Fungal community succession contributes to product maturity during the co-composting of chicken manure and crop residues

Microbial inoculant accelerated pig slurry maturation at low-temperature anaerobic digestion: Performance and mechanism

This study investigated the impact of microbial inoculants on maturing pig slurry during anaerobic digestion (AD) at psychrophilic temperatures (10 °C). A simulation experiment was conducted with two treatments: pig slurry alone (CK) and pig slurry supplemented with microbial inoculants (MA). The MA treatment achieved faster maturity than CK, as evidenced by an improved germination index (achieving 70 % in advance) and a reduced content of organic pollutants, which was attributed to an increased relative abundance of hydrolytic microorganisms (7-21 %) and decreased pathogens (6-9 %) at the early stage (<42 (d)). Microbial inoculants influenced pig slurry microorganisms by serving as keystone taxa (B_OTU229 (f_Ruminococcaceae) and F_OTU76 (s_Acremonium alcalophilum)), and stimulating new keystone taxa (B_OTU423 (g_NK4A214) and F_OTU25 (g_Clavulina)) through associative interactions, thereby intensifying saprotrophic and carbon cycling processes, and accelerating maturation. These results provide a biological strategy for maturing pig slurry and help elucidate the mechanisms underlying microbial effects.

Effects of Trichoderma harzianum combined with Phanerochaete chrysosporium on lignin degradation and humification during chicken manure and rice husk composting

The purpose of this study was to investigate the effects of combined treatment of Trichoderma harzianum and Phanerochaete chrysosporium on lignin degradation and humification during aerobic composting. Chicken manure (CM) and rice husk (RH) were used as organic raw materials for composting. The basic physicochemical analysis indicated that the combined addition of Trichoderma harzianum and Phanerochaete chrysosporium effectively improved lignin degradation rate (16.60%), increased humic acid (HA) content (22.70 g/kg), and the germination index (GI) reached 110.99%. Fungal community revealed that the relative abundance of Ascomycota was 37.46-68.85%, 9.57-60.35%, 58.02-91.76%, 0.98-91.60% in CK, T1, T2, T3 and Basidiomycota was 7.81-36.03%, 7.84-3.55%, 4.42-9.60%, 0.06-8.05% in CK, T1, T2, T3 (in phylum); the relative abundance of Kazachstania was 0.001-68.48%, 0.62-14.60%, 7.06-25.45%, 0.001-38.16% in CK, T1, T2, T3 and Diutina was 2.67-7.97%, 1.11-34.42%, 15.79-64.41%, 0.25-35.34% in CK, T1, T2, T3 (in genus) during the composting. Especially, the combined addition of Trichoderma harzianum and Phanerochaete chrysosporium had more negative impact on the activity of Basidiomycota compared with CK and other treatments and Trichoderma harzianum treatment had the strongest inhibitory effect on Tausonia abundance compared with CK and other treatments. Correlation analysis indicated that moisture content influenced fungal community structure (r = -0.740, p < 0.01) which affected lignin degradation (r = -0.952, p < 0.01) and compost maturity level in the composting process. Fungi Functional Guild (FUNGuild) and correlation heatmap demonstrated that T3 could enhance the relative abundance of endophyte which may had the potential to improve the degradation of lignin. This study confirmed the positive effects of the combination of Trichoderma harzianum and Phanerochaete chrysosporium in enhancing lignin degradation and promoting compost maturity, providing a foundation for a deeper understanding of the mechanisms involved in lignin degradation and humification processes influenced by the fungal community during composting, ultimately contributing to the efficient utilization of agricultural waste resources.

Feedstock optimization with low carbon to nitrogen ratio during algal sludge aerobic composting: Quality and gaseous emissions

This study investigated compost quality and gaseous emissions during the algal sludge composting. The experiment explored the feasibility of low initial carbon to nitrogen (C/N) ratio composting by using different volume ratios of algal sludge and spent mushroom substrates (1:1, 1:2, 1:3, and 1:4, corresponding to C/N ratios of 9.5, 12.3, 14.6, 16.0, respectively). The results showed that increasing the proportion of algal sludge in the initial material led to a longer maturation time and higher nitrogen losses but also enhanced the mineralization of organic nitrogen (converted to NH4+ and NO3-) and reduced carbon losses. The addition of carbon-rich bulking agents within a certain range improved the diversity and interactions of bacterial communities during algal sludge composting. In conclusion, considering the nitrogen and carbon lost, retained, and made available across the four treatments, treatment 3 (C/N = 14.6) appears to be the optimal choice for low C/N composting.

