphic region of the Glycoside Hydrolase GH63 gene, encoding exo-acting α-glucosidases, in basidiomycetes. These primers were validated on 125 different fungal genomic DNAs, and GH63 amplification yield was compared with that of already published functional markers targeting genes coding for laccases, N-acetylhexosaminidases, cellobiohydrolases and class II peroxidases. Specific amplicons were recovered for 95% of the fungal species tested, and GH63 amplification success was strikingly higher than rates obtained with other functional genes. We downloaded the GH63 sequences from 483 fungal genomes publicly available at the JGI mycocosm database. GH63 was present in 461 fungal genomes belonging to all phyla, except Microsporidia and Neocallimastigomycota divisions. Moreover, the phylogenetic trees built with both GH63 and Rpb1 protein sequences revealed that GH63 is also a promising phylogenetic marker. Finally, a very high proportion of GH63 proteins was predicted to be secreted. This molecular tool could be a new phylogenetic marker of fungal species as well as potential indicator of functional diversity of basidiomycetes fungal communities in term of secretory capacities.

Primer Sets Developed for Functional Genes Reveal Shifts in Functionality of Fungal Community in Soils

Phylogenetic diversity of soil microbes is a hot topic at the moment. However, the molecular tools for the assessment of functional diversity in the fungal community are less developed than tools based on genes encoding the ribosomal operon. Here 20 sets of primers targeting genes involved mainly in carbon cycling were designed and/or validated and the functioning of soil fungal communities along a chronosequence of land abandonment from agriculture was evaluated using them. We hypothesized that changes in fungal community structure during secondary succession would lead to difference in the types of genes present in soils and that these changes would be directional. We expected an increase in genes involved in degradation of recalcitrant organic matter in time since agriculture. Out of the investigated genes, the richness of the genes related to carbon cycling was significantly higher in fields abandoned for longer time. The composition of six of the genes analyzed revealed significant differences between fields abandoned for shorter and longer time. However, all genes revealed significant variance over the fields studied, and this could be related to other parameters than the time since agriculture such as pH, organic matter, and the amount of available nitrogen. Contrary to our initial hypothesis, the genes significantly different between fields were not related to the decomposition of more recalcitrant matter but rather involved in degradation of cellulose and hemicellulose.

Comparison of pectin-degrading fungal communities in temperate forests using glycosyl hydrolase family 28 pectinase primers targeting Ascomycete fungi

Fungi have developed a wide assortment of enzymes to break down pectin, a prevalent polymer in plant cell walls that is important in plant defense and structure. One enzyme family used to degrade pectin is the glycosyl hydrolase family 28 (GH28). In this study we developed primers for the amplification of GH28 coding genes from a database of 293 GH28 sequences from 40 fungal genomes. The primers were used to successfully amplify GH28 pectinases from all Ascomycota cultures tested, but only three out of seven Basidiomycota cultures. In addition, we further tested the primers in PCRs on metagenomic DNA extracted from senesced tree leaves from different forest ecosystems, followed by cloning and sequencing. Taxonomic specificity for Ascomycota GH28 genes was tested by comparing GH28 composition in leaves to internal transcribed spacer (ITS) amplicon composition using pyrosequencing. All sequences obtained from GH28 primers were classified as Ascomycota; in contrast, ITS sequences indicated that fungal communities were up to 39% Basidiomycetes. Analysis of leaf samples indicated that both forest stand and ecosystem type were important in structuring fungal communities. However, site played the prominent role in explaining GH28 composition, whereas ecosystem type was more important for ITS composition, indicating possible genetic drift between populations of fungi. Overall, these primers will have utility in understanding relationships between fungal community composition and ecosystem processes, as well as detection of potentially pathogenic Ascomycetes.

Fungal Communities in Soils: Soil Organic Matter Degradation

Stable isotope probing (SIP) provides the opportunity to label decomposer microorganisms that build their biomass on a specific substrate. In combination with high-throughput sequencing, SIP allows for the identification of fungal community members involved in a particular decomposition process. Further information can be gained through gene-targeted metagenomics and metatranscriptomics, opening the possibility to describe the pool of genes catalyzing specific decomposition reactions in situ and to identify the diversity of genes that are expressed. When combined with gene descriptions of fungal isolates from the same environment, specific biochemical reactions involved in decomposition can be linked to individual fungal taxa. Here we describe the use of these methods to explore the cellulolytic fungal community in forest litter and soil.

