Innovations in CAZyme gene diversity and its modification for biorefinery applications

For sustainable growth, concept of biorefineries as recourse to the "fossil derived" energy source is important. Here, the Carbohydrate Active enZymes (CAZymes) play decisive role in generation of biofuels and related sugar-based products utilizing lignocellulose as a carbon source. Given their industrial significance, extensive studies on the evolution of CAZymes have been carried out. Various bacterial and fungal organisms have been scrutinized for the development of CAZymes, where advance techniques for strain enhancement such as CRISPR and analysis of specific expression systems have been deployed. Specific Omic-based techniques along with protein engineering have been adopted to unearth novel CAZymes and improve applicability of existing enzymes. In-Silico computational research and functional annotation of new CAZymes to synergy experiments are being carried out to devise cocktails of enzymes for use in biorefineries. Thus, with the establishment of these technologies, increased diversity of CAZymes with broad span of functions and applications is seen.

Improved endoglucanase production and mycelial biomass of some ericoid fungi

Fungal species associated with ericaceous plant roots produce a number of enzymes and other bio-active metabolites in order to enhance survival of their host plants in natural environments. This study focussed on endoglucanase production from root associated ericoid mycorrhizal and dark septate endophytic fungal isolates. Out of the five fungal isolates screened, Leohumicola sp. (ChemRU330/PPRI 13195) had the highest relative enzyme activity and was tested along with isolates belonging to Hyloscyphaceae (EdRU083/PPRI 17284) and Leotiomycetes (EdRU002/PPRI 17261) for endoglucanase production under different pH and nutritional conditions that included: carbon sources, nitrogen sources and metal ions, at an optimum temperature of 28 °C. An optimal of pH 5.0 produced enzyme activity of 3.99, 2.18 and 4.31 (U/mg protein) for isolates EdRU083, EdRU002 and Leohumicola sp. respectively. Increased enzyme activities and improved mycelial biomass production were obtained in the presence of supplements such as potassium, sodium, glucose, maltose, cellobiose, tryptone and peptone. While NaFe-EDTA and Co2+ inhibited enzyme activity. The potential role of these fungi as a source of novel enzymes is an ongoing objective of this study.

Differences in carbon source utilisation by orchid mycorrhizal fungi from common and endangered species of Caladenia (Orchidaceae)

Terrestrial orchids depend on orchid mycorrhizal fungi (OMF) as symbionts for their survival, growth and nutrition. The ability of OMF from endangered orchid species to compete for available resources with OMF from common species may affect the distribution, abundance and therefore conservation status of their orchid hosts. Eight symbiotically effective OMF from endangered and more common Caladenia species were tested for their ability to utilise complex insoluble and simple soluble carbon sources produced during litter degradation by growth with different carbon sources in liquid medium to measure the degree of OMF variation with host conservation status or taxonomy. On simple carbon sources, fungal growth was assessed by biomass. On insoluble substrates, ergosterol content was assessed using ultra-performance liquid chromatography (UPLC). The OMF grew on all natural materials and complex carbon sources, but produced the greatest biomass on xylan and starch and the least on bark and chitin. On simple carbon sources, the greatest OMF biomass was measured on most hexoses and disaccharides and the least on galactose and arabinose. Only some OMF used sucrose, the most common sugar in green plants, with possible implications for symbiosis. OMF from common orchids produced more ergosterol and biomass than those from endangered orchids in the Dilatata and Reticulata groups but not in the Patersonii and Finger orchids. This suggests that differences in carbon source utilisation may contribute to differences in the distribution of some orchids, if these differences are retained on site.

