Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

Pure lignin induces overexpression of cytochrome P450 (CYP) encoding genes and brings insights into the lignocellulose depolymerization by Trametes villosa

Trametes villosa is a remarkable white-rot fungus (WRF) with the potential to be applied in lignocellulose conversion to obtain chemical compounds and biofuels. Lignocellulose breakdown by WRF is carried out through the secretion of oxidative and hydrolytic enzymes. Despite the existing knowledge about this process, the complete molecular mechanisms involved in the regulation of this metabolic system have not yet been elucidated. Therefore, in order to understand the genes and metabolic pathways regulated during lignocellulose degradation, the strain T. villosa CCMB561 was cultured in media with different carbon sources (lignin, sugarcane bagasse, and malt extract). Subsequently, biochemical assays and differential gene expression analysis by qPCR and high-throughput RNA sequencing were carried out. Our results revealed the ability of T. villosa CCMB561 to grow on lignin (AL medium) as the unique carbon source. An overexpression of Cytochrome P450 was detected in this medium, which may be associated with the lignin O-demethylation pathway. Clusters of up-regulated CAZymes-encoding genes were identified in lignin and sugarcane bagasse, revealing that T. villosa CCMB561 acts simultaneously in the depolymerization of lignin, cellulose, hemicellulose, and pectin. Furthermore, genes encoding nitroreductases and homogentisate-1,2-dioxygenase that act in the degradation of organic pollutants were up-regulated in the lignin medium. Altogether, these findings provide new insights into the mechanisms of lignocellulose degradation by T. villosa and confirm the ability of this fungal species to be applied in biorefineries and in the bioremediation of organic pollutants.

Whole-genome sequencing and comparative genomic analyses of the medicinal fungus Sanguinoderma infundibulare in Ganodermataceae

Sanguinoderma infundibulare is a newly discovered species of Ganodermataceae known to have high medicinal and ecological values. In this study, the whole-genome sequencing and comparative genomic analyses were conducted to further understand Ganodermataceae's genomic structural and functional characteristics. Using the Illumina NovaSeq and PacBio Sequel platforms, 88 scaffolds were assembled to obtain a 48.99-Mb high-quality genome of S. infundibulare. A total of 14,146 protein-coding genes were annotated in the whole genome, with 98.6% of complete benchmarking universal single-copy orthologs (BUSCO) scores. Comparative genomic analyses were conducted among S. infundibulare, Sanguinoderma rugosum, Ganoderma lucidum, and Ganoderma sinense to determine their intergeneric differences. The 4 species were found to share 4,011 orthogroups, and 24 specific gene families were detected in the genus Sanguinoderma. The gene families associated with carbohydrate esterase in S. infundibulare were significantly abundant, which was reported to be involved in hemicellulose degradation. One specific gene family in Sanguinoderma was annotated with siroheme synthase, which may be related to the typical characteristics of fresh pore surface changing to blood red when bruised. This study enriched the available genome data for the genus Sanguinoderma, elucidated the differences between Ganoderma and Sanguinoderma, and provided insights into the characteristics of the genome structure and function of S. infundibulare.

Molecular insights into the microbial degradation of sediment-derived DOM in a macrophyte-dominated lake under aerobic and hypoxic conditions

The mineralization of dissolved organic matter (DOM) in sediments is an important factor leading to the eutrophication of macrophyte-dominated lakes. However, the changes in the molecular characteristics of sediment-derived DOM during microbial degradation in macrophyte-dominated lakes are not well understood. In this study, the microbial degradation process of sediment-derived DOM in Lake Caohai under aerobic and hypoxic conditions was investigated using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomics. The results revealed that the microbial degradation of sediment-derived DOM in macrophyte-dominated lakes was more intense under aerobic conditions. The microorganisms mainly metabolized the protein-like substances in the macrophyte-dominated lakes, and the carbohydrate-active enzyme genes and protein/lipid-like degradation genes played key roles in sediment-derived DOM degradation. Organic compounds with high H/C ratios such as lipids, carbohydrates, and protein/lipid-like compounds were preferentially removed by microorganisms during microbial degradation. Meanwhile, there was an increase in the abundance of organic molecular formula with a high aromaticity such as tannins and unsaturated hydrocarbons with low molecular weight and low double bond equivalent. In addition, aerobic/hypoxic environments can alter microbial metabolic pathways of sediment-derived DOM by affecting the relative abundance of microbial communities (e.g., Gemmatimonadetes and Acidobacteria) and functional genes (e.g., ABC.PE.P1 and ABC.PE.P) in macrophyte-dominated lakes. The abundances of lipids, unsaturated hydrocarbons, and protein compounds in aerobic environments decreased by 58 %, 50 %, and 44 %, respectively, compared to in hypoxic environments under microbial degradation. The results of this study deepen our understanding of DOM biodegradation in macrophyte-dominated lakes under different redox environments and provide new insights into nutrients releases from sediment and continuing eutrophication in macrophyte-dominated lakes.

Transcriptional effects of carbon and nitrogen starvation on Ganoderma boninense, an oil palm phytopathogen

BACKGROUND

Ganoderma boninense is a phytopathogen of oil palm, causing basal and upper stem rot diseases.

METHODS

The genome sequence was used as a reference to study gene expression during growth in a starved carbon (C) and nitrogen (N) environment with minimal sugar and sawdust as initial energy sources. This study was conducted to mimic possible limitations of the C-N nutrient sources during the growth of G. boninense in oil palm plantations.

RESULTS

Genome sequencing of an isolate collected from a palm tree in West Malaysia generated an assembly of 67.12 Mb encoding 19,851 predicted genes. Transcriptomic analysis from a time course experiment during growth in this starvation media identified differentially expressed genes (DEGs) that were found to be associated with 29 metabolic pathways. During the active growth phase, 26 DEGs were related to four pathways, including secondary metabolite biosynthesis, carbohydrate metabolism, glycan metabolism and mycotoxin biosynthesis. G. boninense genes involved in the carbohydrate metabolism pathway that contribute to the degradation of plant cell walls were up-regulated. Interestingly, several genes associated with the mycotoxin biosynthesis pathway were identified as playing a possible role in pathogen-host interaction. In addition, metabolomics analysis revealed six metabolites, maltose, xylobiose, glucooligosaccharide, glycylproline, dimethylfumaric acid and arabitol that were up-regulated on Day2 of the time course experiment.

CONCLUSIONS

This study provides information on genes expressed by G. boninense in metabolic pathways that may play a role in the initial infection of the host.

Whole genome structural predictions reveal hidden diversity in putative oxidative enzymes of the lignocellulose-degrading ascomycete Parascedosporium putredinis NO1

IMPORTANCE

An annotated reference genome has revealed P. putredinis NO1 as a useful resource for the identification of new lignocellulose-degrading enzymes for biorefining of woody plant biomass. Utilizing a "structure-omics"-based searching strategy, we identified new potentially lignocellulose-active sequences that would have been missed by traditional sequence searching methods. These new identifications, alongside the discovery of novel enzymatic functions from this underexplored lineage with the recent discovery of a new phenol oxidase that cleaves the main structural β-O-4 linkage in lignin from P. putredinis NO1, highlight the underexplored and poorly represented family Microascaceae as a particularly interesting candidate worthy of further exploration toward the valorization of high value biorenewable products.

Degradation of polypropylene by fungi Coniochaeta hoffmannii and Pleurostoma richardsiae

The urgent need for better disposal and recycling of plastics has motivated a search for microbes with the ability to degrade synthetic polymers. While microbes capable of metabolizing polyurethane and polyethylene terephthalate have been discovered and even leveraged in enzymatic recycling approaches, microbial degradation of additive-free polypropylene (PP) remains elusive. Here we report the isolation and characterization of two fungal strains with the potential to degrade pure PP. Twenty-seven fungal strains, many isolated from hydrocarbon contaminated sites, were screened for degradation of commercially used textile plastic. Of the candidate strains, two identified as Coniochaeta hoffmannii and Pleurostoma richardsiae were found to colonize the plastic fibers using scanning electron microscopy (SEM). Further experiments probing degradation of pure PP films were performed using C. hoffmannii and P. richardsiae and analyzed using SEM, Raman spectroscopy and Fourier transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR). The results showed that the selected fungi were active against pure PP, with distinct differences in the bonds targeted and the degree to which each was altered. Whole genome and transcriptome sequencing was conducted for both strains and the abundance of carbohydrate active enzymes, GC content, and codon usage bias were analyzed in predicted proteomes for each. Enzymatic assays were conducted to assess each strain's ability to degrade naturally occurring compounds as well as synthetic polymers. These investigations revealed potential adaptations to hydrocarbon-rich environments and provide a foundation for further investigation of PP degrading activity in C. hoffmannii and P. richardsiae.