Fungal traits that drive ecosystem dynamics on land

Fungi contribute extensively to a wide range of ecosystem processes, including decomposition of organic carbon, deposition of recalcitrant carbon, and transformations of nitrogen and phosphorus. In this review, we discuss the current knowledge about physiological and morphological traits of fungi that directly influence these processes, and we describe the functional genes that encode these traits. In addition, we synthesize information from 157 whole fungal genomes in order to determine relationships among selected functional genes within fungal taxa. Ecosystem-related traits varied most at relatively coarse taxonomic levels. For example, we found that the maximum amount of variance for traits associated with carbon mineralization, nitrogen and phosphorus cycling, and stress tolerance could be explained at the levels of order to phylum. Moreover, suites of traits tended to co-occur within taxa. Specifically, the genetic capacities for traits that improve stress tolerance-β-glucan synthesis, trehalose production, and cold-induced RNA helicases-were positively related to one another, and they were more evident in yeasts. Traits that regulate the decomposition of complex organic matter-lignin peroxidases, cellobiohydrolases, and crystalline cellulases-were also positively related, but they were more strongly associated with free-living filamentous fungi. Altogether, these relationships provide evidence for two functional groups: stress tolerators, which may contribute to soil carbon accumulation via the production of recalcitrant compounds; and decomposers, which may reduce soil carbon stocks. It is possible that ecosystem functions, such as soil carbon storage, may be mediated by shifts in the fungal community between stress tolerators and decomposers in response to environmental changes, such as drought and warming.

PCR primers to study the diversity of expressed fungal genes encoding lignocellulolytic enzymes in soils using high-throughput sequencing

Plant biomass degradation in soil is one of the key steps of carbon cycling in terrestrial ecosystems. Fungal saprotrophic communities play an essential role in this process by producing hydrolytic enzymes active on the main components of plant organic matter. Open questions in this field regard the diversity of the species involved, the major biochemical pathways implicated and how these are affected by external factors such as litter quality or climate changes. This can be tackled by environmental genomic approaches involving the systematic sequencing of key enzyme-coding gene families using soil-extracted RNA as material. Such an approach necessitates the design and evaluation of gene family-specific PCR primers producing sequence fragments compatible with high-throughput sequencing approaches. In the present study, we developed and evaluated PCR primers for the specific amplification of fungal CAZy Glycoside Hydrolase gene families GH5 (subfamily 5) and GH11 encoding endo-β-1,4-glucanases and endo-β-1,4-xylanases respectively as well as Basidiomycota class II peroxidases, corresponding to the CAZy Auxiliary Activity family 2 (AA2), active on lignin. These primers were experimentally validated using DNA extracted from a wide range of Ascomycota and Basidiomycota species including 27 with sequenced genomes. Along with the published primers for Glycoside Hydrolase GH7 encoding enzymes active on cellulose, the newly design primers were shown to be compatible with the Illumina MiSeq sequencing technology. Sequences obtained from RNA extracted from beech or spruce forest soils showed a high diversity and were uniformly distributed in gene trees featuring the global diversity of these gene families. This high-throughput sequencing approach using several degenerate primers constitutes a robust method, which allows the simultaneous characterization of the diversity of different fungal transcripts involved in plant organic matter degradation and may lead to the discovery of complex patterns in gene expression of soil fungal communities.

Fungal Community Responses to Past and Future Atmospheric CO2 Differ by Soil Type

Soils sequester and release substantial atmospheric carbon, but the contribution of fungal communities to soil carbon balance under rising CO2 is not well understood. Soil properties likely mediate these fungal responses but are rarely explored in CO2 experiments. We studied soil fungal communities in a grassland ecosystem exposed to a preindustrial-to-future CO2 gradient (250 to 500 ppm) in a black clay soil and a sandy loam soil. Sanger sequencing and pyrosequencing of the rRNA gene cluster revealed that fungal community composition and its response to CO2 differed significantly between soils. Fungal species richness and relative abundance of Chytridiomycota (chytrids) increased linearly with CO2 in the black clay (P < 0.04, R(2) > 0.7), whereas the relative abundance of Glomeromycota (arbuscular mycorrhizal fungi) increased linearly with elevated CO2 in the sandy loam (P = 0.02, R(2) = 0.63). Across both soils, decomposition rate was positively correlated with chytrid relative abundance (r = 0.57) and, in the black clay soil, fungal species richness. Decomposition rate was more strongly correlated with microbial biomass (r = 0.88) than with fungal variables. Increased labile carbon availability with elevated CO2 may explain the greater fungal species richness and Chytridiomycota abundance in the black clay soil, whereas increased phosphorus limitation may explain the increase in Glomeromycota at elevated CO2 in the sandy loam. Our results demonstrate that soil type plays a key role in soil fungal responses to rising atmospheric CO2.

