An investigation of the biodiversity of thermophilic and thermotolerant fungal species in composts using culture-based and molecular techniques

Fungal Colonization of the Airways of Patients with Cystic Fibrosis: the Role of the Environmental Reservoirs

Filamentous fungi frequently colonize the airways of patients with cystic fibrosis and may cause severe diseases, such as the allergic bronchopulmonary aspergillosis. The most common filamentous fungi capable to chronically colonize the respiratory tract of the patients are Aspergillus fumigatus and Scedosporium species. Defining the treatment strategy may be challenging, the number of available drugs being limited and some of the causative agents being multiresistant microorganisms. The knowledge of the fungal niches in the outdoor and indoor environment is needed for understanding the origin of the contamination of the patients. In light of the abundance of some of the causative molds in compost, agricultural and flower fields, occupational activities related to such environments should be discouraged for patients with cystic fibrosis (CF). In addition, the microbiological monitoring of their indoor environment, including analysis of air and dust on surfaces, is essential to propose preventive measures aiming to reduce the exposure to environmental molds. Nevertheless, some specific niches were also identified in the indoor environment, in relation with humidity which favors the growth of thermotolerant molds. Potted plants were reported as indoor reservoirs for Scedosporium species. Likewise, Exophiala dermatitidis may be spread in the kitchen via dishwashers. However, genotype studies are still required to establish the link between dishwashers and colonization of the airways of CF patients by this black yeast. Moreover, as nothing is known regarding the other filamentous fungi associated with CF, further studies should be conducted to identify other potential specific niches in the habitat.

Microbial agents obtained from tomato straw composting effectively promote tomato straw compost maturation and improve compost quality

Appropriate management of agricultural organic waste (AOW) presents a significant obstacle in the endeavor to attain sustainable agricultural development. The proper management of AOW is a necessity for sustainable agricultural development. This can be done skillfully by incorporating microbial agents in the composting procedure. In this study, we isolated relevant bacteria strains from tomato straw AOW, which demonstrated efficient degradation of lignocellulose without any antagonistic effects in them. These strains were then combined to create a composite microbial agent called Zyco Shield (ZS). The performance of ZS was compared with a commercially effective microorganism (EM) and a control CK. The results indicate that the ZS treatment significantly prolonged the elevated temperature phase of the tomato straw pile, showing considerable degradation of lignocellulosic material. This substantial degradation did not happen in the EM and CK treatments. Moreover, there was a temperature rise of 4-6 ℃ in 2 days of thermophilic phase, which was not the case in the EM and CK treatments. Furthermore, the inoculation of ZS substantially enhanced the degradation of organic waste derived from tomato straw. This method increased the nutrient content of the resulting compost and elevated the enzymatic activity of lignocellulose-degrading enzymes, while reducing the urease enzyme activity within the pile. The concentrations of NH4+-N and NO3--N showed increases of (2.13% and 47.51%), (14.81% and 32.17%) respectively, which is again very different from the results of the EM and CK treatments. To some extent, the alterations observed in the microbial community and the abundance of functional microorganisms provide indirect evidence supporting the fact that the addition of ZS microbial agent facilitates the composting process of tomato straw. Moreover, we confirmed the degradation process of tomato straw through X-ray diffraction, Fourier infrared spectroscopy, and by scanning electron microscopy to analyze the role of ZS microbial inoculum composting. Consequently, reinoculation compost strains improves agricultural waste composting efficiency and enhances product quality.

Regulation of fungal communities during pig manure composting

The role of protein shell (PS) amendment in altering the fungal community during pig manure (PM) composting was investigated. Six different dosages of PS based on the dry weight of PM (0 %, 2.5 %, 5 %, 7.5 %, 10 %, and 12 %; T1-T6, respectively) were mixed with wheat straw to make the initial feedstock and composted for 42 days. The results showed that Ascomycota, Basidiomycota, and Giomeromycota were the most abundant phyla in all treatments. However, the relative abundance of Giomeromycota was the highest in the control treatment, although a substantially greater population was observed in all treatments. Genus abundance declined steadily from T1 to T6; however, T4 and T6 had smaller populations. Correlation analysis also suggested that T6 amendment increased the overall fungal dynamics and organic matter degradation. Thus, T6 was more efficient to enhance the overall fungal population and dynamics with considerable network connections among all the analyzed parameters.

Moderately delayed maturation of composting promotes the reduction of guild-plant pathogenic fungi within vegetable waste

The relationships among the relative abundance of guild-plant pathogenic fungi, compost maturation index, and microbial community variation during vegetable waste composting, which are influenced by the C/N ratio, remain poorly understood. To address this, fungal communities were analyzed in composting treatments with C/N ratios of approximately 15 (CN15) and 25 (CN25), using vegetable waste as the primary raw material. The CN15 treatment showed greater microbial community variation and a better overall compost maturation index value than the CN25 treatment. However, the CN25 treatment had a greater decline in plant-pathogenic fungi than the CN15 treatment. Notably, the relative abundance of guild-plant pathogenic fungi was significantly negatively related to the compost maturity index in the CN25 treatment, while no significant relationship was observed in the CN15 treatment. This study suggests that the moderately delayed maturation of composting is beneficial for reducing guild-plant pathogenic fungi in vegetable waste.

Investigation of underlying links between nitrogen transformation and microorganisms' network modularity in the novel static aerobic composting of dairy manure by "stepwise verification interaction analysis"

Conventional composting is a viable method treating agricultural solid waste, and microorganisms and nitrogen transformation are the two major components of this proces. Unfortunately, conventional composting is time-consuming and laborious, and limited efforts have been made to mitigate these problems. Herein, a novel static aerobic composting technology (NSACT) was developed and employed for the composting of cow manure and rice straw mixtures. During the composting process, physicochemical parameters were analyzed to evaluate the quality of compost products, and microbial abundance dynamics were determined using high-throughput sequencing technique. The results showed that NSACT achieved compost maturity within 17 days as the thermophilic stage (≥55 °C) lasted for 11 days. GI, pH, and C/N were 98.71 %, 8.38, and 19.67 in the top layer, 92.32 %, 8.24, and 22.38 in the middle layer, 102.08 %, 8.33, and 19.95 in the bottom layer. These observations indicate compost products maturated and met the requirements of current legislation. Compared with fungi, bacterial communities dominated NSACT composting system. Based on the stepwise verification interaction analysis (SVIA), the novel combination utilization of multiple statistical analyses (Spearman, RDA/CCA, Network modularity, and Path analyses), bacterial genera Norank Anaerolineaceae (-0.9279*), norank Gemmatimonadetes (1.1959*), norank Acidobacteria (0.6137**) and unclassified Proteobacteria (-0.7998*), and fungi genera Myriococcum thermophilum (-0.0445), unclassified Sordariales (-0.0828*), unclassified Lasiosphaeriaceae (-0.4174**), and Coprinopsis calospora (-0.3453*) were the identified key microbial taxa affecting NH₄⁺-N, NO₃^--N, TKN and C/N transformation in the NSACT composting matrix respectively. This work revealed that NSACT successfully managed cow manure-rice straw wastes and significantly shorten the composting period. Interestingly, most microorganisms observed in this composting matrix acted in a synergistic manner, promoting nitrogen transformation.