Dominant influence of plants on soil microbial carbon cycling functions during natural restoration of degraded karst vegetation

The impacts of natural restoration projects on soil microbial carbon (C) cycling functions have not been well recognized despite their wide implementation in the degraded karst areas of southwest China. In this study, metagenomic sequencing assays were conducted on functional genes and microorganisms related to soil C-cycling at three natural restoration stages (shrubbery, TG; secondary forest, SG; old-growth forest, OG) in the southeast of Guizhou Province, China. The aims were to investigate the changes in microbial potentials responsible for soil C cycling and the underlying driving forces. The natural restoration resulted in vegetation establishment at all three restoration stages, rendering alterations of soil microbial C cycle functions as indicated by metagenomic gene assays. When TG was restored into OG, the number and diversity of genes and microorganisms involved in soil C cycling remained unchanged, but their composition underwent significant shifts. Specifically, microbial potentials for soil C decomposition exhibited an increase driven by the collaborative efforts of plants and soils, while microbial potentials for soil C biosynthesis displayed an initial upswing followed by a subsequent decline which was primarily influenced by plants alone. In comparison to soil nutrients, it was determined that plant diversities served as the primary driving factor for the alterations in microbial carbon cycle potentials. Soil microbial communities involved in C cycling were predominantly attributed to Proteobacteria (31.87%-40.25%) and Actinobacteria (11.29%-26.07%), although their contributions varied across the three restoration stages. The natural restoration of degraded karst vegetation thus influences soil microbial C cycle functions by enhancing C decomposition potentials and displaying a nuanced pattern of biosynthesis potentials, primarily influenced by above-ground plants. These results provide valuable new insights into the regulation of soil C cycling during the restoration of degraded karst vegetation from genetic and microbial perspectives.

Comparative Genomic Analysis and Metabolic Potential Profiling of a Novel Culinary-Medicinal Mushroom, Hericium rajendrae (Basidiomycota)

Hericium rajendrae is an emerging species in the genus Hericium with few members. Despite being highly regarded due to its rarity, knowledge about H. rajendrae remains limited. In this study, we sequenced, de novo assembled, and annotated the complete genome of H. rajendrae NPCB A08, isolated from the Qinling Mountains in Shaanxi, China, using the Illumina NovaSeq and Nanopore PromethION technologies. Comparative genomic analysis revealed similarities and differences among the genomes of H. rajendrae, H. erinaceus, and H. coralloides. Phylogenomic analysis revealed the divergence time of the Hericium genus, while transposon analysis revealed evolutionary characteristics of the genus. Gene family variation reflected the expansion and contraction of orthologous genes among Hericium species. Based on genomic bioinformation, we identified the candidate genes associated with the mating system, carbohydrate-active enzymes, and secondary metabolite biosynthesis. Furthermore, metabolite profiling and comparative gene clusters analysis provided strong evidence for the biosynthetic pathway of erinacines in H. rajendrae. This work provides the genome of H. rajendrae for the first time, and enriches the genomic content of the genus Hericium. These findings also facilitate the application of H. rajendrae in complementary drug research and functional food manufacturing, advancing the field of pharmaceutical and functional food production involving H. rajendrae.

A repertoire of candidate effector proteins of the fungus Ceratocystis cacaofunesta

The genus Ceratocystis includes many phytopathogenic fungi that affect different plant species. One of these is Ceratocystis cacaofunesta, which is pathogenic to the cocoa tree and causes Ceratocystis wilt, a lethal disease for the crop. However, little is known about how this pathogen interacts with its host. The knowledge and identification of possible genes encoding effector proteins are essential to understanding this pathosystem. The present work aimed to predict genes that code effector proteins of C. cacaofunesta from a comparative analysis of the genomes of five Ceratocystis species available in databases. We performed a new genome annotation through an in-silico analysis. We analyzed the secretome and effectorome of C. cacaofunesta using the characteristics of the peptides, such as the presence of signal peptide for secretion, absence of transmembrane domain, and richness of cysteine residues. We identified 160 candidate effector proteins in the C. cacaofunesta proteome that could be classified as cytoplasmic (102) or apoplastic (58). Of the total number of candidate effector proteins, 146 were expressed, presenting an average of 206.56 transcripts per million. Our database was created using a robust bioinformatics strategy, followed by manual curation, generating information on pathogenicity-related genes involved in plant interactions, including CAZymes, hydrolases, lyases, and oxidoreductases. Comparing proteins already characterized as effectors in Sordariomycetes species revealed five groups of protein sequences homologous to C. cacaofunesta. These data provide a valuable resource for studying the infection mechanisms of these pathogens in their hosts.

Advances in microbial pretreatment for biorefining of perennial grasses

Perennial grasses are potentially abundant sources of biomass for biorefineries, which can produce high yields with low input requirements, and many added environmental benefits. However, perennial grasses are highly recalcitrant to biodegradation and may require pretreatment before undergoing many biorefining pathways. Microbial pretreatment uses the ability of microorganisms or their enzymes to deconstruct plant biomass and enhance its biodegradability. This process can enhance the enzymatic digestibility of perennial grasses, enabling saccharification with cellulolytic enzymes to produce fermentable sugars and derived fermentation products. Similarly, microbial pretreatment can increase the methanation rate when the grasses are used to produce biogas through anaerobic digestion. Microorganisms can also increase the digestibility of the grasses to improve their quality as animal feed, enhance the properties of grass pellets, and improve biomass thermochemical conversion. Metabolites produced by fungi or bacteria during microbial pretreatment, such as ligninolytic and cellulolytic enzymes, can be further recovered as added-value products. Additionally, the action of the microorganisms can release chemicals with commercialization potential, such as hydroxycinnamic acids and oligosaccharides, from the grasses. This review explores the recent advances and remaining challenges in using microbial pretreatment for perennial grasses with the goal of obtaining added-value products through biorefining. It emphasizes recent trends in microbial pretreatment such as the use of microorganisms as part of microbial consortia or in unsterilized systems, the use and development of microorganisms and consortia capable of performing more than one biorefining step, and the use of cell-free systems based on microbial enzymes. KEY POINTS: • Microorganisms or enzymes can reduce the recalcitrance of grasses for biorefining • Microbial pretreatment effectiveness depends on the grass-microbe interaction • Microbial pretreatment can generate value added co-products to enhance feasibility.

Genomic insights into Aspergillus sydowii 29R-4-F02: unraveling adaptive mechanisms in subseafloor coal-bearing sediment environments

Introduction

Aspergillussydowii is an important filamentous fungus that inhabits diverse environments. However, investigations on the biology and genetics of A. sydowii in subseafloor sediments remain limited.

Methods

Here, we performed de novo sequencing and assembly of the A. sydowii 29R-4-F02 genome, an isolate obtained from approximately 2.4 km deep, 20-million-year-old coal-bearing sediments beneath the seafloor by employing the Nanopore sequencing platform.

Results and Discussion

The generated genome was 37.19 Mb with GC content of 50.05%. The final assembly consisted of 11 contigs with N50 of 4.6 Mb, encoding 12,488 putative genes. Notably, the subseafloor strain 29R-4-F02 showed a higher number of carbohydrate-active enzymes (CAZymes) and distinct genes related to vesicular fusion and autophagy compared to the terrestrial strain CBS593.65. Furthermore, 257 positively selected genes, including those involved in DNA repair and CAZymes were identified in subseafloor strain 29R-4-F02. These findings suggest that A. sydowii possesses a unique genetic repertoire enabling its survival in the extreme subseafloor environments over tens of millions of years.

Effects of Different Nitrogen Levels on Lignocellulolytic Enzyme Production and Gene Expression under Straw-State Cultivation in Stropharia rugosoannulata

Stropharia rugosoannulata has been used in environmental engineering to degrade straw in China. The nitrogen and carbon metabolisms are the most important factors affecting mushroom growth, and the aim of this study was to understand the effects of different nitrogen levels on carbon metabolism in S. rugosoannulata using transcriptome analysis. The mycelia were highly branched and elongated rapidly in A3 (1.37% nitrogen). GO and KEGG enrichment analyses revealed that the differentially expressed genes (DEGs) were mainly involved in starch and sucrose metabolism; nitrogen metabolism; glycine, serine and threonine metabolism; the MAPK signaling pathway; hydrolase activity on glycosyl bonds; and hemicellulose metabolic processes. The activities of nitrogen metabolic enzymes were highest in A1 (0.39% nitrogen) during the three nitrogen levels (A1, A2 and A3). However, the activities of cellulose enzymes were highest in A3, while the hemicellulase xylanase activity was highest in A1. The DEGs associated with CAZymes, starch and sucrose metabolism and the MAPK signaling pathway were also most highly expressed in A3. These results suggested that increased nitrogen levels can upregulate carbon metabolism in S. rugosoannulata. This study could increase knowledge of the lignocellulose bioconversion pathways and improve biodegradation efficiency in Basidiomycetes.

Biological significance of carbohydrate active enzymes and searching their inhibitors for therapeutic applications

Glycans are the most abundant and diverse group of biomolecules with a crucial role in all the biological processes. Their structural and functional diversity is not genetically encoded, but depends on Carbohydrate Active Enzymes (CAZymes) which carry out all catalytic activities in terms of synthesis, modification, and degradation. CAZymes comprise large families of enzymes with specific functions and are widely used for various commercial applications ranging from biofuel production to textile and food industries with impact on biorefineries. To understand the structure and functional mechanism of these CAZymes for their modification for industrial use, together with knowledge of therapeutic aspects of their dysfunction associated with various diseases, CAZyme inhibitors can be used as a valuable tool. In search for new inhibitors, the screening of various secondary metabolites using high-throughput techniques and rational design techniques have been explored. The inhibitors can thus help tune CAZymes and are emerging as a potential research interest.