Understanding plant cell-wall remodelling during the symbiotic interaction between Tuber melanosporum and Corylus avellana using a carbohydrate microarray

A combined approach, using a carbohydrate microarray as a support for genomic data, has revealed subtle plant cell-wall remodelling during Tuber melanosporum and Corylus avellana interaction. Cell walls are involved, to a great extent, in mediating plant-microbe interactions. An important feature of these interactions concerns changes in the cell-wall composition during interaction with other organisms. In ectomycorrhizae, plant and fungal cell walls come into direct contact, and represent the interface between the two partners. However, very little information is available on the re-arrangement that could occur within the plant and fungal cell walls during ectomycorrhizal symbiosis. Taking advantage of the Comprehensive Microarray Polymer Profiling (CoMPP) technology, the current study has had the aim of monitoring the changes that take place in the plant cell wall in Corylus avellana roots during colonization by the ascomycetous ectomycorrhizal fungus T. melanosporum. Additionally, genes encoding putative plant cell-wall degrading enzymes (PCWDEs) have been identified in the T. melanosporum genome, and RT-qPCRs have been performed to verify the expression of selected genes in fully developed C. avellana/T. melanosporum ectomycorrhizae. A localized degradation of pectin seems to occur during fungal colonization, in agreement with the growth of the ectomycorrhizal fungus through the middle lamella and with the fungal gene expression of genes acting on these polysaccharides.

Reduced genomic potential for secreted plant cell-wall-degrading enzymes in the ectomycorrhizal fungus Amanita bisporigera, based on the secretome of Trichoderma reesei

Based on the analysis of its genome sequence, the ectomycorrhizal (ECM) basidiomycetous fungus Laccaria bicolor was shown to be lacking many of the major classes of secreted enzymes that depolymerize plant cell wall polysaccharides. To test whether this is also a feature of other ECM fungi, we searched a survey genome database of Amanita bisporigera with the proteins found in the secretome of Trichoderma reesei (syn. Hypocrea jecorina), a biochemically well-characterized industrial fungus. Additional proteins were also used as queries to compensate for major groups of cell-wall-degrading enzymes lacking in the secretome of T. reesei and to substantiate conclusions drawn from the T. reesei collection. By MS/MS-based "shotgun" proteomics, 80 proteins were identified in culture filtrates of T. reesei strain RUTC30 grown on corn cell walls and in a commercial "cellulase" preparation, Spezyme CP. The two T. reesei enzyme preparations were qualitatively and quantitatively similar, the most striking difference being the lack of at least five major peptidases from the commercial enzyme mixture. Based on our analysis of A. bisporigera, this ECM fungus is deficient in many major classes of cell-wall-degrading enzymes, including both glycosyl hydrolases and carbohydrate esterases. By comparison, the genomes of the saprophytic basidiomycetes Coprinopsis cinerea and Galerina marginata (using a genome survey sequence approximately equivalent in depth to that of A. bisporigera) have, like T. reesei, a much more complete complement of cell-wall-degrading enzymes.

Mycorrhizal fungi as drivers of ecosystem processes in heathland and boreal forest biomes

The importance of mycorrhizas in heathland and boreal forest biomes, which together cover much of the landmass of the Northern Hemisphere and store most of the global stocks of carbon, is reviewed. The taxonomic affinities of the organisms forming these symbiotic partnerships are assessed, and the distinctive structural features of the ericoid mycorrhizas of heathland dwarf shrubs and the ectomycorrhizas of boreal forest trees are described. It is stressed that neither in terms of the geographical distribution of the plants nor in terms of the occurrence of their characteristic mycorrhizas in the soil profile should these biomes be considered to be mutually exclusive. What unites them is their apparent affinity for acidic organic soils of inherently low accessibility of the major nutrients nitrogen (N) and phosphorus (P). These properties relate directly to the nature of the nutrient-poor recalcitrant litter produced by their host plants and through positive-feedback mechanisms that are reinforced by selective removal of labile nutrients by the mycorrhizas. We suggest that coevolution of these plant litter traits with mycorrhizal associations that are adapted to them has been one of the defining features of these ecosystems. Ericoid and ectomycorrhizal fungi have biochemical and physiological attributes that make them highly efficient at scavenging for organic sources of N and P in surface soil horizons. In so doing, they restrict supplies of these elements to the decomposer communities. Case studies involving exploitation of N and P in defined organic substrates are described. In both biomes the dominant plants depend upon the abilities of their fungal partners to recover nutrients, so the symbioses control nutrient cycles, productivity, species composition, and functioning of these ecosystems. It is in this context that the fungal symbionts are here considered to be drivers of nutritional processes in their respective biomes. Through their influences upon the quality of carbon residues mycorrhizal fungi must also affect the sink-source balance for this key element in soil. There is an urgent need for the evaluation of the relative contributions of symbiotic and saprotrophic components of the microflora to the processes of carbon storage and cycling in these biomes, particularly in the context of global climate change and impacts of anthropogenic pollutant N deposition.Key words: carbon sequestration, peatlands, C/N ratios, carbon and nutrient cycles.