Regulating pH and Phanerochaete chrysosporium inoculation improved the humification and succession of fungal community at the cooling stage of composting

This study aimed to explore the effect of regulating pH and Phanerochaete chrysosporium inoculation at the cooling stage of composting on the lignocellulose degradation, humification process and related precursors as well as fungal community for secondary fermentation. Results showed that composting with P. chrysosporium inoculation and pH regulation (T4) had 58% cellulose decomposition, 73% lignin degradation and improved enzyme activities for lignin decomposition. There was 81.98% increase of humic substance content and more transformation of polyphenols and amino acids in T4 compared to control. Inoculating P. chrysosporium affected the fungal community diversity, and regulating pH helped to increase the colonization of P. chrysosporium. Network analysis showed that the network complexity and synergy between microorganisms was improved in T4. Correlation and Random Forest analysis suggested that enriched Phanerochaete and Thermomyces in the mature stage of T4 were key taxa for lignocellulose degradation, and humic acid formation by accumulating precursors.

Yeast community succession in cow dung composting process

Yeast complexes in the composting process of cow dung prepared to fertilize the soil for growing vegetables and fruits were studied. The average abundance of yeasts changed during the four temperature stages of the composting process. The highest abundance of yeasts, 1.38 × 10⁴ cfu/g, was observed in the second stage of heating from 20 to 40 °C; the lowest was studied in the stage with the highest temperature (65 °C), 1.68 × 10³ cfu/g. A total of 19 yeast species were observed and identified: 11 ascomycetes and 8 basidiomycetes, belonging to five subphyla of Fungi: Saccharomycotina (10), Pezizomycotina (1), Agaricomycotina (5), Pucciniomycotina (2), and Ustilaginomycotina (1). The greatest diversity of yeasts was found in the initial (20 °C) and second (heating up to 40 °C) temperature stages of composting (Aureobasidium pullulans (yeast-like fungus), Candida parapsilosis, Candida saitoana, Candida santamariae, Candida tropicalis, Curvibasidium cygneicollum, Cutaneotrichosporon moniliforme, Debaryomyces fabryi, Debaryomyces hansenii, Filobasidium magnum, Kazachstania sp., Moesziomyces bullatus, Naganishia globosa, Papiliotrema flavescens, Rhodotorula mucilaginosa, Scheffersomyces insectosa, Torulaspora delbrueckii, Vanrija musci), and the lowest in the stage of maximum heating (65 °C) (C. parapsilosis, C. tropicalis, Cyberlindnera jadinii).The opportunistic yeasts C. parapsilosis and C. tropicalis were obtained not only in the initial, second and third temperature stages of the composting process, but also in mature compost in the final stage prepared for soil application. This study shows that the cow dung, used in the farm studied did not meet the microbiological safety criteria. The reduction of opportunistic yeast species was not achieved with the composting method used. The likelihood of these species entering agricultural products via compost and soil and developing as endophytes in the internal tissues of fruits is very high. Since some strains of opportunistic Candida species from cow dung exhibited virulent characteristics (they produced hydrolytic enzymes and were resistant to antifungal compounds), additional phenotypic and genetic studies of the compost strains and their comparison with clinical isolates should be pursued.

Effect of the Presence of Lignin from Woodflour on the Compostability of PHA-Based Biocomposites: Disintegration, Biodegradation and Microbial Dynamics

Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) has gained attention as a possible substitute for conventional polymers that could be integrated into the organic recycling system. Biocomposites with 15% of pure cellulose (TC) and woodflour (WF) were prepared to analyze the role of lignin on their compostability (58 °C) by tracking the mass loss, CO₂ evolution, and the microbial population. Realistic dimensions for typical plastic products (400 µm films), as well as their service performance (thermal stability, rheology), were taken into account in this hybrid study. WF showed lower adhesion with the polymer than TC and favored PHBV thermal degradation during processing, also affecting its rheological behavior. Although all materials disintegrated in 45 days and mineralized in less than 60 days, lignin from woodflour was found to slow down the bioassimilation of PHBV/WF by limiting the access of enzymes and water to easier degradable cellulose and polymer matrix. According to the highest and the lowest weight loss rates, TC incorporation allowed for higher mesophilic bacterial and fungal counts, while WF seemed to hinder fungal growth. At the initial steps, fungi and yeasts seem to be key factors in facilitating the later metabolization of the materials by bacteria.

Role of fungal communities and their interaction with bacterial communities on carbon and nitrogen component transformation in composting with different phosphate additives

The aim of the study was to compare the succession of fungal community and their interaction with bacterial community during pig manure composting with different phosphate additives and further to identify microbial roles on the transformation of carbon and nitrogen (C&N) components and compost maturity. The results showed that the composition of fungal community was significantly affected by pH in composting and acidic phosphate might postpone the C&N degradation process. Network analysis showed that phosphate additives, especially acidic additives, could increase the interaction of microbial community but acidic phosphate decreased the core fungi:bacteria ratio. Redundancy analysis indicated that the interactions between bacterial and fungal communities played more roles than individual contribution of bacteria or fungi for C&N conversion of composting. Structural equation modeling suggested that bacterial community was positively directly correlated to C&N loss and the participation of fungal community significantly benefited the maturity of composting. pH exhibited a great intermediated role for driving C&N conversion, maturity, and safety of composts by regulating bacterial and fungal community in composting with phosphate addition, which suggested a fast-composting way based on pH regulation by additives.

Evaluation of fungal community assembly and function during food waste composting with Aneurinibacillus sp. LD3 inoculant

The objective of this work was to evaluate the fungal community assembly and function during food waste composting with Aneurinibacillus sp. LD3 (LD3) inoculant. Inoculation reduced the content of total organic carbon, moisture content, nitrate nitrogen, and nitrite nitrogen. The LD3 inoculant was able to drive the changes in the assembly of the fungal community. In particular, inoculation with LD3 not only increased the relative abundance of Ascomycota and Trichocomaceae_unclassified for lignocellulose degradation at the mesophilic and cooling stages but also reduced the relative abundances of the opportunistic human pathogen Candida. Saprotroph was the predominant fungal trophic mode in composting, and inoculation with LD3 has a better inactivation effect on animal and plant pathogenic fungi during composting. Furthermore, the variation of the fungal community after inoculation with LD3 was the largest explained by temperature (30.64%). These results implied that LD3 significantly regulated fungal composition and function of food waste composting.

Core fungal species strengthen microbial cooperation in a food-waste composting process

In ecosystem engineering research, the contribution of microbial cooperation to ecosystem function has been emphasized. Fungi are one of the predominant decomposers in composting, but thus far, less attention has been given to fungal than to bacterial cooperation. Therefore, network and cohesion analyses were combined to reveal the correlation between fungal cooperation and organic matter (OM) degradation in ten composting piles. Positive cohesion, reflecting the cooperation degree, was positively linked to the degradation rate of OM. From the community perspective, core species (i.e., Candida tropicalis, Issatchenkia orientails, Kazachstania exigua, and Dipodascus australiensis) with high occurrence frequency and abundance were the key in regulating positive cohesion. These species were highly relevant to functional genera associated with OM degradation in both fungal and bacterial domains. Therefore, focusing on these core fungal species might be an appropriate strategy for targeted regulation of functional microbes and promotion of degradation rates.