Diversity and dynamics of the microbial community on decomposing wheat straw during mushroom compost production

The development of communities of three important composting players including actinobacteria, fungi and clostridia was explored during the composting of wheat straw for mushroom production. The results revealed the presence of highly diversified actinobacteria and fungal communities during the composting process. The diversity of the fungal community, however, sharply decreased in the mature compost. Furthermore, an apparent succession of both actinobacteria and fungi with intensive changes in the composition of communities was demonstrated during composting. Notably, cellulolytic actinomycetal and fungal genera represented by Thermopolyspora, Microbispora and Humicola were highly enriched in the mature compost. Analysis of the key cellulolytic genes revealed their prevalence at different composting stages including several novel glycoside hydrolase family 48 exocellulase lineages. The community of cellulolytic microbiota also changed substantially over time. The prevalence of the diversified cellulolytic microorganisms holds the great potential of mining novel lignocellulose decomposing enzymes from this specific ecosystem.

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.

Microbial genomics, transcriptomics and proteomics: new discoveries in decomposition research using complementary methods

Molecular methods for the analysis of biomolecules have undergone rapid technological development in the last decade. The advent of next-generation sequencing methods and improvements in instrumental resolution enabled the analysis of complex transcriptome, proteome and metabolome data, as well as a detailed annotation of microbial genomes. The mechanisms of decomposition by model fungi have been described in unprecedented detail by the combination of genome sequencing, transcriptomics and proteomics. The increasing number of available genomes for fungi and bacteria shows that the genetic potential for decomposition of organic matter is widespread among taxonomically diverse microbial taxa, while expression studies document the importance of the regulation of expression in decomposition efficiency. Importantly, high-throughput methods of nucleic acid analysis used for the analysis of metagenomes and metatranscriptomes indicate the high diversity of decomposer communities in natural habitats and their taxonomic composition. Today, the metaproteomics of natural habitats is of interest. In combination with advanced analytical techniques to explore the products of decomposition and the accumulation of information on the genomes of environmentally relevant microorganisms, advanced methods in microbial ecophysiology should increase our understanding of the complex processes of organic matter transformation.

Ascomycota members dominate fungal communities during straw residue decomposition in arable soil

This study investigated the development of fungal community composition in arable soil during the degradation of straw residue. We explored the short-term responses of the fungal community over 28 days of decomposition in soil using culture-independent polymerase chain reaction in combination with a clone library and denaturing gradient gel electrophoresis (DGGE). Fungal cellobiohydrolase I (cbhI) genes in the soil were also characterized, and their diversity suggested the existence of a different cellulose decomposer. The DGGE profiles based on fungal internal transcribed spacer analysis showed different successions of fungal populations during residue decomposition. Members of Lecythophora and Sordariales were dominant in the early succession, while Hypocrea and Engyodontium were better adapted in the late succession. The succession of fungal communities might be related to changes of residue quality during decomposition. Collectively, sequences assigned to Ascomycota members were dominant at different stages of the fungal succession during decomposition, revealing that they were key drivers responsible for residue degradation in the arable soil tested.

Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens

Plants represent a large reservoir of organic carbon comprised primarily of recalcitrant polymers that most metazoans are unable to deconstruct. Many herbivores gain access to nutrients in this material indirectly by associating with microbial symbionts, and leaf-cutter ants are a paradigmatic example. These ants use fresh foliar biomass as manure to cultivate gardens composed primarily of Leucoagaricus gongylophorus, a basidiomycetous fungus that produces specialized hyphal swellings that serve as a food source for the host ant colony. Although leaf-cutter ants are conspicuous herbivores that contribute substantially to carbon turnover in Neotropical ecosystems, the process through which plant biomass is degraded in their fungus gardens is not well understood. Here we present the first draft genome of L. gongylophorus, and, using genomic and metaproteomic tools, we investigate its role in lignocellulose degradation in the gardens of both Atta cephalotes and Acromyrmex echinatior leaf-cutter ants. We show that L. gongylophorus produces a diversity of lignocellulases in ant gardens and is likely the primary driver of plant biomass degradation in these ecosystems. We also show that this fungus produces distinct sets of lignocellulases throughout the different stages of biomass degradation, including numerous cellulases and laccases that likely play an important role in lignocellulose degradation. Our study provides a detailed analysis of plant biomass degradation in leaf-cutter ant fungus gardens and insight into the enzymes underlying the symbiosis between these dominant herbivores and their obligate fungal cultivar.