Inoculation with effective microorganisms agent enhanced fungal diversity in the secondary fermentation process

Microbial inoculations have emerged as a key approach to address the low natural microbial activity of traditional composting technologies. It is crucial for successfully promoting manure composting to understand the influences of microbial inoculations on fungal communities and its mechanisms. To investigate the effects of microbial inoculation on diversity characteristics, tropic mode, and co-occurrence network of fungal communities during composting, an aerobic composting experiment of chicken manure inoculated with microbial agents was performed. The results showed that microbial inoculations enhanced fungal richness and diversity during the secondary fermentation, promoted beneficial fungi, and restrained pathogenic microbes. Microbial inoculation facilitated saprophytic fungi and symbiotic fungi, augmented fungal network complexity and cooperation during the first fermentation, concurrently impeding fungal network complexity and cooperation during the secondary fermentation. These results provide technical guidance for composting process optimization and compost product quality improving, which was beneficial to promote soil quality and mitigating agricultural non-point source pollution.

Integrated assessment of the chemical, microbiological and ecotoxicological effects of a bio-packaging end-of-life in compost

The present study aimed to i) assess the disintegration of a novel bio-packaging during aerobic composting (2 and 6 % tested concentrations) and evaluate the resulting compost ii) analyse the ecotoxicity of bioplastics residues on earthworms; iii) study the microbial communities during composting and in 'earthworms' gut after their exposure to bioplastic residues; iv) correlate gut microbiota with ecotoxicity analyses; v) evaluate the chemico-physical characterisation of bio-packaging after composting and earthworms' exposure. Both tested concentrations showed disintegration of bio-packaging close to 90 % from the first sampling time, and compost chemical analyses identified its maturity and stability at the end of the process. Ecotoxicological assessments were then conducted on Eisenia fetida regarding fertility, growth, genotoxic damage, and impacts on the gut microbiome. The bioplastic residues did not influence the earthworms' fertility, but DNA damages were measured at the highest bioplastic dose tested. Furthermore bioplastic residues did not significantly affect the bacterial community during composting, but compost treated with 2 % bio-packaging exhibited greater variability in the fungal communities, including Mortierella, Mucor, and Alternaria genera, which can use bioplastics as a carbon source. Moreover, bioplastic residues influenced gut bacterial communities, with Paenibacillus, Bacillus, Rhizobium, Legionella, and Saccharimonadales genera being particularly abundant at 2 % bioplastic concentration. Higher concentrations affected microbial composition by favouring different genera such as Pseudomonas, Ureibacillus, and Streptococcus. For fungal communities, Pestalotiopsis sp. was found predominantly in earthworms exposed to 2 % bioplastic residues and is potentially linked to its role as a microplastics degrader. After composting, Attenuated Total Reflection analysis on bioplastic residues displayed evidence of ageing with the formation of hydroxyl groups and amidic groups after earthworm exposure.

Performance evaluation and microbial community succession analysis of co-composting treatment of refinery waste activated sludge

Refinery waste activated sludge (RWAS) is riched in organic matter with energy recovery value, while unique petroleum components in RWAS may pose challenges to the recycling process. Aerobic composting technology is an effective means of organic solid waste resource treatment, which can convert organic solid waste into fertilizer for agriculture. This study explores the effect of petroleum components on the performance of RWAS composting by co-composting it with chicken manure. The results showed that more than 65% of petroleum was removed by aerobic composting. After composting, germination index (GI) exceeded 80%, and a humic acid to fulvic acid ratio (HA/FA) was greater than 1. These results signified that the petroleum components slightly affect the harmless and recycling of RWAS. The microbial community succession found that Firmicutes (54.11-91.96%) and Ascomycota (82.35-97.21%) emerged as the dominant phyla during the thermophilic phase of composting. Thermobifida, norank_f__Limnochordaceae and Kernia were the key microorganism in the degradation of petroleum and the humification of composting, and reduced the phytotoxicity of composting products. Redundancy analysis found that the degradation of petroleum was conducive to the formation of humic acid. These findings indicate that aerobic composting technology can remove petroleum components in RWAS and convert them into composted fertilizers, providing key technical support for managing RWAS in a sustainable and environmentally friendly manner.