Magnesite driven the complementary effects of core fungi by optimizing the physicochemical parameters in pig manure composting

The effects of magnesite (MS) on fungi communities and the core fungi complementarity during pig manure (PM) composting were explored. Different dosage of MS [0% (T1), 2.5% (T2), 5% (T3), 7.5% (T4) and 10% (T5)] as amendments mixed with PM for 42 days composting. The results showed the dominant of phyla were Ascomycota (78.87%), Neocallimastigomycota (41.40%), Basidiomycota (30.81%) and Aphelidiomycota (29.44%). From day 7 to 42, the abundance of Ascomycota and Aphelidiomycota were increased from 7.75% to 42.41% to 57.27%-78.87% and 0-0.70% to 11.73%-29.44% among all treatments. Nevertheless, the phyla abundance of Neocallimastigomycota and Basidiomycota decreased from day 7 to 42. The co-occurrence network indicated that the high additive amendment could enhance the core fungi complementarity effects capacity. The 10% MS addition was a promisable candidate to optimum fungal communities, and causing a better compost quality. This study illustrated the potential and fungi communities changing of MS as additives in composting.

Co-composting with cow dung and subsequent vermicomposting improve compost quality of spent mushroom

In order to determine a feasible degrading process for spent mushroom (SMS) with high lignin content, the present work used cow dung (CD), SMS, and a mixture of CD and SMS as substrates and evaluated the effects of vermicomposting on the microflora and the quality of composting products. Bacterial (R² = 0.548, P = 0.001) and fungal (R² = 0.314, P = 0.005) community both were different between composting and vermicomposting. Vermicomposting and substrates affected enzyme activities indirectly by affecting ammonium, pH, total carbon, richness, and bacterial community composition. These results suggested that appropriate regulation of environmental factors may increase microbial activity. An increase in ion-exchange capacity (up to 139.8%), pH (6.9%), and nitrate (71.1%) and a decrease in total carbon (31.2%) and carbon/nitrogen ratio (32.1%) in vermicomposting indicated that earthworms could further improve product quality. Co-composting with CD and integrated subsequent vermicomposting efficiently promoted the maturity of SMS.

Effects of residual monensin in livestock manure on nitrogen transformation and microbial community during "crop straw feeding-substrate fermentation-mushroom cultivation" recycling system

Although crop-livestock integration recycling systems improve nitrogen (N) utilization in agroecosystems, there are limited studies regarding impacts of residual antibiotics in livestock manure on N transformation in entire recycling system. The objective was to evaluate effects of feeding monensin on N recycling during "straw feeding-substrate fermentation-mushroom cultivation". This experiment contained 3 steps. During straw feeding, beef cattle were allocated into 2 groups and fed diets with or without monensin, respectively. During fermentation, beef cattle manure (with or without monensin) and straw (corn or wheat) and were co-fermented for 35 d to produce substrates. During cultivation, Agaricus bisporus was cultivated on 4 substrates to recycle N in the form of mushrooms. Rates of N retention during fermentation were significant higher for monensin and corn straw treatments and there was an significant interaction between straw and antibiotic on N retention rate during cultivation. However, residual monensin significantly reduced amount of recycled N during entire recycling system, due to changes in N transformation-associated enzyme activity, ammonification and denitrification plus microbial community structure and succession. Specifically, residual monensin inhibited growth of dominant bacterial phylum Bacteroidetes and fungal phylum Neocallimastigomycota, and increased bacterial phylla Actinobacteriota and Firmicutes. These alterations in functional microbes increased N retention rates but reduced mushroom yields in antibiotic treatments during cultivation. In conclusion, monensin decreased the N recycling rate in recycling system, but also reduced N losses during fermentation by inhibiting ammonification and denitrification, so, avoiding antibiotics usage is an effective strategy to improve the efficiency of recycling systems.

Lignocellulosics in plant cell wall and their potential biological degradation

Lignocellulosic materials are composed of three main structural polymers: hemicellulose, cellulose, and lignin. Cellulose is a long chain molecule of glucose requiring a small number of enzymes for degradation due to its simple structure while lignin is a complex polymer of phenylpropane making its biochemical decomposition difficult. Under anaerobic conditions, lignocellulose breakdown is much easier and more rapid than aerobic conditions. Various studies have been carried out to estimate the rate of degradation of lignocellulosic materials. Microorganisms play a key role in the degradation of lignocellulosic materials because they produce a variety of hydrolytic enzymes including cellulase, proteases, xylanases, lipases, laccase, and phosphatases during the degradation of lignocellulosic materials. Based on the body of literature, microorganismal activity can provide useful information about the process of organic matter decomposition.

The microbial mechanisms of enhanced humification by inoculation with Phanerochaete chrysosporium and Trichoderma longibrachiatum during biogas residues composting

This study investigated effects of composite microbes (CMs) (Phanerochaete chrysosporium and Trichoderma longibrachiatum) on humification during co-composting of biogas residue, spent mushroom substrate and rice straw. Results showed that CMs inoculation elevated degradation ratios of cellulose, hemicellulose and lignin by 7.86%, 8.87% and 6.45%, and contents of humus and humic acid were correspondingly promoted by 15.5% and 23.6%, respectively. Relative abundances of bacteria associated with refractory macromolecules degradation (Flavobacterium, Anseongella and Actinomadura) and cellulolytic fungi (Hypocreales_Incertae_sedis, Hypocreaceae and Psathyrellaceae) were raised by CMs addition. Redundancy analysis demonstrated a positive correlation between microbial communities and temperature, fulvic acid and lignocellulose contents. Moreover, CMs inoculation promoted pathways of xenobiotics biodegradation and metabolism, and biosynthesis of other secondary metabolites, which was closely associated with lignocellulose degradation and humus formation. These results suggested that biological inoculation could enhance composting efficiency and improve compost quality, benefiting biogas residues composting.

Dynamics of fungal species related to nitrogen transformation and their network patterns during cattle manure-corn straw with biochar composting

Fungi are reputed to play a significant role in the composting matrix as decomposers of recalcitrant organic materials like cellulose and lignin. However, information on the fungi communities' roles in nitrogen transformation under a compost-biochar mixture is scarce. This study investigated shifts in fungal species mediating N transformation and their network patterns in cattle manure-corn straw (CMCS) and CMCS plus biochar (CMCB) composting using high-throughput sequencing data. The results revealed that the addition of biochar altered fungal richness and diversity and significantly influenced their compositions during composting. Biochar also altered the compost fungal network patterns; CMCS had a more complex network with higher positive links than CMCB, suggesting stable niche overlap. The consistent agreement of multivariate analyses (redundancy, network, regression, Mantel and path analyses) indicated that Ciliophora_sp in CMCS and unclassified_norank_Pleosporales in CMCB were the key fungal species mediating total N transformation, whereas Scedosporium_prolificans in CMCS and unclassified_Microascaceae in CMCB were identified as major predictive indices determining NO₃^--N transformation. Also, Coprinopsis cinerea and Penicillium oxalicum were the predictive factors for NH₄⁺-N transformation in CMCS and CMCB during composting. These results indicated that the effects of biochar on N conversions in composting could be unraveled using multivariate analyses on fungi community evolution, network patterns, and metabolism.