The First Whole Genome Sequencing of Agaricus bitorquis and Its Metabolite Profiling

Agaricus bitorquis, an emerging wild mushroom with remarkable biological activities and a distinctive oversized mushroom shape, has gained increasing attention in recent years. Despite its status as an important resource of wild edible fungi, knowledge about this mushroom is still limited. In this study, we used the Illumina NovaSeq and Nanopore PromethION platforms to sequence, de novo assemble, and annotate the whole genome and mitochondrial genome (mitogenome) of the A. bitorquis strain BH01 isolated from Bosten Lake, Xinjiang Province, China. Using the genome-based biological information, we identified candidate genes associated with mating type and carbohydrate-active enzymes in A. bitorquis. Cluster analysis based on P450 of basidiomycetes revealed the types of P450 members of A. bitorquis. Comparative genomic, mitogenomic, and phylogenetic analyses were also performed, revealing interspecific differences and evolutionary features of A. bitorquis and A. bisporus. In addition, the molecular network of metabolites was investigated, highlighting differences in the chemical composition and content of the fruiting bodies of A. bitorquis and A. bisporus. The genome sequencing provides a comprehensive understanding and knowledge of A. bitorquis and the genus Agaricus mushrooms. This work provides valuable insights into the potential for artificial cultivation and molecular breeding of A. bitorquis, which will facilitate the development of A. bitorquis in the field of edible mushrooms and functional food manufacture.

Linking processes to community functions—insights into litter decomposition combining fungal metatranscriptomics and environmental NMR profiling

In forest ecosystems, decomposition is essential for carbon and nutrient cycling and therefore a key process for ecosystem functioning. During the decomposition process, litter chemistry, involved decomposer organisms, and enzymatic activity change interdependently. Chemical composition of the litter is the most complex and dynamic component in the decomposition process and therefore challenging to assess holistically. In this study, we aimed to characterize chemical shifts during decomposition and link them to changes in decomposer fungal activity. We characterized the chemical composition of freshly fallen autumn leaves of European beech (Fagus sylvatica) and the corresponding leaf litter after 1 year of decomposition by proton nuclear magnetic resonance spectroscopy. We further tested the applicability of spiking experiments for qualitative and quantitative characterization of leaves and litter chemistry. The composition and transcriptional activity of fungal communities was assessed by high-throughput Illumina sequencing in the same litter samples. We were able to distinguish freshly fallen leaves from 1-year-old litter based on their chemical composition. Chemical composition of leaves converged among regions with progressing decomposition. Fungal litter communities differed in composition among regions, but they were functionally redundant according to the expression of genes encoding litter degrading enzymes (CAZymes). Fungi of the saprotrophic genera Mycena and Chalara correlated with transcription of litter-degrading CAZymes in 1-year-old litter. Forestry measures influenced the diversity and transcription rate of the detected CAZymes transcripts in litter. Their expression was primarily predicted by composition of the soluble chemical fraction of the litter. Environmental NMR fingerprints thus proved valuable for inferring ecological contexts. We propose and discuss a holistic framework to link fungal activity, enzyme expression, and chemical composition.

Genomic and Metabolomic Analyses of the Medicinal Fungus Inonotus hispidus for Its Metabolite's Biosynthesis and Medicinal Application

Inonotus hispidus mushroom is a traditional medicinal fungus with anti-cancer, antioxidation, and immunomodulatory activities, and it is used in folk medicine as a treatment for indigestion, cancer, diabetes, and gastric illnesses. Although I. hispidus is recognized as a rare edible medicinal macrofungi, its genomic sequence and biosynthesis potential of secondary metabolites have not been investigated. In this study, using Illumina NovaSeq combined with the PacBio platform, we sequenced and de novo assembled the whole genome of NPCB_001, a wild I. hispidus isolate from the Aksu area of Xinjiang Province, China. Comparative genomic and phylogenomic analyses reveal interspecific differences and evolutionary traits in the genus Inonotus. Bioinformatics analysis identified candidate genes associated with mating type, polysaccharide synthesis, carbohydrate-active enzymes, and secondary metabolite biosynthesis. Additionally, molecular networks of metabolites exhibit differences in chemical composition and content between fruiting bodies and mycelium, as well as association clusters of related compounds. The deciphering of the genome of I. hispidus will deepen the understanding of the biosynthesis of bioactive components, open the path for future biosynthesis research, and promote the application of Inonotus in the fields of drug research and functional food manufacturing.

Homokaryotic High-Quality Genome Assembly of Medicinal Fungi Wolfiporia hoelen Reveals Auto-Regulation and High-Temperature Adaption of Probable Two-Speed Genome

Sclerotia of Wolfiporia hoelen are one of the most important traditional Chinese medicines and are commonly used in China, Japan, Korea, and other Asian countries. In the present study, we presented the first high-quality homokaryotic genome of W. hoelen with 14 chromosomes which was evaluated with assembly index, telomere position detection, and whole-genome collinearity. A 64.44 Mb genome was assembled with a Contig N50 length of 3.76 Mb. The imbalanced distribution of transposons and chromosome characters revealed the probable two-speed genome of W. hoelen. High consistency between methylation and transposon conserved the genome stability. The expansion of the gene family about signal transduction and nutritional transport has intimate relationships with sclerotial formation. Up-regulation of expression for distinctive decomposition enzymes, ROS clearance genes, biosynthesis of unsaturated fatty acids, and change of the cell wall components maintained high-speed growth of mycelia that may be the high-temperature adaption strategy of W. hoelen. Further, the analysis of mating-control genes demonstrated that HD3 probably had no function on mating recognition, with the HD protein in a distant genetic with known species. Overall, the high-quality genome of W. hoelen provided crucial information for genome structure and stability, high-temperature adaption, and sexual and asexual process.

Carbohydrate active enzyme system in rumen fungi: a review

Hydrolysis and dehydration reactions of carbohydrates, which are used as energy raw materials by all living things in nature, are controlled by Carbohydrate Active Enzyme (CAZy) systems. These enzymes are also used in different industrial areas today. There are different types of microorganisms that have the CAZy system and are used in the industrial sector. Apart from current organisms, there are also rumen fungi within the group of candidate microorganisms with the CAZy system. It has been reported that xylanase (EC3.2.1.8 and EC3.2.1.37) enzyme, a member of the glycoside hydrolase enzyme family obtained from Trichoderma sp. and used especially in areas such as bread, paper, and feed industry, is more synthesized in rumen fungi such as Orpinomyces sp. and Neocallimastix sp. Therefore, this study reviews Neocallimastixsp., Orpinomyces sp., Caecomyces sp., Piromyces sp., and Anaeromyces sp., registered in the CAZy and Mycocosm database for rumen fungi to have both CAZy enzyme activity and to be an alternative microorganism in the industry. Furthermore the CAZy enzyme activities of the strains are investigated. The review shows thatNeocallimax sp. and Orpinomyces sp. areconsidered as candidate microorganisms.

Role of ascomycete and basidiomycete fungi in meeting established and emerging sustainability opportunities: a review

Fungal biomass is the future's feedstock. Non-septate Ascomycetes and septate Basidiomycetes, famously known as mushrooms, are sources of fungal biomass. Fungal biomass, which on averagely comprises about 34% protein and 45% carbohydrate, can be cultivated in bioreactors to produce affordable, safe, nontoxic, and consistent biomass quality. Fungal-based technologies are seen as attractive, safer alternatives, either substituting or complementing the existing standard technology. Water and wastewater treatment, food and feed, green technology, innovative designs in buildings, enzyme technology, potential health benefits, and wealth production are the key sectors that successfully reported high-efficiency performances of fungal applications. This paper reviews the latest technical know-how, methods, and performance of fungal adaptation in those sectors. Excellent performance was reported indicating high potential for fungi utilization, particularly in the sectors, yet to be utilized and improved on the existing fungal-based applications. The expansion of fungal biomass in the industrial-scale application for the sustainability of earth and human well-being is in line with the United Nations' Sustainable Development Goals.

Comparative Genomics of Three Aspergillus Strains Reveals Insights into Endophytic Lifestyle and Endophyte-Induced Plant Growth Promotion

Aspergillus includes both plant pathogenic and beneficial fungi. Although endophytes beneficial to plants have high potential for plant growth promotion and improving stress tolerance, studies on endophytic lifestyles and endophyte-plant interactions are still limited. Here, three endophytes belonging to Aspergillus, AS31, AS33, and AS42, were isolated. They could successfully colonize rice roots and significantly improved rice growth. The genomes of strains AS31, AS33, and AS42 were sequenced and compared with other Aspergillus species covering both pathogens and endophytes. The genomes of AS31, AS33, and AS42 were 36.8, 34.8, and 35.3 Mb, respectively. The endophytic genomes had more genes encoding carbohydrate-active enzymes (CAZymes) and small secreted proteins (SSPs) and secondary metabolism gene clusters involved in indole metabolism than the pathogens. In addition, these endophytes were able to improve Pi (phosphorus) accumulation and transport in rice by inducing the expression of Pi transport genes in rice. Specifically, inoculation with endophytes significantly increased Pi contents in roots at the early stage, while the Pi contents in inoculated shoots were significantly increased at the late stage. Our results not only provide important insights into endophyte-plant interactions but also provide strain and genome resources, paving the way for the agricultural application of Aspergillus endophytes.