Geneious plugins for the access of PlasmoDB and PiroplasmaDB databases

The bioinformatics software, Geneious, provides a useful platform for researchers to retrieve and analyse genomic and functional genomics information. However, the main databases that the software is able to access are hosted by NCBI (National Center for Biotechnology Information). The databases of EuPathDB (Eukaryotic Pathogen Database Resources), such as PlasmoDB and PiroplasmaDB, collect more specific and detailed information about eukaryotic pathogens than those kept in NCBI databases. Two plugins for Geneious, one for PlasmaDB and one for PiroplasmaDB were developed. When installed, users can use search facilities to find and import gene and protein sequences from the EuPathDB databases. Users can then use the functions of Geneious to process the sequence information. When information unique to PlasmoDB and PiroplasmaDB is required, the user can access results linked with the gene/protein sequence via the default web browser. The plugins are freely available from the Victorian Bioinformatics Consortium website. The plugins can be modified to access any of the databases of EuPathDB.

Fungal community on decomposing leaf litter undergoes rapid successional changes

Fungi are considered the primary decomposers of dead plant biomass in terrestrial ecosystems. However, current knowledge regarding the successive changes in fungal communities during litter decomposition is limited. Here we explored the development of the fungal community over 24 months of litter decomposition in a temperate forest with dominant Quercus petraea using 454-pyrosequencing of the fungal internal transcribed spacer (ITS) region and cellobiohydrolase I (cbhI) genes, which encode exocellulases, to specifically address cellulose decomposers. To quantify the involvement of phyllosphere fungi in litter decomposition, the fungal communities in live leaves and leaves immediately before abscission were also analysed. The results showed rapid succession of fungi with dramatic changes in the composition of the fungal community. Furthermore, most of the abundant taxa only temporarily dominated in the substrate. Fungal diversity was lowest at leaf senescence, increased until month 4 and did not significantly change during subsequent decomposition. Highly diverse community of phyllosphere fungi inhabits live oak leaves 2 months before abscission, and these phyllosphere taxa comprise a significant share of the fungal community during early decomposition up to the fourth month. Sequences assigned to the Ascomycota showed highest relative abundances in live leaves and during the early stages of decomposition. In contrast, the relative abundance of sequences assigned to the Basidiomycota phylum, particularly basidiomycetous yeasts, increased with time. Although cellulose was available in the litter during all stages of decomposition, the community of cellulolytic fungi changed substantially over time. The results indicate that litter decomposition is a highly complex process mediated by various fungal taxa.

The irreversible loss of a decomposition pathway marks the single origin of an ectomycorrhizal symbiosis

Microbial symbioses have evolved repeatedly across the tree of life, but the genetic changes underlying transitions to symbiosis are largely unknown, especially for eukaryotic microbial symbionts. We used the genus Amanita, an iconic group of mushroom-forming fungi engaged in ectomycorrhizal symbioses with plants, to identify both the origins and potential genetic changes maintaining the stability of this mutualism. A multi-gene phylogeny reveals one origin of the symbiosis within Amanita, with a single transition from saprotrophic decomposition of dead organic matter to biotrophic dependence on host plants for carbon. Associated with this transition are the losses of two cellulase genes, each of which plays a critical role in extracellular decomposition of organic matter. However a third gene, which acts at later stages in cellulose decomposition, is retained by many, but not all, ectomycorrhizal species. Experiments confirm that symbiotic Amanita species have lost the ability to grow on complex organic matter and have therefore lost the capacity to live in forest soils without carbon supplied by a host plant. Irreversible losses of decomposition pathways are likely to play key roles in the evolutionary stability of these ubiquitous mutualisms.