Combined addition of biochar and garbage enzyme improving the humification and succession of fungal community during sewage sludge composting

The influences of combination of garbage enzyme and biochar on total organic carbon (TOC) degradation, humification and the fungal succession during sewage sludge (SS) composting were established. Results showed that the GE and BC + GE treatments significantly increased the enzyme activity of fluorescein diacetate hydrolase (FDA) and increased the TOC degradation rate by 9.8% and 21.9% relative to control. The excitation-emission matrix (EEM) combined with the percentage fluorescence response (Pi, n) also proved that the combination of BC and GE promoted fulvic acid-like and humic-like substances production, and thus increased humification. Furthermore, the combination of BC and GE effectively decreased the relative abundance of Unclassified_k_Fugni, while increased the abundance of Ascomycota and Basidiomycota compared with control. The four genera, Pseudeurotium, Talaromyces, Trichoderma, and Penicillium, were the main fungi for the humification. Comparatively, the combined of BC and GE showed the optimal performance for TOC degradation and humification during SS composting.

Influence of microbial inoculants on co-composting of lignocellulosic crop residues with farm animal manure: A review

The rapidly developing agro-industry generates huge amounts of lignocellulosic crop residues and animal manure worldwide. Although co-composting represents a promising and cost-effective method to treat various agricultural wastes simultaneously, poor composting efficiency prolongs total completion time and deteriorates the quality of the final product. However, supplementation of the feedstock with beneficial microorganisms can mitigate these negative effects by facilitating the decomposition of recalcitrant materials, enhancing microbial enzyme activity, and promoting maturation and humus formation during the composting process. Nevertheless, the influence of microbial inoculation may vary greatly depending on certain factors, such as start-up parameters, structure of the feedstock, time of inoculation, and composition of the microbial cultures used. The purpose of this contribution is to review recent developments in co-composting procedures involving different lignocellulosic crop residues and farm animal manure combined with microbial inoculation strategies. To evaluate the effectiveness of microbial additives, the results reported in a large number of peer-reviewed articles were compared in terms of composting process parameters (i.e., temperature, microbial activity, total organic carbon and nitrogen contents, decomposition rate of lignocellulose fractions, etc.) and compost characteristics (humification, C/N ratio, macronutrient content, and germination index). Most studies confirmed that the use of microbial amendments in the co-composting process is an efficient way to facilitate biodegradation and improve the sustainable management of agricultural wastes. Overall, this review paper provides insights into various inoculation techniques, identifies the limitations and current challenges of co-composting, especially with microbial inoculation, and recommends areas for further research in this field.

Co-composting of cotton residues with olive mill wastewater: process monitoring and evaluation of the diversity of culturable microbial populations

With the aim to recommend an integrated alternative for the combined treatment of olive mill wastewater (OMW) and cotton residues (CR), and the production of high value and environmentally friendly products, two compost piles were set up. The first pile (control, pile 1) consisted of ginned CR, whereas the second (pile 2) was made of CR with the addition of OMW. A series of physicochemical parameters and the culturable microbial diversity in both piles were assessed. Co-composting (pile 2) displayed higher temperatures during the whole process, a prolonged second thermophilic phase and temperature values higher than 40 °C even after the thermophilic stage. Comparing the physicochemical parameters of the pile 2 with those of the pile 1, it was deduced that pH in the former was more acidic during the onset of the process; the EC values were higher throughout the process, while the levels of ammonium and nitrate nitrogen, as well as the NH₄⁺/NO₃^- ratios, were lower at most of the sampling dates. By evaluating the abovementioned results, it was estimated that the co-composting process headed sooner toward stability and maturity, Isolated microorganisms from both piles were identified as members of the genera Brevibacillus, Serratia, Klebsiella, and Aspergillus, whereas active thermotolerant diazotrophs were detected in both piles at the 2nd thermophilic phase emerging a promising prospect upon further evaluation for enhancing the end-product quality. Our findings indicate that co-composting is an interesting approach for the exploitation of large quantities of agro-industrial residues with a final product suitable for improving soil fertility and health.

Characterization of Thermophilic Lignocellulolytic Microorganisms in Composting

Composting involves the selection of a microbiota capable of resisting the high temperatures generated during the process and degrading the lignocellulose. A deep understanding of the thermophilic microbial community involved in such biotransformation is valuable to improve composting efficiency and to provide thermostable biomass-degrading enzymes for biorefinery. This study investigated the lignocellulose-degrading thermophilic microbial culturome at all the stages of plant waste composting, focusing on the dynamics, enzymes, and thermotolerance of each member of such a community. The results revealed that 58% of holocellulose (cellulose plus hemicellulose) and 7% of lignin were degraded at the end of composting. The whole fungal thermophilic population exhibited lignocellulose-degrading activity, whereas roughly 8-10% of thermophilic bacteria had this trait, although exclusively for hemicellulose degradation (xylan-degrading). Because of the prevalence of both groups, their enzymatic activity, and the wide spectrum of thermotolerance, they play a key role in the breakdown of hemicellulose during the entire process, whereas the degradation of cellulose and lignin is restricted to the activity of a few thermophilic fungi that persists at the end of the process. The xylanolytic bacterial isolates (159 strains) included mostly members of Firmicutes (96%) as well as a few representatives of Actinobacteria (2%) and Proteobacteria (2%). The most prevalent species were Bacillus licheniformis and Aeribacillus pallidus. Thermophilic fungi (27 strains) comprised only four species, namely Thermomyces lanuginosus, Talaromyces thermophilus, Aspergillus fumigatus, and Gibellulopsis nigrescens, of whom A. fumigatus and T. lanuginosus dominated. Several strains of the same species evolved distinctly at the stages of composting showing phenotypes with different thermotolerance and new enzyme expression, even not previously described for the species, as a response to the changing composting environment. Strains of Bacillus thermoamylovorans, Geobacillus thermodenitrificans, T. lanuginosus, and A. fumigatus exhibiting considerable enzyme activities were selected as potential candidates for the production of thermozymes. This study lays a foundation to further investigate the mechanisms of adaptation and acquisition of new traits among thermophilic lignocellulolytic microorganisms during composting as well as their potential utility in biotechnological processing.