Comparative analysis of genome-based CAZyme cassette in Antarctic Microbacterium sp. PAMC28756 with 31 other Microbacterium species

BACKGROUND

The genus Microbacterium belongs to the family Microbacteriaceae and phylum Actinobacteria. A detailed study on the complete genome and systematic comparative analysis of carbohydrate-active enzyme (CAZyme) among the Microbacterium species would add knowledge on metabolic and environmental adaptation. Here we present the comparative genomic analysis of CAZyme using the complete genome of Antarctic Microbacterium sp. PAMC28756 with other complete genomes of 31 Microbacterium species available.

OBJECTIVE

The genomic and CAZyme comparison of Microbacterium species and to rule out the specific features of CAZyme for the environmental and metabolic adaptation.

METHODS

Bacterial source were collected from NCBI database, CAZyme annotation of Microbacterium species was analyzed using dbCAN2 Meta server. Cluster of orthologous groups (COGs) analysis was performed using the eggNOG4.5 database. Whereas, KEGG database was used to compare and obtained the functional genome annotation information in carbohydrate metabolism and glyoxylate cycle.

RESULTS

Out of 32 complete genomes of Microbacterium species, strain No. 7 isolated from Activated Sludge showed the largest genomic size at 4.83 Mb. The genomic size of PAMC28756 isolated from Antarctic lichen species Stereocaulons was 3.54 Mb, the G + C content was 70.4% with 3,407 predicted genes, of which 3.36% were predicted CAZyme. In addition, while comparing the Glyoxylate cycle among 32 bacteria, except 10 strains, all other, including our strain have Glyoxylate pathway. PAMC28756 contained the genes that degrade cellulose, hemicellulose, amylase, pectinase, chitins and other exo-and endo glycosidases. Utilizing these polysaccharides can provides source of energy in an extreme environment. In addition, PAMC28756 assigned the (10.15%) genes in the carbohydrate transport and metabolism functional group closely related to the CAZyme for polysaccharides degradation.

CONCLUSIONS

The genomic content and CAZymes distribution was varied in Microbacterium species. There was the presence of more than 10% genes in the carbohydrate transport and metabolism functional group closely related to the CAZyme for polysaccharides degradation. In addition, occurrence of glyoxylate cycle for alternative utilization of carbon sources suggest the adaptation of PAMC28756 in the harsh microenvironment.

Systems biology-guided understanding of white-rot fungi for biotechnological applications: a review

Plant-derived biomass is the most abundant biogenic carbon source on Earth. Despite this, only a small clade of organisms known as white-rot fungi (WRF) can efficiently break down both the polysaccharide and lignin components of plant cell walls. This unique ability imparts a key role for WRF in global carbon cycling and highlights their potential utilization in diverse biotechnological applications. To date, research on WRF has primarily focused on their extracellular ‘digestive enzymes’ whereas knowledge of their intracellular metabolism remains underexplored. Systems biology is a powerful approach to elucidate biological processes in numerous organisms, including WRF. Thus, here we review systems biology methods applied to WRF to date, highlight observations related to their intracellular metabolism, and conduct comparative extracellular proteomic analyses to establish further correlations between WRF species, enzymes, and cultivation conditions. Lastly, we discuss biotechnological opportunities of WRF as well as challenges and future research directions.

Advanced research tools for fungal diversity and its impact on forest ecosystem

Fungi are dominant ecological participants in the forest ecosystems, which play a major role in recycling organic matter and channeling nutrients across trophic levels. Fungal populations are shaped by plant communities and environmental parameters, and in turn, fungal communities also impact the forest ecosystem through intrinsic participation of different fungal guilds. Mycorrhizal fungi result in conservation and stability of forest ecosystem, while pathogenic fungi can bring change in forest ecosystem, by replacing the dominant plant species with new or exotic plant species. Saprotrophic fungi, being ecological regulators in the forest ecosystem, convert dead tree logs into reusable constituents and complete the ecological cycles of nitrogen and carbon. However, fungal communities have not been studied in-depth with respect to functional, spatiotemporal, or environmental parameters. Previously, fungal diversity and its role in shaping the forest ecosystem were studied by traditional and laborious cultural methods, which were unable to achieve real-time results and draw a conclusive picture of fungal communities. This review highlights the latest advances in biological methods such as next-generation sequencing and meta'omics for observing fungal diversity in the forest ecosystem, the role of different fungal groups in shaping forest ecosystem, forest productivity, and nutrient cycling at global scales.

Whole-Genome Sequencing and Analysis of the White-Rot Fungus Ceriporia lacerata Reveals Its Phylogenetic Status and the Genetic Basis of Lignocellulose Degradation and Terpenoid Synthesis

Ceriporia lacerata is an endophytic white-rot fungus that has lignocellulolytic and terpenoid-biosynthetic abilities. However, little is known about the genomic architecture of this fungus, even at the genus level. In this study, we present the first de novo genome assembly of C. lacerata (CGMCC No. 10485), based on PacBio long-read and Illumina short-read sequencing. The size of the C. lacerata genome is approximately 36 Mb (N50, 3.4 Mb). It encodes a total of 13,243 genes, with further functional analysis revealing that these genes are primarily involved in primary metabolism and host interactions in this strain's saprophytic lifestyle. Phylogenetic analysis based on ITS demonstrated a primary evolutionary position for C. lacerata, while the phylogenetic analysis based on orthogroup inference and average nucleotide identity revealed high-resolution phylogenetic details in which Ceriporia, Phlebia, Phlebiopsis, and Phanerochaete belong to the same evolutionary clade within the order Polyporales. Annotation of carbohydrate-active enzymes across the genome yielded a total of 806 genes encoding enzymes that decompose lignocellulose, particularly ligninolytic enzymes, lytic polysaccharides monooxygenases, and enzymes involved in the biodegradation of aromatic components. These findings illustrate the strain's adaptation to woody habitats, which requires the degradation of lignin and various polycyclic aromatic hydrocarbons. The terpenoid-production potential of C. lacerata was evaluated by comparing the genes of terpenoid biosynthetic pathways across nine Polyporales species. The shared genes highlight the major part of terpenoid synthesis pathways, especially the mevalonic acid pathway, as well as the main pathways of sesquiterpenoid, monoterpenoid, diterpenoid, and triterpenoid synthesis, while the strain-specific genes illustrate the distinct genetic factors determining the synthesis of structurally diverse terpenoids. This is the first genomic analysis of a species from this genus that we are aware of, and it will help advance functional genome research and resource development of this important fungus for applications in renewable energy, pharmaceuticals, and agriculture.

Anti-inflammatory Effect of a Novel Pectin Polysaccharide From Rubus chingii Hu on Colitis Mice

Rubus chingii Hu has been used as a functional food for a long time. A novel pectin polysaccharide named RCHP-S from R. chingii Hu was structurally identified and explored its anti-inflammatory effect on colitis mice. RCHP-S was composed of mannose, rhamnose, glucuronic acid, galacturonic acid, glucose, galactose, and arabinose. NMR spectroscopy and methylation analysis showed that RCHP-S was mainly composed of HG-type pectin domains but also contains a small amount of RG-I. The anti-inflammatory tests indicated that the mouse macrophage RAW 264.7 cells pretreated with RCHP-S could show a significant inhibitory effect on the mRNA level of iNOS, IL-1β, IL-6, and TNF-α in vitro. Polysaccharide RCHP-S reduced the enteritis symptoms in dextran sulfate sodium (DSS)-induced colitis mice by inhibiting released inflammatory factors. These results indicated that the R. chingii Hu polysaccharide can be used as food additives for the treatment of intestinal inflammation.

Penicillium Ochrochloron RLS11 Secretome Containing Carbohydrate-Active Enzymes Improves Commercial Enzyme Mixtures During Sugarcane Straw Saccharification

Filamentous fungi are prolific producers of carbohydrate-active enzymes (CAZymes) and important agents that carry out plant cell wall degradation in natural environments. The number of fungal species is frequently reported in the millions range, with a huge diversity and genetic variability, reflecting on a vast repertoire of CAZymes that these organisms can produce. In this study, we evaluated the ability of previously selected ascomycete and basidiomycete fungi to produce plant cell wall-degrading enzyme (PCWDE) activities and the potential of the culture supernatants to increase the efficiency of the Cellic® CTec2/HTec2 for steam-exploded sugarcane straw saccharification. The culture supernatant of Penicillium ochrochloron RLS11 showed a promising supplementation effect on Cellic® CTec2/HTec2, and we conducted the whole-genome sequencing and proteomic analysis for this fungus. The size of the assembled genome was 38.06 Mbp, and a total of 12,015 protein-coding genes were identified. The repertoire of PCWDE-coding genes was comparatively high among Penicillium spp. and showed an expansion in important cellulases and xylanases families, such as GH3, GH6, GH7, and GH11. The proteomic analysis indicated cellulases that probably enhanced the biomass saccharification performance of the Cellic® CTec2/HTec2, which included enzymes from GH3, GH6, and GH7 families.