Development of markers for simple sequence repeat-rich regions that discriminate between Pisolithus albus and P. microcarpus

Inter-simple sequence repeat PCR (ISSR-PCR) was used to develop markers for simple sequence repeat-rich (SSR) regions for investigation of genetic relatedness of Pisolithus isolates collected from eastern mainland Australia. Primers were designed to amplify ten SSR-rich regions and these were used to screen 14 Pisolithus isolates. Two amplified loci showed size polymorphisms among the isolates (regarded as polymorphic), two were monomorphic for all isolates, while the remainder amplified alleles for only some isolates. UPGMA analysis of the alleles for each isolate at each locus together with ITS-RFLP analysis, separated the isolates into groups. These two groups appear to correspond to isolates that ITS sequence data have previously separated as P. albus and P. microcarpus.

Mycorrhizas and nutrient cycling in ecosystems - a journey towards relevance?

Progress towards understanding the extent to which mycorrhizal fungi are involved in the mobilization of nitrogen (N) and phosphorus (P) from natural substrates is reviewed here. While mycorrhiza research has emphasized the role of the symbiosis in facilitation of capture of these nutrients in ionic form, attention has shifted since the mid-1980s to analysing the mycorrhizal fungal abilities to release N and P from the detrital materials of microbial faunal and plant origins, which are the primary sources of these elements in terrestrial ecosystems. Ericoid, and some ectomycorrhizal fungi have the potential to be directly involved in attack both on structural polymers, which may render nutrients inaccessible, and in mobilization of N and P from the organic polymers in which they are sequestered. The advantages to the plant of achieving intervention in the microbial mobilization-immobilization cycles are stressed. While the new approaches may initially lack the precision achieved in studies of readily characterized ionic forms of N and P, they do provide insights of greater ecological relevance. The results support the hypothesis that selection has favoured ericoid and ectomycorrhizal systems with well developed saprotrophic capabilities in those ecosystems characterized by retention of N and P as organic complexes in the soil. The need for further investigation of the abilities of arbuscular mycorrhizal fungi to intervene in nutrient mobilization processes is stressed.

Glucosidase inhibitor from Umbilicaria esculenta

Inhibitory activity toward beta-glucosidase was detected in extracts of the lichen, Umbilicaria esculenta. The extract showed strong inhibition of disaccharide hydrolytic enzymes of mold and mammalian origin, but weak or no inhibition of polysaccharide hydrolytic enzymes except glucoamylase and laminarinase. The inhibitor in the extract was very stable, retaining more than 95% of its activity when treated with heat, acid, alkali, and some hydrolytic enzymes. Purified inhibitor was identified as 1-deoxynojirimycin (1,5-dideoxy-1,5-immino-D-glucitol) by NMR spectrometry, which was known to be produced by Streptomyces sp. and the plant Morus sp. Extracts from Parmelia austrosinensis, Parmelia praesorediosa, and an unidentified lichen species, showed glucosidase inhibitory activities similar to U. esculenta.