Community-level dormancy potential regulates bacterial beta-diversity succession during the co-composting of manure and crop residues

This study aimed to disclose the bacterial diversity succession during the co-composting of manure and crop residues and to provide new insight into the role of community-level dormancy potential in diversity succession. Illumina sequencing and PICRUSt-estimated metagenomes were used for this purpose. The bacterial richness and phylogenetic diversity decreased in the early and middle stages of composting and were maintained to a stable status in the late stage. Both composting phases and raw materials impacted the aforementioned alpha diversity significantly, while the composting phases had a greater (80%-94%) impact than the raw materials (1%-18%). Bacterial beta-diversity succession exhibited selectivity as the composting proceeded, and the dominant taxa changed into salt- and heat-resistant genera such as Bacillus, Glycomyces, and Halocella. Meanwhile, Georgenia, Actinomadura, and Ruminofilibacter were identified as the dominant predictor taxa of bacterial community succession in composting. Roughly, the abundance of genes underlying dormancy strategies, including sporulation factors (spo0A gene), toxin-antitoxin systems (dinJ/yafP, mazF/E, hipA/O, and relA/E genes), and resuscitation-promoting factors (rpfC gene), increased as composting proceeded and reached the highest in the thermophilic or maturation phases. Co-occurring relationships between bacterial communities and genes underlying dormancy strategies in different composting phases comprised multiple associations dominated by positive edges (50%-97%). The stability in genes underlying dormancy strategies and aggregate dormancy potential had a positive linear correlation with that in bacterial beta diversity (R² = 0.26-0.42; P < 0.05), but not related significantly to that in richness and phylogenetic diversity. This study highlighted the importance of understanding how community-level dormancy strategies mediated microbial succession in composting to better predict compost maturity and product quality.

Changes of fungal diversity in fine coal gasification slag amendment pig manure composting

The purpose of this study was to investigate fungal diversity and relative abundance (RA) during pig manure composting via high-throughput sequencing approach. Fine coal gasification slag (FCGS) (0%, 2%, 4%, 6%, 8% and 10%) were added into composting raw materials as additive and performed 42 days. Adjust C/N and moisture to 30 and 65%. Results showed that dominant phyla were Ascomycota (99.62%) and Basidiomycota (0.38%). The main genera were Epicoccum (1.26%), Alternaria (83.35%), Aspergillus (12.08%) and Gibberella (1.69%). 10% treatment got the higher abundance and operational taxonomic units number from rank abundance curve and petals diagram. Compared with control, FCGS amendment composting could increase the sanitary time (3-7 d) and total nitrogen (0.05-12.03%). The principal component analysis was considered that FCGS treatments and control had significantly difference. The RA of fungi varied among all treatments. Therefore, 10% treatment was a potential candidate to enhance fungal diversity and composting quality.

Improved strategies to efficiently isolate thermophilic, thermotolerant, and heat-resistant fungi from compost and soil

Thermophilic, thermotolerant and heat-resistant fungi developed different physiological traits, enabling them to sustain or even flourish under elevated temperatures, which are life-hostile for most other eukaryotes. With the growing demand of heat-stable molecules in biotechnology and industry, the awareness of heat-adapted fungi as a promising source of respective enzymes and biomolecules is still increasing. The aim of this study was to test two different strategies for the efficient isolation and identification of distinctly heat-adapted fungi from easily accessible substrates and locations. Eight compost piles and ten soil sites were sampled in combination with different culture-dependent approaches to describe suitable strategies for the isolation and selection of thermophilous fungi. Additionally, an approach with a heat-shock treatment, but without elevated temperature incubation led to the isolation of heat-resistant mesophilic species. The cultures were identified based on morphology, DNA barcodes, and microsatellite fingerprinting. In total, 191 obtained isolates were assigned to 31 fungal species, from which half are truly thermophilic or thermotolerant, while the other half are heat-resistant fungi. A numerous amount of heat-adapted fungi was isolated from both compost and soil samples, indicating the suitability of the used approaches and that the richness and availability of those organisms in such environments are substantially high.

Diversity and composition of the North Sikkim hot spring mycobiome using a culture-independent method

Fungi are considered to be the most resilient and economically important microbial community that can easily survive and optimally grow under a wide range of growth conditions. Thermophilic fungi from the geothermal sources have been less pondered upon and lie unexplored. Here, a microbiome approach was conducted to understand the concealed world of the environmental mycobiota from the two hot springs of North Sikkim district located in North-east India. The solfataric muds from the hot springs were analyzed. In both the samples, on the basis of genus level classification, genus Fusarium had the highest abundance followed by Colletotrichum, Pochonia, Pyricularia, Neurospora, etc. Analyzing the predicted genes, the functional proteins of New Yume Samdung mycobiome were found to be dominated by the genera Fusarium (22%), Trichoderma (12%), and Aspergillus (11%), whereas in the case of Old Yume Samdung, it was dominated by the genera Aspergillus (11%), Saccharomyces (6%), and Fusarium (5%). Interestingly, in the studied mycobiome, environmental yeasts were also detected. From the functional metagenomics, sulfate adenylatetransferase (SAT) proteins for sulfur assimilation were found in some of the fungal reads. Toxin protein reads such as AM-toxin biosynthesis proteins, AF-toxin biosynthesis proteins, Gliotoxin biosynthesis proteins, and aflatoxin biosynthesis proteins were detected in the mycobiomes.

Response of bacterial and fungal communities to high petroleum pollution in different soils

Petroleum pollution of soils is a major environmental problem. Soil microorganisms can decompose a significant fraction of petroleum hydrocarbons in soil at low concentrations (1-5%). This characteristic can be used for soil remediation after oil pollution. Microbial community dynamics and functions are well studied in cases of moderate petroleum pollution, while cases with heavy soil pollution have received much less attention. We studied bacterial and fungal successions in three different soils with high petroleum contents (6 and 25%) in a laboratory experiment. The proportion of aliphatic and aromatic compounds decreased by 4-7% in samples with 6% pollution after 120 days of incubation but remained unchanged in samples with 25% hydrocarbons. The composition of the microbial community changed significantly in all cases. Oil pollution led to an increase in the relative abundance of bacteria such as Actinobacteria and the candidate TM7 phylum (Saccaribacteria) and to a decrease in that of Bacteroidetes. The gene abundance (number of OTUs) of oil-degrading bacteria (Rhodococcus sp., candidate class TM7-3 representative) became dominant in all soil samples, irrespective of the petroleum pollution level and soil type. The fungal communities in unpolluted soil samples differed more significantly than the bacterial communities. Nonmetric multidimensional scaling revealed that in the polluted soil, successions of fungal communities differed between soils, in contrast to bacterial communities. However, these successions showed similar trends: fungi capable of lignin and cellulose decomposition, e.g., from the genera Fusarium and Mortierella, were dominant during the incubation period.

Patterns of fungal community succession triggered by C/N ratios during composting

Accumulating evidence indicates that the functional rather than taxonomic composition of microbial communities is closely correlated to local environmental factors. While composting is a widely accepted practice, specific knowledge of how fungal functional groups interact during the composting process remains limited. To address this, the impact of the initial C/N ratio of composting material on fungal community was analyzed in order to reveal the succession of functional diversity. Compared with the raw materials, the final composting product significantly reduced the relative abundances of plant and animal pathogens. Abundances of plant and animal pathogens, as well as dung saprotrophs, were negatively correlated with compost maturity, while abundances of wood saprotrophs exhibited positive correlations. Specific OTUs that showing highly abundant in each treatment were expected to compete for environmental preferences (niches) and/or interact with each other in positive (facilitative) ways. OTU2 (wood saprotroph) exhibiting the highest occurrence was negatively related to OTU7 (animal pathogen) and OTU4 (plant pathogen) during the mesophilic phase. Taken together, high-efficiency composting is represented as pattern variations of fungal community with a process of gradual decline of plant and animal pathogens as well as dung saprotrophs.