Hybrid Assembly Improves Genome Quality and Completeness of Trametes villosa CCMB561 and Reveals a Huge Potential for Lignocellulose Breakdown

Trametes villosa is a wood-decaying fungus with great potential to be used in the bioconversion of agro-industrial residues and to obtain high-value-added products, such as biofuels. Nonetheless, the lack of high-quality genomic data hampers studies investigating genetic mechanisms and metabolic pathways in T. villosa, hindering its application in industry. Herein, applying a hybrid assembly pipeline using short reads (Illumina HiSeq) and long reads (Oxford Nanopore MinION), we obtained a high-quality genome for the T. villosa CCMB561 and investigated its genetic potential for lignocellulose breakdown. The new genome possesses 143 contigs, N50 of 1,009,271 bp, a total length of 46,748,415 bp, 14,540 protein-coding genes, 22 secondary metabolite gene clusters, and 426 genes encoding Carbohydrate-Active enzymes. Our CAZome annotation and comparative genomic analyses of nine Trametes spp. genomes revealed T. villosa CCMB561 as the species with the highest number of genes encoding lignin-modifying enzymes and a wide array of genes encoding proteins for the breakdown of cellulose, hemicellulose, and pectin. These results bring to light the potential of this isolate to be applied in the bioconversion of lignocellulose and will support future studies on the expression, regulation, and evolution of genes, proteins, and metabolic pathways regarding the bioconversion of lignocellulosic residues.

Fungal lignocellulolytic enzymes and lignocellulose: A critical review on their contribution to multiproduct biorefinery and global biofuel research

The continuous increase in the global energy demand has diminished fossil fuel reserves and elevated the risk of environmental deterioration and human health. Biorefinery processes involved in producing bio-based energy-enriched chemicals have paved way to meet the energy demands. Compared to the thermochemical processes, fungal system biorefinery processes seems to be a promising approach for lignocellulose conversion. It also offers an eco-friendly and energy-efficient route for biofuel generation. Essentially, ligninolytic white-rot fungi and their enzyme arsenals degrade the plant biomass into structural constituents with minimal by-products generation. Hemi- or cellulolytic enzymes from certain soft and brown-rot fungi are always favoured to hydrolyze complex polysaccharides into fermentable sugars and other value-added products. However, the cost of saccharifying enzymes remains the major limitation, which hinders their application in lignocellulosic biorefinery. In the past, research has been focused on the role of lignocellulolytic fungi in biofuel production; however, a cumulative study comprising the contribution of the lignocellulolytic enzymes in biorefinery technologies is still lagging. Therefore, the overarching goal of this review article is to discuss the major contribution of lignocellulolytic fungi and their enzyme arsenal in global biofuel research and multiproduct biorefinery.

Draft genome sequences of strains CBS6241 and CBS6242 of the basidiomycetous yeast Filobasidium floriforme

The Tremellomycetes are a species-rich group within the basidiomycete fungi; however, most analyses of this group to date have focused on pathogenic Cryptococcus species within the order Tremellales. Recent genome-assisted studies of other Tremellomycetes have identified interesting features with respect to biotechnological applications as well as the evolution of genes involved in mating and sexual development. Here, we report genome sequences of two strains of Filobasidium floriforme, a species from the order Filobasidiales, which branches basally to the Tremellales, Trichosporonales, and Holtermanniales. The assembled genomes of strains CBS6241 and CBS6242 are 27.4 Mb and 26.4 Mb in size, respectively, with 8314 and 7695 predicted protein-coding genes. Overall sequence identity at nucleic acid level between the strains is 97%. Among the predicted genes are pheromone precursor and pheromone receptor genes as well as two genes encoding homedomain (HD) transcription factors, which are predicted to be part of the mating type (MAT) locus. Sequence analysis indicates that CBS6241 and CBS6242 carry different alleles for both the pheromone/receptor genes as well as the HD transcription factors. Orthology inference identified 1482 orthogroups exclusively found in F. floriforme, some of which were involved in carbohydrate transport and metabolism. Subsequent CAZyme repertoire characterization identified 267 and 247 enzymes for CBS6241 and CBS6242, respectively, the second highest number of CAZymes among the analyzed Tremellomycete species. In addition, F. floriforme contains five CAZymes absent in other species and several plant-cell-wall degrading CAZymes with the highest copy number in Tremellomycota, indicating the biotechnological potential of this species.

Genomic Studies of White-Rot Fungus Cerrena unicolor SP02 Provide Insights into Food Safety Value-Added Utilization of Non-Food Lignocellulosic Biomass

Cerrena unicolor is an ecologically and biotechnologically important wood-degrading basidiomycete with high lignocellulose degrading ability. Biological and genetic investigations are limited in the Cerrena genus and, thus, hinder genetic modification and commercial use. The aim of the present study was to provide a global understanding through genomic and experimental research about lignocellulosic biomass utilization by Cerrena unicolor. In this study, we reported the genome sequence of C. unicolor SP02 by using the Illumina and PacBio 20 platforms to obtain trustworthy assembly and annotation. This is the combinational 2nd and 3rd genome sequencing and assembly of C. unicolor species. The generated genome was 42.79 Mb in size with an N50 contig size of 2.48 Mb, a G + C content of 47.43%, and encoding of 12,277 predicted genes. The genes encoding various lignocellulolytic enzymes including laccase, lignin peroxidase, manganese peroxidase, cytochromes P450, cellulase, xylanase, α-amylase, and pectinase involved in the degradation of lignin, cellulose, xylan, starch, pectin, and chitin that showed the C. unicolor SP02 potentially have a wide range of applications in lignocellulosic biomass conversion. Genome-scale metabolic analysis opened up a valuable resource for a better understanding of carbohydrate-active enzymes (CAZymes) and oxidoreductases that provide insights into the genetic basis and molecular mechanisms for lignocellulosic degradation. The C. unicolor SP02 model can be used for the development of efficient microbial cell factories in lignocellulosic industries. The understanding of the genetic material of C. unicolor SP02 coding for the lignocellulolytic enzymes will significantly benefit us in genetic manipulation, site-directed mutagenesis, and industrial biotechnology.

Metagenomic insights into soil microbial communities involved in carbon cycling along an elevation climosequences

Diversity and community composition of soil microorganisms along the elevation climosequences have been widely studied, while the microbial metabolic potential, particularly in regard to carbon (C) cycling, remains unclear. Here, a metagenomic analysis of C related genes along five elevations ranging from 767 to 4190 m at Mount Kilimanjaro was analysed to evaluate the microbial organic C transformation capacities in various ecosystems. The highest gene abundances for decomposition of moderate mineralizable compounds, i.e. carbohydrate esters, chitin and pectin were found at the mid-elevations with hump-shaped pattern, where the genes for decompositions of recalcitrant C (i.e. lignin) and easily mineralizable C (i.e. starch) showed the opposite trend (i.e. U-shaped pattern), due to high soil pH and seasonality in both low and high elevations. Notably, the gene abundances for the decompositions of starch, carbohydrate esters, chitin and lignin had positive relationships with corresponding C compounds, indicating the consistent responses of microbial functional profiles and metabolites to elevation climosequences. Understanding of adaptation of microbial communities, potential function and metabolites to elevation climosequences and their influencing factors provided a new insight for the regulation of terrestrial C storage.

Niche adaptation promoted the evolutionary diversification of tiny ocean predators

Unicellular eukaryotic predators play a crucial role in the functioning of the ocean ecosystem by recycling nutrients and energy that are channeled to upper trophic levels. Traditionally, these evolutionarily diverse organisms have been combined into a single functional group (heterotrophic flagellates), overlooking their organismal differences. Here, we investigated four evolutionarily related species belonging to one cosmopolitan group of uncultured marine picoeukaryotic predators: marine stramenopiles (MAST)-4 (species A, B, C, and E). Co-occurrence and distribution analyses in the global surface ocean indicated contrasting patterns in MAST-4A and C, suggesting adaptation to different temperatures. We then investigated whether these spatial distribution patterns were mirrored by MAST-4 genomic content using single-cell genomics. Analyses of 69 single cells recovered 66 to 83% of the MAST-4A/B/C/E genomes, which displayed substantial interspecies divergence. MAST-4 genomes were similar in terms of broad gene functional categories, but they differed in enzymes of ecological relevance, such as glycoside hydrolases (GHs), which are part of the food degradation machinery in MAST-4. Interestingly, MAST-4 species featuring a similar GH composition (A and C) coexcluded each other in the surface global ocean, while species with a different set of GHs (B and C) appeared to be able to coexist, suggesting further niche diversification associated with prey digestion. We propose that differential niche adaptation to temperature and prey type has promoted adaptive evolutionary diversification in MAST-4. We show that minute ocean predators from the same phylogenetic group may have different biogeography and genomic content, which needs to be accounted for to better comprehend marine food webs.

Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation

BACKGROUND

The Arthrobacter group is a known set of bacteria from cold regions, the species of which are highly likely to play diverse roles at low temperatures. However, their survival mechanisms in cold regions such as Antarctica are not yet fully understood. In this study, we compared the genomes of 16 strains within the Arthrobacter group, including strain PAMC25564, to identify genomic features that help it to survive in the cold environment.

RESULTS

Using 16 S rRNA sequence analysis, we found and identified a species of Arthrobacter isolated from cryoconite. We designated it as strain PAMC25564 and elucidated its complete genome sequence. The genome of PAMC25564 is composed of a circular chromosome of 4,170,970 bp with a GC content of 66.74 % and is predicted to include 3,829 genes of which 3,613 are protein coding, 147 are pseudogenes, 15 are rRNA coding, and 51 are tRNA coding. In addition, we provide insight into the redundancy of the genes using comparative genomics and suggest that PAMC25564 has glycogen and trehalose metabolism pathways (biosynthesis and degradation) associated with carbohydrate active enzyme (CAZymes). We also explain how the PAMC26654 produces energy in an extreme environment, wherein it utilizes polysaccharide or carbohydrate degradation as a source of energy. The genetic pattern analysis of CAZymes in cold-adapted bacteria can help to determine how they adapt and survive in such environments.

CONCLUSIONS

We have characterized the complete Arthrobacter sp. PAMC25564 genome and used comparative analysis to provide insight into the redundancy of its CAZymes for potential cold adaptation. This provides a foundation to understanding how the Arthrobacter strain produces energy in an extreme environment, which is by way of CAZymes, consistent with reports on the use of these specialized enzymes in cold environments. Knowledge of glycogen metabolism and cold adaptation mechanisms in Arthrobacter species may promote in-depth research and subsequent application in low-temperature biotechnology.

Physiological Characteristics and Comparative Secretome Analysis of Morchella importuna Grown on Glucose, Rice Straw, Sawdust, Wheat Grain, and MIX Substrates

Morels (Morchella sp.) are economically important edible macro-fungi, which can grow on various synthetic or semi-synthetic media. However, the complex nutritional metabolism and requirements of these fungi remain ill-defined. This study, based on the plant biomass commonly used in the artificial cultivation of morels, assessed and compared the growth characteristics and extracellular enzymes of Morchella importuna cultivated on glucose, rice straw, sawdust, wheat grain, and a mixture of equal proportions of the three latter plant substrates (MIX). M. importuna could grow on all five tested media but displayed significant variations in mycelial growth rate, biomass, and sclerotium yield on the different media. The most suitable medium for M. importuna was wheat and wheat-containing medium, followed by glucose, while rice straw and sawdust were the least suitable. A total of 268 secretory proteins were identified by liquid chromatography coupled with tandem mass spectrometry detection. Functional classification and label-free comparative analysis of these proteins revealed that carbohydrate-active enzyme (CAZYme) proteins were the predominant component of the secretome of M. importuna, followed by protease, peptidase, and other proteins. The abundances of CAZYme proteins differed among the tested media, ranging from 64% on glucose to 88% on rice straw. The CAZYme classes of glycoside hydrolases and carbohydrate-binding module were enriched in the five secretomes. Furthermore, the enzyme activities of CMCase, lignase, amylase, xylase, pNPCase, and pNPGase were detected during the continuous culture of M. importuna in MIX medium, and the relative expression of the corresponding genes were detected by quantitative real-time PCR. The combined data of growth potential, secretome, extracellular enzyme activity, and gene expression on different substrates inferred that M. importuna was weak in lignocellulose degradation but a good starch decomposer. Specifically, in terms of the degradation of cellulose, the ability to degrade cellulose into oligosaccharides was weaker compared with further degradation into monosaccharides, and this might be the speed-limiting step of cellulose utilization in M. importuna. In addition, M. importuna had a strong ability to decompose various hemicellulose glycosidic bonds, especially α- and β-galactosidase. Only a very few lignin-degradation-related proteins were detected, and these were in low abundance, consistent with the presence of weak lignin degradation ability. Furthermore, the presence of lipase and chitinase implied that M. importuna was capable of decomposition of its own mycelia in vitro. The study provides key data that facilitates a further understanding of the complex nutritional metabolism of M. importuna.

Hybrid Genome Assembly for Predicting Functional Potential of a Novel Streptomyces Strain as Plant Biomass Valorisation Agent

Environmental bioremediation relies heavily on the realized potential of efficient bioremediation agents or microbial strains of interest. Identifying suitable microbial agents for plant biomass waste valorization requires (i) high-quality genome assemblies to predict the full metabolic and functional potential, (ii) accurate mapping of lignocellulose metabolizing enzymes. However, fragmented nature of the sequenced genomes often limits the prediction ability due to breaks occurring in coding sequences. To address these challenges and as part of our ongoing agri-culturomics efforts, we have performed a hybrid genome assembly using Illumina and Nanopore reads with modified assembly protocol, for a novel Streptomyces strain isolated from the rhizosphere niche of green leafy vegetables grown in a commercial urban farm. High-quality genome was assembled with the size of 8.6 Mb in just two contigs with N50 of 8,542,030 and coverage of 383X. This facilitated identification and complete arrangement of approximately 248 CAZymes and 38 biosynthetic gene clusters in the genome. Multiple gene clusters consisting of cellulases and hemicellulases associated with substrate recognition domain were identified in the genome. Genes for lignin, chitin, and even some aromatic compounds degradation were found in the Streptomyces sp. genome which makes it a promising candidate for lignocellulosic waste valorization.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-021-00935-5.

Comparative Genomics: Insights on the Pathogenicity and Lifestyle of Rhizoctonia solani

Proper management of agricultural disease is important to ensure sustainable food security. Staple food crops like rice, wheat, cereals, and other cash crops hold great export value for countries. Ensuring proper supply is critical; hence any biotic or abiotic factors contributing to the shortfall in yield of these crops should be alleviated. Rhizoctonia solani is a major biotic factor that results in yield losses in many agriculturally important crops. This paper focuses on genome informatics of our Malaysian Draft R. solani AG1-IA, and the comparative genomics (inter- and intra- AG) with four AGs including China AG1-IA (AG1-IA_KB317705.1), AG1-IB, AG3, and AG8. The genomic content of repeat elements, transposable elements (TEs), syntenic genomic blocks, functions of protein-coding genes as well as core orthologous genic information that underlies R. solani’s pathogenicity strategy were investigated. Our analyses show that all studied AGs have low content and varying profiles of TEs. All AGs were dominant for Class I TE, much like other basidiomycete pathogens. All AGs demonstrate dominance in Glycoside Hydrolase protein-coding gene assignments suggesting its importance in infiltration and infection of host. Our profiling also provides a basis for further investigation on lack of correlation observed between number of pathogenicity and enzyme-related genes with host range. Despite being grouped within the same AG with China AG1-IA, our Draft AG1-IA exhibits differences in terms of protein-coding gene proportions and classifications. This implies that strains from similar AG do not necessarily have to retain similar proportions and classification of TE but must have the necessary arsenal to enable successful infiltration and colonization of host. In a larger perspective, all the studied AGs essentially share core genes that are generally involved in adhesion, penetration, and host colonization. However, the different infiltration strategies will depend on the level of host resilience where this is clearly exhibited by the gene sets encoded for the process of infiltration, infection, and protection from host.

Comparative Analysis of Carbohydrate Active Enzymes in the Flammulina velutipes var. lupinicola Genome

The purpose of this study was to determine the genome sequence of Flammulina velutipes var. lupinicola based on next-generation sequencing (NGS) and to identify the genes encoding carbohydrate-active enzymes (CAZymes) in the genome. The optimal assembly (71 kmer) based on ABySS de novo assembly revealed a total length of 33,223,357 bp (49.53% GC content). A total of 15,337 gene structures were identified in the F. velutipes var. lupinicola genome using ab initio gene prediction method with Funannotate pipeline. Analysis of the orthologs revealed that 11,966 (96.6%) out of the 15,337 predicted genes belonged to the orthogroups and 170 genes were specific for F. velutipes var. lupinicola. CAZymes are divided into six classes: auxiliary activities (AAs), glycosyltransferases (GTs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycoside hydrolases (GHs), and carbohydrate-binding modules (CBMs). A total of 551 genes encoding CAZymes were identified in the F. velutipes var. lupinicola genome by analyzing the dbCAN meta server database (HMMER, Hotpep, and DIAMOND searches), which consisted of 54-95 AAs, 145-188 GHs, 55-73 GTs, 6-19 PLs, 13-59 CEs, and 7-67 CBMs. CAZymes can be widely used to produce bio-based products (food, paper, textiles, animal feed, and biofuels). Therefore, information about the CAZyme repertoire of the F. velutipes var. lupinicola genome will help in understanding the lignocellulosic machinery and in-depth studies will provide opportunities for using this fungus for biotechnological and industrial applications.