Cloning and sequence analysis of the cellobiohydrolase I genes from some basidiomycetes

Genes encoding the cellobiohydrolase enzyme (CBHI), designated as cbhI, were isolated from the basidiomycetes Auricularia fuscosuccinea, Pleurotus giganteus, P. eryngii, P. ostreatus, and P. sajor-caju. Initially, the fungal genomic DNA was extracted using a modified cetyltrimethyl ammonium bromide (CTAB) protocol and used as a DNA template. The cbhI genes were then amplified and cloned using the pGEM-T Easy Vector Systems. The sizes of these PCR amplicons were between 700~800 bp. The DNA sequences obtained were similar showing high identity to the cbhI gene family. These cbhI genes were partial consisting of three coding regions and two introns. The deduced amino acid sequences exhibited significant similarity to those of fungal CBHI enzymes belonging to glycosyl hydrolase family 7.

Soil fungal cellobiohydrolase I gene (cbhI) composition and expression in a loblolly pine plantation under conditions of elevated atmospheric CO2 and nitrogen fertilization

The simultaneous increase of atmospheric CO(2) and nitrogen (N) deposition to terrestrial ecosystems is predicted to alter plant productivity and, consequently, to change the amount and quality of above- and belowground carbon entering forest soils. It is not known how such changes will impact the composition and function of soil fungal communities that play a key role in degrading complex carbon. We sequenced the fungal cellobiohydrolase I gene (cbhI) from soil DNA and cDNA to compare the richness and composition of resident and expressed cbhI genes at a U.S. Department of Energy free air-carbon dioxide enrichment (FACE) site (NC), which had been exposed to elevated atmospheric CO(2) and/or N fertilization treatment for several years. Our results provide evidence that the richness and composition of the cellulolytic fungi surveyed in this study were distinct in the DNA- and cDNA-based gene surveys and were dominated by Basidiomycota that have low or no representation in public databases. The surveys did not detect differences in richness or phylum-level composition of cbhI-containing, cellulolytic fungi that correlated with elevated CO(2) or N fertilization at the time of sampling.

Active and total microbial communities in forest soil are largely different and highly stratified during decomposition

Soils of coniferous forest ecosystems are important for the global carbon cycle, and the identification of active microbial decomposers is essential for understanding organic matter transformation in these ecosystems. By the independent analysis of DNA and RNA, whole communities of bacteria and fungi and its active members were compared in topsoil of a Picea abies forest during a period of organic matter decomposition. Fungi quantitatively dominate the microbial community in the litter horizon, while the organic horizon shows comparable amount of fungal and bacterial biomasses. Active microbial populations obtained by RNA analysis exhibit similar diversity as DNA-derived populations, but significantly differ in the composition of microbial taxa. Several highly active taxa, especially fungal ones, show low abundance or even absence in the DNA pool. Bacteria and especially fungi are often distinctly associated with a particular soil horizon. Fungal communities are less even than bacterial ones and show higher relative abundances of dominant species. While dominant bacterial species are distributed across the studied ecosystem, distribution of dominant fungi is often spatially restricted as they are only recovered at some locations. The sequences of cbhI gene encoding for cellobiohydrolase (exocellulase), an essential enzyme for cellulose decomposition, were compared in soil metagenome and metatranscriptome and assigned to their producers. Litter horizon exhibits higher diversity and higher proportion of expressed sequences than organic horizon. Cellulose decomposition is mediated by highly diverse fungal populations largely distinct between soil horizons. The results indicate that low-abundance species make an important contribution to decomposition processes in soils.

Comparative assessment of fungal cellobiohydrolase I richness and composition in cDNA generated using oligo(dT) primers or random hexamers

Understanding soil fungal distribution and activities, particularly at the level of gene expression, is important in unveiling mechanisms regulating their activities in situ. Recent identification of fungal genes involved in carbon cycling has provided the foundation for developing reverse-transcriptase PCR assays to monitor spatiotemporal gene expression patterns in soils and other complex microbial systems. The polyadenylated 3' ends of eukaryotic mRNA transcripts enables the use of oligo(dT) primers for cDNA synthesis, but this can result in the overrepresentation of the 3' end of transcripts in cDNA pools. In an effort to increase the uniformity of transcripts represented in cDNA pools, random hexamers have been used. The use of both priming methods is abundant in the literature, but we do not know how these methods perform relative to each other. We performed comparative richness and compositional analyses of the fungal glycosyl hydrolase family 7 cellobiohydrolase I gene cbhI amplified from soil cDNAs that had been generated using either oligo(dT) primers or random hexamers. Our results demonstrate that similar cbhI richness and composition were recovered using both approaches. Richness estimates and compositional profiles of cbhI sequence libraries generated from random hexamer-primed cDNA were more variable than from libraries generated from oligo(dT) primed cDNA. However, our overall results indicate that, on average, comparable richness and composition were recovered from soil cDNAs when either priming method was used.