Thermotolerant and Thermophilic Mycobiota in Different Steps of Compost Maturation

Composting is a complex process in which various micro-organisms, mainly fungi and bacteria, are involved. The process depends on a large number of factors (biological, chemical, and physical) among which microbial populations play a fundamental role. The high temperatures that occur during the composting process indicate the presence of thermotolerant and thermophilic micro-organisms that are key for the optimization of the process. However, the same micro-organisms can be harmful (allergenic, pathogenic) for workers that handle large quantities of material in the plant, and for end users, for example, in the indoor environment (e.g., pots in houses and offices). Accurate knowledge of thermotolerant and thermophilic organisms present during the composting stages is required to find key organisms to improve the process and estimate potential health risks. The objective of the present work was to study thermotolerant and thermophilic mycobiota at different time points of compost maturation. Fungi were isolated at four temperatures (25, 37, 45, and 50 °C) from compost samples collected at five different steps during a 21-day compost-maturation period in an active composting plant in Liguria (northwestern Italy). The samples were subsequently plated on three different media. Our results showed a high presence of fungi with an order of magnitude ranging from 1 × 10⁴ to 3 × 10⁵ colony-forming units (CFU) g⁻¹. The isolated strains, identified by means of specific molecular tools (ITS, beta-tubulin, calmodulin, elongation factor 1-alpha, and LSU sequencing), belonged to 45 different species. Several thermophilic species belonging to genera Thermoascus and Thermomyces were detected, which could be key during composting. Moreover, the presence of several potentially harmful fungal species, such as Aspergillus fumigatus, A. terreus, and Scedosporium apiospermum, were found during the whole process, including the final product. Results highlighted the importance of surveying the mycobiota involved in the composting process in order to: (i) find solutions to improve efficiency and (ii) reduce health risks.

Metabolites from Two Dominant Thermophilic Fungal Species Thermomyces lanuginosus and Scytalidium thermophilum

Thermomyces lanuginosus and Scytalidium thermophilum are among the most ubiquitous thermophilic fungi in compost and soil. Chemical study on these two prevalent strains collected from Yunnan led to isolation of 23 metabolites, including one new metabolite, therlanubutanolide, and 15 known compounds, isolated from the YGP culture broth of Thermomyces lanuginosus and 7 known compounds isolated from Scytalidium thermophilum, respectively. Therlanubutanolide shared the quite similar features of the same carbon skeleton and saturation as natural hexadecanoic acids. This was the first reported discovery of such a lactone as natural occurring metabolite. All the compounds were reported for the first time from thermophilic fungi. Among them, N-[(2S,3R,4E,8E)-1,3-dihydroxy-9-methyloctadeca-4,8-dien-2-yl]acetamide was for the first time reported to be a naturally occurring metabolite and its NMR data was first provided in this study. A type of PKS-derived metabolites, three 3,4-dihydronaphthalen-1(2H)-ones, which were widely found in plant pathogenic fungi as phytotoxins and reported to have antimicrobial activity, were obtained from both dominant thermophilic fungi. The frequent occurrence of such PKS phytotoxins in these two thermophilic fungi might suggest particular ecological interest.

Assessment of bacterial and fungal communities in a full-scale thermophilic sewage sludge composting pile under a semipermeable cover

Bacterial and fungal communities in a full-scale composting pile were investigated, with sewage sludge and a vegetal bulking agent as starting materials. Bacillales and Actinomycetales were predominant throughout the process, showing significant abundance. Ascomycota was the predominant fungal phylum during the thermophilic phase, with a shift to Basidiomycota at the end of the process. The bulking material was the principal contributor to both communities by the end of the process, with a signal above 50%. The presence of genera, such as Pedomicrobium, Ureibacillus and Tepidimicrobium at the end of the process, and Chaetomium and Arthrographis in the maturation phase, showed an inverse correlation with indicators of organic matter stabilisation. A semipermeable cover was an effective technology for excluding pathogens. These results indicate that changes in the microbial population and their interrelation with operational variables could represent a useful tool for monitoring composting processes.

Succession of fungal dynamics and their influence on physicochemical parameters during pig manure composting employing with pine leaf biochar

The effects of pine leaf biochar (PLB) on fungal community during pig manure composting were investigated. Five different doses of PLB [0% (T1), 2.5% (T2), 5% (T3), 10% (T4) and 15% (T5)] were mixed with mixture of pig manure and sawdust (2:1) for 50 days of composting. The present results indicated that fungal diversity increased more obvious in biochar amendment treatments than control (T1) and that the highest was recorded in T4 treatment. Basidiomycota, Ascomycota and Mucoromycota were the most three abundant phyla in all the treatments, while Heterobasidion, Pezoloma, Mucor, Geastrum, Talaromyces and Cystofilobasidium were the richness genera. In addition, network analysis indicated that fungal community abundance was significantly (p < 0.05) associated with temperature, pH, CO₂ and CH₄ emission and the seed germination index. In summary, the 10% PLB amendment (T4) was a potential option to strengthen fungal diversity and improve the composting efficiency as well as compost quality.

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

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

A novel thermostable D-amino acid oxidase of the thermophilic fungus Rasamsonia emersonii strain YA

d-Amino acid oxidase (DAAO) is a valuable flavoenzyme capable of being used in various practical applications, such as in determining d-amino acids and producing a material for semisynthetic cephalosporins, requiring higher thermal stability, higher catalytic activity, and broad substrate specificity. In this study, we isolated the thermophilic fungus Rasamsonia emersonii strain YA, which can grow on several d-amino acids as the sole nitrogen source, from a compost and characterized DAAO (ReDAAO) of the fungus. ReDAAO expressed in Escherichia coli exhibited significant oxidase activity against various neutral and basic d-amino acids, in particular hydrophobic d-amino acids. In addition, the enzyme also significantly acted on cephalosporin C, a starting material for semisynthetic antibiotics, and d-Glu, a general substrate for d-aspartate oxidase but not for DAAO, showing its unique and practically useful substrate specificity. The apparent k_cat and K_m values of the enzyme toward good substrates were comparable to those of higher catalytic fungal DAAOs, and the thermal stability (T₅₀ value of ~60 °C) was comparable to that of a thermophilic bacterial DAAO and significantly higher than that of other eukaryotic DAAOs. These results highlight the great potential of ReDAAO for use in practical applications.

Effect of phosphogypsum addition in the composting process on the physico-chemical proprieties and the microbial diversity of the resulting compost tea

Phosphoric acid production and olive oil production are among the most important economical sectors in Tunisia. However, they generate huge amounts of wastes (phosphogypsum, olive mill waste water, and olive pomace). In a previous study, we used phosphogypsum (PG), in co-composting with organic wastes. Three composts were produced; their PG content was of 0 (AT), 10 (A10), and 30% (A30). In the present study, we focused on their derived compost teas. The physico-chemical characterization of the different compost teas showed that those from A10 and A30 composts presented higher P and Ca contents than that from control one (AT). The microbial characterization using DGGE showed a noticeable microbial diversity in the different compost teas and that the addition of 10% and 30% PG in the compost had different effects on the compost tea microbial diversity. The identification results showed that the addition of 10 and 30% of PG did not affect the presence of PGPR (plant growth-promoting rhizobacteria) and fungal soil antagonists in the compost teas. Two PGPRs were isolated from AT and A30 compost teas, and their effect on the growth of potato plants in vitro was evaluated.