Transcriptome Profiling-Based Analysis of Carbohydrate-Active Enzymes in Aspergillus terreus Involved in Plant Biomass Degradation

Given the global abundance of plant biomass residues, potential exists in biorefinery-based applications with lignocellulolytic fungi. Frequently isolated from agricultural cellulosic materials, Aspergillus terreus is a fungus efficient in secretion of commercial enzymes such as cellulases, xylanases and phytases. In the context of biomass saccharification, lignocellulolytic enzyme secretion was analyzed in a strain of A. terreus following liquid culture with sugarcane bagasse (SB) (1% w/v) and soybean hulls (SH) (1% w/v) as sole carbon source, in comparison to glucose (G) (1% w/v). Analysis of the fungal secretome revealed a maximum of 1.017 UI.mL^–1 xylanases after growth in minimal medium with SB, and 1.019 UI.mL^–1 after incubation with SH as carbon source. The fungal transcriptome was characterized on SB and SH, with gene expression examined in comparison to equivalent growth on G as carbon source. Over 8000 genes were identified, including numerous encoding enzymes and transcription factors involved in the degradation of the plant cell wall, with significant expression modulation according to carbon source. Eighty-nine carbohydrate-active enzyme (CAZyme)-encoding genes were identified following growth on SB, of which 77 were differentially expressed. These comprised 78% glycoside hydrolases, 8% carbohydrate esterases, 2.5% polysaccharide lyases, and 11.5% auxiliary activities. Analysis of the glycoside hydrolase family revealed significant up-regulation for genes encoding 25 different GH family proteins, with predominance for families GH3, 5, 7, 10, and 43. For SH, from a total of 91 CAZyme-encoding genes, 83 were also significantly up-regulated in comparison to G. These comprised 80% glycoside hydrolases, 7% carbohydrate esterases, 5% polysaccharide lyases, 7% auxiliary activities (AA), and 1% glycosyltransferases. Similarly, within the glycoside hydrolases, significant up-regulation was observed for genes encoding 26 different GH family proteins, with predominance again for families GH3, 5, 10, 31, and 43. A. terreus is a promising species for production of enzymes involved in the degradation of plant biomass. Given that this fungus is also able to produce thermophilic enzymes, this first global analysis of the transcriptome following cultivation on lignocellulosic carbon sources offers considerable potential for the application of candidate genes in biorefinery applications.

The Biocontrol Root-Oomycete, Pythium Oligandrum, Triggers Grapevine Resistance and Shifts in the Transcriptome of the Trunk Pathogenic Fungus, Phaeomoniella Chlamydospora

The worldwide increase in grapevine trunk diseases, mainly esca, represents a major threat for vineyard sustainability. Biocontrol of a pioneer fungus of esca, Phaeomoniella chlamydospora, was investigated here by deciphering the tripartite interaction between this trunk-esca pathogen, grapevine and the biocontrol-oomycete, Pythium oligandrum. When P. oligandrum colonizes grapevine roots, it was observed that the wood necroses caused by P. chlamydospora were significantly reduced. Transcriptomic analyses of plant and fungus responses were performed to determine the molecular events occurring, with the aim to relate P.chlamydospora degradation of wood to gene expression modulation. Following P. oligandrum-root colonization, major transcriptomic changes occurred both, in the grapevine-defense system and in the P. chlamydospore-virulence factors. Grapevine-defense was enhanced in response to P. chlamydospora attacks, with P. oligandrum acting as a plant-systemic resistance inducer, promoting jasmonic/ethylene signaling pathways and grapevine priming. P. chlamydospora pathogenicity genes, such as those related to secondary metabolite biosynthesis, carbohydrate-active enzymes and transcription regulators, were also affected in their expression. Shifts in grapevine responses and key-fungal functions were associated with the reduction of P. chlamydospora wood necroses. This study provides evidence of wood fungal pathogen transcriptional changes induced by a root biocontrol agent, P. oligandrum, in which there is no contact between the two microorganisms.

Complete Genome Sequence and Carbohydrates-Active EnZymes (CAZymes) Analysis of Lactobacillus paracasei DTA72, a Potential Probiotic Strain with Strong Capability to Use Inulin

The whole genome sequence of Lactobacillus paracasei DTA72, isolated from healthy infant feces, is reported, along with the Carbohydrates-Active enZymes (CAZymes) analysis and an in silico safety assessment. Strain DTA72 had previously demonstrated some interesting potential probiotic features, such as a good resistance to gastrointestinal conditions and an anti-Listeria activity. The 3.1 Mb sequenced genome consists of 3116 protein-coding sequences distributed on 340 SEED subsystems. In the present study, we analyzed the fermentation capability of strain DTA72 on six different carbohydrate sources, namely, glucose, fructose, lactose, galactose, xylose, and inulin by using phenotypical and genomic approaches. Interestingly, L. paracasei DTA72 evidenced the best growth performances on inulin with a much shorter lag phase and higher number of cells at the stationary phase in comparison with all the sugars tested. The CAZyme analysis using the predicted amino acid sequences detected 80 enzymes, distributed into the five CAZymes classes. Moreover, the in silico analysis revealed the absence of blood hemolytic genes, transmissible antibiotic resistances, and plasmids in DTA72. The results described in this study, together with those previously reported and particularly the strong capability to utilize inulin as energy source, make DTA72 a very interesting potential probiotic strain to be considered for the production of synbiotic foods. The complete genome data have been deposited in GenBank under the accession number WUJH00000000.

Degradative Ability of Mushrooms Cultivated on Corn Silage Digestate

The current management practice of digestate from biogas plants involves its use for land application as a fertilizer. Nevertheless, the inadequate handling of digestate may cause environmental risks due to losses of ammonia, methane and nitrous oxide. Therefore, the key goals of digestate management are to maximize its value by developing new digestate products, reducing its dependency on soil application and the consequent air pollution. The high nitrogen and lignin content in solid digestate make it a suitable substrate for edible and medicinal mushroom cultivation. To this aim, the mycelial growth rate and degradation capacity of the lignocellulosic component from corn silage digestate, undigested wheat straw and their mixture were investigated on Cyclocybe aegerita, Coprinus comatus, Morchella importuna, Pleurotus cornucopiae and Pleurotus ostreatus. The structural modification of the substrates was performed by using attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy. Preliminary in vitro results demonstrated the ability of P. ostreatus, P. cornucopiae and M. importuna to grow and decay hemicellulose and lignin of digestate. Cultivation trials were carried out on C. aegerita, P. cornucopiae and P. ostreatus. Pleurotus ostreatus showed the highest biological efficiency and fruiting body production in the presence of the digestate; moreover, P. ostreatus and P. cornucopiae were able to degrade the lignin. These results provide attractive perspectives both for more sustainable digestate management and for the improvement of mushroom cultivation efficiency.

Bioprospecting Microbial Diversity for Lignin Valorization: Dry and Wet Screening Methods

Lignin is an abundant cell wall component, and it has been used mainly for generating steam and electricity. Nevertheless, lignin valorization, i.e. the conversion of lignin into high value-added fuels, chemicals, or materials, is crucial for the full implementation of cost-effective lignocellulosic biorefineries. From this perspective, rapid screening methods are crucial for time- and resource-efficient development of novel microbial strains and enzymes with applications in the lignin biorefinery. The present review gives an overview of recent developments and applications of a vast arsenal of activity and sequence-based methodologies for uncovering novel microbial strains with ligninolytic potential, novel enzymes for lignin depolymerization and for unraveling the main metabolic routes during growth on lignin. Finally, perspectives on the use of each of the presented methods and their respective advantages and disadvantages are discussed.

Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer

BACKGROUND

Cultivation-independent methods, including metagenomics, are tools for the exploration and discovery of biotechnological compounds produced by microbes in natural environments. Glycoside hydrolases (GHs) enzymes are extremely desired and important in the industry of production for goods and biofuel and removal of problematic biofilms and exopolysaccharide (EPS). Biofilms and EPS are complex, requiring a wide range of enzymes for a complete degradation. The aim of this study was to identify potential GH microbial producers and GH genes with biotechnological potential, using EPS-complex structure (WH15EPS) of Acidobacteria Granulicella sp. strain WH15 as an enrichment factor, in cultivation-independent and cultivation-dependent methods. We performed stable isotope probing (SIP) combined with metagenomics on topsoil litter amended with WH15EPS and coupled solid culture-EPS amended medium with metagenomics.