Simulated atmospheric N deposition alters fungal community composition and suppresses ligninolytic gene expression in a northern hardwood forest

High levels of atmospheric nitrogen (N) deposition may result in greater terrestrial carbon (C) storage. In a northern hardwood ecosystem, exposure to over a decade of simulated N deposition increased C storage in soil by slowing litter decay rates, rather than increasing detrital inputs. To understand the mechanisms underlying this response, we focused on the saprotrophic fungal community residing in the forest floor and employed molecular genetic approaches to determine if the slower decomposition rates resulted from down-regulation of the transcription of key lignocellulolytic genes, by a change in fungal community composition, or by a combination of the two mechanisms. Our results indicate that across four Acer-dominated forest stands spanning a 500-km transect, community-scale expression of the cellulolytic gene cbhI under elevated N deposition did not differ significantly from that under ambient levels of N deposition. In contrast, expression of the ligninolytic gene lcc was significantly down-regulated by a factor of 2-4 fold relative to its expression under ambient N deposition. Fungal community composition was examined at the most southerly of the four sites, in which consistently lower levels of cbhI and lcc gene expression were observed over a two-year period. We recovered 19 basidiomycete and 28 ascomycete rDNA 28S operational taxonomic units; Athelia, Sistotrema, Ceratobasidium and Ceratosebacina taxa dominated the basidiomycete assemblage, and Leotiomycetes dominated the ascomycetes. Simulated N deposition increased the proportion of basidiomycete sequences recovered from forest floor, whereas the proportion of ascomycetes in the community was significantly lower under elevated N deposition. Our results suggest that chronic atmospheric N deposition may lower decomposition rates through a combination of reduced expression of ligninolytic genes such as lcc, and compositional changes in the fungal community.

Reverse transcription-PCR methods significantly impact richness and composition measures of expressed fungal cellobiohydrolase I genes in soil and litter

The importance of soil fungi in complex carbon degradation and the recent identification of genes involved in this process have sparked considerable interest in examining fungal gene expression in situ. Expression of target eukaryotic genes is commonly examined using reverse transcription (RT)-PCR, during which single-stranded (ss) complementary DNA (cDNA) is synthesized from an oligo (dT) primer and the gene of interest is subsequently amplified by PCR using gene specific primers. Another method that is being increasingly employed in environmental gene expression studies is SMART PCR, which generates and amplifies double-stranded (ds) complementary DNA (cDNA) from sscDNA using PCR, prior to gene-specific PCR. We performed a replicated comparison of these two methods using RNA extracted from forest soil and litter to determine if the two approaches yielded comparable results. Richness, composition and reproducibility of gene expression profiles of the fungal glycosyl hydrolase family 7 (GH7) cellobiohydrolase I gene (cbhI) were examined when amplified from sscDNA or dscDNA synthesized using SMART PCR. In the dscDNA libraries from soil or litter samples, richness was significantly reduced and the composition was altered relative to sscDNA libraries. Library composition was significantly more reproducible among replicate sscDNA libraries than among parallel dscDNA libraries from litter. In sum, the reduced richness and altered composition produced in the dscDNA libraries could substantially influence ecological interpretations of the data. Defining the factors underpinning the methodological biases will potentially aid in optimizing the design of gene expression studies in soils and other complex environmental samples.

Mining metagenomes for novel cellulase genes

Cellulases hydrolyze the β-1,4 linkages of cellulose and are widely used in food, brewing and wine, animal feed, textiles and laundry, and pulp and paper industries, especially for hydrolyzing cellulosic materials into sugars, which can be fermented to produce useful products such as ethanol. Metagenomics has become an alternative approach to conventional culture-dependent methods as it allows exhaustive mining of microbial genomes in their natural environments. This review covers the current state of research and challenges in mining novel cellulase genes from the metagenomes of various environments, and discusses the potential biotechnological applications of metagenome-derived cellulases.