Positive impact of biochar alone and combined with bacterial consortium amendment on improvement of bacterial community during cow manure composting

The present work studied to evaluate the effectiveness under the interaction of bacterial consortium and biochar applied to give impetus to bacterial community activities among cow manure composting. High-throughput sequencing technique and six treatments were carried out: T2, T3 and T6 were single apply of bacteria culture (C), 12%wood biochar (12%WB) and 12%wheat straw biochar (12%WSB), respectively, while T4 and T5 were bacterial consortium combined with 12%WB and 12%WSB respectively, and T1 was used as control. The conclusion shows that the richness of bacterial community were most prosperity in T5 and T4 that in line with the statistical analysis angle of curves and cluster. The dominate phyla of Firmicutes, Proteobacteria and Bacteroidetes were accounted to 31.36%, 34.79% and 33.85%, the superior genera were Dysgonomonas (16.55%), Empedobater (9.39%), Atopostipes (13.42%), Tissierella (8.25%), Marinimicrobium (14.45%) and Pseudomonas (9%). Overall, bacterial consortium combined with biochar could stimulate microbe activity to accelerate degradation, enhance richness and alter specific selection of bacterial community.

Dynamics of fungal diversity and interactions with environmental elements in response to wheat straw biochar amended poultry manure composting

The fungal dynamics and its correlation with physicochemical and gaseous emission were investigated using metagenomics and Heat map illustrator (HEMI). Five different concentrations of wheat straw biochar (WSB) were applied to poultry manure (PM) and composted for 50 days; those without the WSB treatment were used as a control. The results revealed the dominant phyla to be Chytridiomycota, Mucoromycota, Ascomycota and Basidiomycota, while Batrachochytrium, Rhizophagus, Mucor, and Puccinia were the superior genera. In particular, the diversity of Chytridiomycota and Ascomycota was more abundant among all of the treatments. Overall, the diversity of the fungal species was correspondent, but relative abundance varied significantly among all of the composts. Principle Coordinate Analysis (PCoA) and Non-Metric Multi- Dimensional Scaling (NMDS) indicated that different concentrations of WSB applied treatments have significantly distinct fungal communities. In addition, correlation analyses of fungal interactions with environmental elements via HEMI also indicate a clear difference among the treatments. Ultimately, the relative abundance of fungal composition significantly influenced the PM compost treated by the WSB.

Changes in structure and function of fungal community in cow manure composting

In this study, dynamic changes in fungal communities, trophic modes and effect factors in 60 days composting of cow manure were analyzed by using high throughput sequencing, FUNGuild and Biolog FF MicroPlate, respectively. Orpinomyces (relative abundance >10.85%) predominated in feedstock, and Mycothermus became the dominating genus (relative abundance >75%) during the active phase. Aerobic composting treatment had a significant effect on fungal trophic modes with pathogenic fungi fading away and wood saprotrophs increasing over composting time. Fungal communities had the higher carbon sources utilization capabilities at the thermophilic phase and mature phase than those in the other periods. Oxidation reduction potential (ORP) significantly increased from -180 to 180 mV during the treatment. Redundancy analysis showed that the succession of fungal community during composting had a significant association with ORP (p < .05). This indicated that aerobic composting treatment not only influenced fungal community structure, but also changed fungal trophic modes and metabolic characteristics.

Compost bacteria and fungi that influence growth and development of Agaricus bisporus and other commercial mushrooms

Mushrooms are an important food crop for many millions of people worldwide. The most important edible mushroom is the button mushroom (Agaricus bisporus), an excellent example of sustainable food production which is cultivated on a selective compost produced from recycled agricultural waste products. A diverse population of bacteria and fungi are involved throughout the production of Agaricus. A range of successional taxa convert the wheat straw into compost in the thermophilic composting process. These initially break down readily accessible compounds and release ammonia, and then assimilate cellulose and hemicellulose into compost microbial biomass that forms the primary source of nutrition for the Agaricus mycelium. This key process in composting is performed by a microbial consortium consisting of the thermophilic fungus Mycothermus thermophilus (Scytalidium thermophilum) and a range of thermophilic proteobacteria and actinobacteria, many of which have only recently been identified. Certain bacterial taxa have been shown to promote elongation of the Agaricus hyphae, and bacterial activity is required to induce production of the mushroom fruiting bodies during cropping. Attempts to isolate mushroom growth-promoting bacteria for commercial mushroom production have not yet been successful. Compost bacteria and fungi also cause economically important losses in the cropping process, causing a range of destructive diseases of mushroom hyphae and fruiting bodies. Recent advances in our understanding of the key bacteria and fungi in mushroom compost provide the potential to improve productivity of mushroom compost and to reduce the impact of crop disease.

Fungal and bacterial successions in the process of co-composting of organic wastes as revealed by 454 pyrosequencing

Composting is viewed as one of the primary methods to treat organic wastes. Co-composting may improve the efficiency of this treatment by establishing the most suitable conditions for decomposers than those present in the individual wastes. Given that bacteria and fungi are the driving agents of composting, information about the composition of their communities and dynamics during composting may improve reproducibility, performance and quality of the final compost as well as help to evaluate the potential human health risk and the choice of the most appropriate application procedure. In this study, the co-composting of mixtures containing two similar components (organic fraction of municipal solid waste and sawdust polluted by oil) and one discriminate component (sewage sludges of different origin) were investigated. Bacterial and fungal community successions in the two mixtures were analyzed during the composting process by determining the change in their structural dynamics using qPCR and 454 pyrosequencing methods in a lab experiment for a period of 270 days. During the initial composting stage, the number of 16S bacterial copies was (3.0±0.2) x 10⁶ and (0.4±0.0) x 10⁷ g^-1, and the Rhodospiralles and Lactobacialles orders dominated. Fungal communities had (2.9±0.0) x10⁵ and (6.1±0.2) x10⁵ ITS copies g^-1, and the Saccharomycetales order dominated. At the end of the thermophilic stage on the 30^th day of composting, bacterial and fungal communities underwent significant changes: dominants changed and their relative abundance decreased. Typical compost residents included Flavobacteriales, Chitinophagaceae and Bacterioidetes for bacteria and Microascaceae, Dothideomycetes, Eurotiomycetes, Sordariomycetes, and Agaricomycetes for fungi. During the later composting stages, the dominating taxa of both bacterial and fungal communities remained, while their relative abundance decreased. In accordance with the change in the dominating OTUs, it was concluded that the dynamics of the bacterial and fungal communities were not similar. Analysis by non-metric multidimensional scaling (NMDS) revealed that the bacterial communities of the two composts became progressively more similar; a similar trend was followed by the fungal community.