RESULTS

SIP metagenome analysis of the soil litter demonstrated that phyla Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes were the most abundant in WH15EPS amended and unamended treatments. The enrichment cultures in solid culture medium coupled to metagenomics demonstrated an enrichment in Proteobacteria, and the metagenome assembly of this enrichment cultures resulted in 4 metagenome-assembled genomes (MAGs) of microbes with low identity (42-86%) to known microorganisms. Among all carbohydrate-active enzymes (CAZymes) retrieved genes, glycoside transferase (GT) was the most abundant family, either in culture-independent or culture-based metagenome datasets. Within the glycoside hydrolases (GHs), GH13 was the most abundant family in both metagenome datasets. In the "heavy" fraction of the culture-independent metagenome SIP dataset, GH109 (α-N-acetylgalactosaminidases), GH117 (agarases), GH50 (agarases), GH32 (invertases and inulinases), GH17 (endoglucanases), and GH71 (mutanases) families were more abundant in comparison with the controls. Those GH families are affiliated to microorganism that are probably capable to degrade WH15EPS and potentially applicable for biofilm deconstruction. Subsequent in culture-based metagenome, the assembled 4 MAGs (unclassified Proteobacteria) also contained GH families of interest, involving mannosidases, lysozymes, galactosidases, and chitinases.

CONCLUSIONS

We demonstrated that functional diversity induced by the presence of WH15EPS in both culture-independent and culture-dependent approaches was enriched in GHs, such as amylases and endoglucanases that could be applied in chemical, pharmaceutical, and food industrial sectors. Furthermore, WH15EPS may be used for the investigation and isolation of yet unknown taxa, such as unclassified Proteobacteria and Planctomycetes, increasing the number of current cultured bacterial representatives with potential biotechnological traits. Video Abstract.

Genome Sequencing and Analysis of the Fungal Symbiont of Sirex noctilio, Amylostereum areolatum: Revealing the Biology of Fungus-Insect Mutualism

Sirex noctilio (F.), together with Amylostereum areolatum, a wood-decaying symbiotic fungus, causes severe damage to Pinus species worldwide. In China, it causes extensive death of Mongolian pine (Pinus sylvestris var. mongolica). There is an obligate dependency mutualism between the woodwasp and its fungus. Studies have suggested that the fungal growth rate affected the size of the wasps: larger adults emerged from sites with a higher fungus growth rate. This genome is the first reported genome sequence of a woodwasp symbiotic fungus. Genome sequence analysis of this fungus would prove the possibility of A. areolatum volatiles affecting the host selection of S. noctilio on a molecular basis. We further clarified that A. areolatum was a strict obligate symbiotic fungus and that it would provide S. noctilio with a suitable environment and with nutrients for the larval growth. These results would lay a foundation for our understanding of the mechanism of this entomogenous symbiosis.

Amylostereum areolatum is the symbiotic fungus of the Eurasian woodwasp, Sirex noctilio, a globally invasive species. The mutualistic symbiont is associated with the woodwasp, assisting the damage process and providing nutrition for its insect partners. Colonization and growth of A. areolatum have essential impacts on the development and spread of S. noctilio, though the mechanism of interaction between the two has been poorly described. In this study, the first genome of this symbiotic fungus was sequenced, assembled, and annotated. The assembled A. areolatum genome was 57.5 Mb (54.51% GC content) with 15,611 protein-coding genes. We identified 580 carbohydrate-active enzymes (CAZymes), 661 genes associated with pathogen-host interactions, and 318 genes encoding transport proteins in total. The genome annotation revealed 10 terpene/phytoene synthases responsible for terpenoid biosynthesis, which could be classified into three clades. Terpene synthase gene clusters in clade II were conserved well across Russulales. In this cluster, genes encoding mevalonate kinase (MK), EGR12 (COG1557), and nonplant terpene cyclases (cd00687) were the known biosynthesis and regulatory genes. Genome sequence analysis of this fungus would prove the possibility of A. areolatum volatiles affecting the host selection of S. noctilio on a molecular basis. We further clarified that A. areolatum was a strict obligate symbiotic fungus. The wasps might protect the fungus before it was introduced into a suitable host substrate by oviposition, while the fungus would provide S. noctilio with a suitable environment and nutrients for the larval growth. These results would lay a foundation for our understanding of the mechanism of this entomogenous symbiosis.

IMPORTANCESirex noctilio (F.), together with Amylostereum areolatum, a wood-decaying symbiotic fungus, causes severe damage to Pinus species worldwide. In China, it causes extensive death of Mongolian pine (Pinus sylvestris var. mongolica). There is an obligate dependency mutualism between the woodwasp and its fungus. Studies have suggested that the fungal growth rate affected the size of the wasps: larger adults emerged from sites with a higher fungus growth rate. This genome is the first reported genome sequence of a woodwasp symbiotic fungus. Genome sequence analysis of this fungus would prove the possibility of A. areolatum volatiles affecting the host selection of S. noctilio on a molecular basis. We further clarified that A. areolatum was a strict obligate symbiotic fungus and that it would provide S. noctilio with a suitable environment and with nutrients for the larval growth. These results would lay a foundation for our understanding of the mechanism of this entomogenous symbiosis.

Prediction of the secretomes of endophytic and nonendophytic fungi reveals similarities in host plant infection and colonization strategies

Endophytic fungi are microorganisms that inhabit internal plant tissues without causing apparent damage. During the infection process, both endophytic and phytopathogenic fungi secrete proteins to resist or supplant the plant's defense mechanisms. This study analyzed the predicted secretomes of six species of endophytic fungi and compared them with predicted secretomes of eight fungal species with different lifestyles: saprophytic, necrotrophic, hemibiotrophic, and biotrophic. The sizes of the predicted secretomes varied from 260 to 1640 proteins, and the predicted secretomes have a wide diversity of CAZymes, proteases, and conserved domains. Regarding the CAZymes in the secretomes of the analyzed fungi, the most abundant CAZyme families were glycosyl hydrolase and serine proteases. Several predicted proteins have characteristics similar to those found in small, secreted proteins with effector characteristics (SSPEC). The most abundant conserved domains, besides those found in the SSPEC, have oxidation activities, indicating that these proteins can protect the fungus against oxidative stress, against domains with protease activity, which may be involved in the mechanisms of nutrition, or against lytic enzymes secreted by the host plant. This study demonstrates that secretomes of endophytic and nonendophytic fungi share an arsenal of proteins important in the process of infection and colonization of host plants.

Genome and secretome analysis of jute endophyte Grammothele lineata strain SDL-CO-2015-1: Insights into its lignocellulolytic structure and secondary metabolite profile

Grammothele lineata strain SDL-CO-2015-1, jute (Corchorus olitorius) endophyte has been reported to produce anti-cancer drug paclitaxel in culture condition. Here we investigated the genome using different bioinformatic tools to find its association with the production of commercially important compounds including taxol. Carbohydrate-active enzymes, proteases, and secretory proteins were annotated revealing a complex endophytic relationship with its plant host. The presences of a diverse range of CAZymes including numerous lignocellulolytic enzymes support its potentiality in biomass degradation. Genome annotation led to the identification of 28 clusters for secondary metabolite biosynthesis. Several biosynthesis gene clusters were identified for terpene biosynthesis from antiSMASH analysis but none could be specifically pinned to taxol synthesis. This study will direct us to understand the genomic organization of endophytic basidiomycetes with a potential for producing numerous commercially important enzymes and secondary metabolites taking G. lineata as a model.

Comparative Genomics Uncovers the Genetic Diversity and Synthetic Biology of Secondary Metabolite Production of Trametes

The carbohydrate-active enzyme (CAZyme) genes of Trametes contribute to polysaccharide degradation. However, the comprehensive analysis of the composition of CAZymes and the biosynthetic gene clusters (BGCs) of Trametes remain unclear. Here, we conducted comparative analysis, detected the CAZyme genes, and predicted the BGCs for nine Trametes strains. Among the 82,053 homologous clusters obtained for Trametes, we identified 8518 core genes, 60,441 accessory genes, and 13,094 specific genes. A large proportion of CAZyme genes were cataloged into glycoside hydrolases, glycosyltransferases, and carbohydrate esterases. The predicted BGCs of Trametes were divided into six strategies, and the nine Trametes strains harbored 47.78 BGCs on average. Our study revealed that Trametes exhibits an open pan-genome structure. These findings provide insights into the genetic diversity and explored the synthetic biology of secondary metabolite production for Trametes.

Whole-genome and time-course dual RNA-Seq analyses reveal chronic pathogenicity-related gene dynamics in the ginseng rusty root rot pathogen Ilyonectria robusta

Ilyonectria robusta causes rusty root rot, the most devastating chronic disease of ginseng. Here, we for the first time report the high-quality genome of the I. robusta strain CD-56. Time-course (36 h, 72 h, and 144 h) dual RNA-Seq analysis of the infection process was performed, and many genes, including candidate effectors, were found to be associated with the progression and success of infection. The gene expression profile of CD-56 showed a trend of initial inhibition and then gradually returned to a profile similar to that of the control. Analyses of the gene expression patterns and functions of pathogenicity-related genes, especially candidate effector genes, indicated that the stress response changed to an adaptive response during the infection process. For ginseng, gene expression patterns were highly related to physiological conditions. Specifically, the results showed that ginseng defenses were activated by CD-56 infection and persisted for at least 144 h thereafter but that the mechanisms invoked were not effective in preventing CD-56 growth. Moreover, CD-56 did not appear to fully suppress plant defenses, even in late stages after infection. Our results provide new insight into the chronic pathogenesis of CD-56 and the comprehensive and complex inducible defense responses of ginseng root to I. robusta infection.