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

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

Stabilisation of spent mushroom substrate for application as a plant growth-promoting organic amendment

Over three million tonnes of spent mushroom substrate (SMS) are produced in Europe every year as a by-product of the cultivation of Agaricus bisporus. The management of SMS has become an increasing challenge for the mushroom production industry, and finding environmentally and economically sustainable solutions for this organic residue is, therefore, highly desirable. Due to its physical properties and nutrient content, SMS has great potential to be employed in agricultural and horticultural sectors, and further contribute to reduce the use of non-renewable resources, such as peat. However, SMS is often regarded as not being stable and/or mature, which hampers its wide use for crop production. Here, we demonstrate the stabilisation of SMS and its subsequent use as organic fertiliser and partial peat replacement in horticulture. The stabilisation was performed in a laboratory-scale composting system, with controlled temperature and aeration. Physical and chemical parameters were monitored during composting and provided information on the progress of the process. Water soluble carbohydrates (WSC) content was found to be the most reliable parameter to predict SMS stability. In situ oxygen consumption indicated the main composting phases, reflecting major changes in microbial activity. The structure of the bacterial community was also found to be a potential predictor of stability, as the compositional changes followed the composting progress. By contrast, the fungal community did not present clear successional process along the experiment. Maturity and quality of the stabilised SMS were assessed in a horticultural growing trial. When used as the sole fertiliser source, SMS was able to support Lolium multiflorum (Italian ryegrass) growth and significantly improved grass yield with a concentration-dependent response, increasing grass biomass up to 300%, when compared to the untreated control. In summary, the results indicated that the method employed was efficient in generating a stable and mature product, which has a great potential to be applied in horticulture. This study represents a step forward in the management of SMS residue, and also provides an alternative to reduce the use of peat in horticulture, alleviating environmental impacts to peatland ecosystems.

Fungal communities in pressmud composting harbour beneficial and detrimental fungi for human welfare

Pressmud is a substrate derived from sugarcane juice filtrate, and around 26-40  kg of this residue are produced per ton of sugarcane. It is mainly used as fertilizer in crops, and its application in the field is often made without any prior treatment, but, in this research, it was studied for the risk this practice poses for human health. This research was stimulated by previous results indicating the presence of opportunistic pathogens in residues used in various composting systems and the extensive use of fresh pressmud in agriculture. Here, It was assessed the fungal diversity present in both fresh and composting pressmud using 454 pyrosequencing. In addition, heat-tolerant fungi were isolated and surveyed for their enzymatic repertoire of biomass-degrading enzymes (cellulase, xylanase, laccase and polygalacturonase). A wide range of opportunistic pathogens was found among the most abundant taxa in the fresh pressmud, such as Lomentospora prolificans (43.13 %), Trichosporon sp. (10.07 %), Candida tropicalis (7.91 %), and Hormographiella aspergillata (8.19 %). This indicates that fresh pressmud might be a putative source of human pathogenic fungi, presenting a potential threat to human health if applied as fertilizer without any treatment. With regard to the heat-tolerant fungi found in this substrate, all the 110 isolates screened were able to produce at least one of the tested enzymes. The pressmud composting process not only effectively reduces the load of pathogenic fungi, but also creates an interesting environment for fungi able to produce thermostable hydrolytic and oxidative enzymes with biotechnological applications.

Early-diverging wood-decaying fungi detected using three complementary sampling methods

Wood-decaying fungi are essential components of degradation systems in forest ecosystems. However, their species diversity and ecological features are largely unknown. Three methods are commonly used to investigate fungal diversity: fruiting body collection, culturing, and environmental DNA analysis. Because no single method fully characterises fungal diversity, complementary approaches using two or more methods are required. However, few studies have compared the different methods and determined the best way to characterise fungal diversity. To this end, we investigated wood-decomposing Dacrymycetes (Agaricomycotina, Basidiomycota) using a complementary approach combining fruiting body collection, culturing, and environmental DNA analysis, thereby offering an effective approach for investigating the diversity of saprotrophic mushrooms. Fruiting body collection, culturing, and environmental DNA analysis detected 11, 10, and 16 operational taxonomic units (OTUs; 25 OTUs in total) and identified three, seven, and seven novel lineages, respectively. The three methods were complementary to each other to detect greater Dacrymycetes diversity. The culturing and environmental DNA analysis identified three early-diverging lineages that were not identified in the fruiting body collection suggesting that diverse lineages lacking observable fruiting bodies remain undiscovered. Such lineages may be important to understand Dacrymycetes evolution. To detect early branches of Dacrymycetes more efficiently, we recommend a combined approach consisting of a primary environmental DNA survey to detect novel lineages and a secondary culture survey to isolate their living mycelia. This approach would be helpful for identifying otherwise-undetectable lineages, and could thus uncover missing links that are important for understanding the evolution of mushroom-forming fungi.

Extrolites of Aspergillus fumigatus and Other Pathogenic Species in Aspergillus Section Fumigati

Aspergillus fumigatus is an important opportunistic human pathogen known for its production of a large array of extrolites. Up to 63 species have been described in Aspergillus section Fumigati, some of which have also been reliably reported to be pathogenic, including A. felis, A. fischeri, A. fumigatiaffinis, A. fumisynnematus, A. hiratsukae, A. laciniosus, A. lentulus, A. novofumigatus, A. parafelis, A. pseudofelis, A. pseudoviridinutans, A. spinosus, A. thermomutatus, and A. udagawae. These species share the production of hydrophobins, melanins, and siderophores and ability to grow well at 37°C, but they only share some small molecule extrolites, that could be important factors in pathogenicity. According to the literature gliotoxin and other exometabolites can be contributing factors to pathogenicity, but these exometabolites are apparently not produced by all pathogenic species. It is our hypothesis that species unable to produce some of these metabolites can produce proxy-exometabolites that may serve the same function. We tabulate all exometabolites reported from species in Aspergillus section Fumigati and by comparing the profile of those extrolites, suggest that those producing many different kinds of exometabolites are potential opportunistic pathogens. The exometabolite data also suggest that the profile of exometabolites are highly specific and can be used for identification of these closely related species.

Thermophilic fungi in the new age of fungal taxonomy

Thermophilic fungi are of wide interest due to their potential to produce heat-tolerant enzymes for biotechnological processes. However, the taxonomy of such organisms remains obscure, especially given new developments in the nomenclature of fungi. Here, we examine the taxonomy of the thermophilic fungi most commonly used in industry in light of the recent taxonomic changes following the adoption of the International Code of Nomenclature for Algae, Fungi and Plants and also based on the movement One Fungus = One Name. Despite the widespread use of these fungi in applied research, several thermotolerant fungi still remain classified as thermophiles. Furthermore, we found that while some thermophilic fungi have had their genomes sequenced, many taxa still do not have barcode sequences of reference strains available in public databases. This lack of basic information is a limiting factor for the species identification of thermophilic fungi and for metagenomic studies in this field. Based on next-generation sequencing, such studies generate large amounts of data, which may reveal new species of thermophilic fungi in different substrates (composting systems, geothermal areas, piles of plant material). As discussed in this study, there are intrinsic problems associated with this method, considering the actual state of the taxonomy of thermophilic fungi. To overcome such difficulties, the taxonomic classification of this group should move towards standardizing the commonly used species names in industry and to assess the possibility of including new systems for describing species based on environmental sequences.