Response of humification process to fungal inoculant in corn straw composting with two different kinds of nitrogen sources

Inoculation is widely used in composting to improve the mineralization process, however, the link of fungal inoculant to humification is rarely proposed. The objective of this study was to investigate the effect of compound fungal inoculation on humification process and fungal community dynamics in corn straw composting with two different kinds of nitrogen sources [pig manure (PM) and urea (UR)]. Structural equation modeling and random forest analysis were conducted to identify key fungi and explore the fungi-mediated humification mechanism. Results showed that fungal inoculation increased the content of humic acids in PM and UR by 71.76 % and 53.01 % compared to control, respectively. High-throughput sequencing indicated that there were more key fungal genera for lignin degradation in PM especially in the later stage of composting, but a more complex fungal (genera) connections with lower humification degree was found in UR. Network analysis and random forest suggested that inoculation promoted dominant genus such as Coprinus, affecting lignocellulose degradation. Structural equation modeling indicated that fungal inoculation could promote humification by direct pathway based on lignin degradation and indirect pathway based on stimulating the indigenous microbes such as Scedosporiu and Coprinus for the accumulation of carboxyl and polyphenol hydroxyl groups. In summary, fungal inoculation is suitable to be used combining with complex nitrogen source such as pig manure in straw composting.

Characterization of fungal microbiome structure in leaf litter compost through metagenomic profiling for harnessing the bio-organic fertilizer potential

Sustainable waste management through composting has gain renewed attention since it could upcycle organic waste into valuable bio-organic fertiliser. This study explored the composition of fungal communities in leaf litter and organic waste composts ecosystems by employing advanced internal transcribed spacer (ITS) metagenomic profiling. This approach provides insights into the diversity, composition, and potential functions of these fungi, offering practical implications for optimising composting processes and enhancing sustainable waste management practices. Various organic composts were collected, including leaf litter composts, from different sources in Delhi-National Capital Region, India, and fungal microbiome composition were characterised through ITS profiling. Results revealed that leaf litter composts and cow dung manure had the highest fungal read counts, while kitchen waste compost had the lowest. Alpha diversity indices, including Chao1 and Shannon, exhibited differences in species richness and diversity among composts, though statistical significance was limited. The leaf composts had relatively higher alpha diversity than the other organic waste composts analysed. The study also identified dominant fungal genera specifically, Wallemia, Geotrichum, Pichia, Mycothermus, Mortierella, Aspergillus, Fusarium, and Basidiobolus, across the compost samples. The presence of beneficial fungal genera like Pichia, Geotrichum, Trichoderma, Mortierella, Basidiobolus, Aspergillus, and others were detected in leaf waste compost and the other organic waste composts. There was also presence of some pathogenic genera viz. Alternaria, Fusarium, and Acremonium, in these composts which underscored the need for proper composting practices and source selection to optimise soil fertility and minimise disease risks in agriculture. Remarkably, leaf compost has highest proportion of beneficial genera with least observed abundance of pathogens. On the other hand, the municipal organic waste compost has least proportion of beneficial genera with higher abundance of pathogens. Overall, these findings contributed to characterisation of composting processes, advancing waste management practices, and enhancing the use of leaf compost as a bio-organic fertiliser.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04028-0.

Enhancement of microbial community dynamics and metabolism in compost through ammonifying cultures inoculation

The efficient use of livestock and poultry manure waste has become a global challenge, with microorganisms playing an important role. To investigate the impact of novel ammonifying microorganism cultures (NAMC) on microbial community dynamics and carbon and nitrogen metabolism, five treatments [5% (v/w) sterilized distilled water, Amm-1, Amm-2, Amm-3, and Amm-4] were applied to cow manure compost. Inoculation with NAMC improved the structure of bacterial and fungal communities, enriched the populations of the functional microorganisms, enhanced the role of specific microorganisms, and promoted the formation of tight modularity within the microbial network. Further functional predictions indicated a significant increase in both carbon metabolism (CMB) and nitrogen metabolism (NMB). During the thermophilic phase, inoculated NAMC treatments boosted carbon metabolism annotation by 10.55%-33.87% and nitrogen metabolism annotation by 26.69%-63.11. Structural equation modeling supported the NAMC-mediated enhancement of NMB and CMB. In conclusion, NAMC inoculation, particularly with Amm-4, enhanced the synergistic interaction between bacteria and fungi. This collaboration promoted enzymatic catabolic and synthetic processes, resultng in positive feedback loops with the endogenous microbial community. Understanding these mechanisms not only unravels how ammonifying microorganisms influence microbial communities but also paves the way for the development of the composting industry and global waste management practices.

Metabolomics analysis of advancing humification mechanism in secondary fermentation of composting by fungal bioaugmentation

The aim of this study was to investigate the differential metabolites and core metabolic pathways caused by fungal bioaugmentation (pH regulation and Phanerochaete chrysosporium inoculation) in secondary fermentation of composting, as well as their roles in advancing humification mechanism. Metabolomics analyses showed that inoculation strengthened the expression of carbohydrate, amino acid, and aromatic metabolites, and pH regulation resulted in the up-regulation of the phosphotransferase system and its downstream carbohydrate metabolic pathways, inhibiting Toluene degradation and driving biosynthesis of aromatic amino acids via the Shikimate pathway. Partial least squares path model suggested that lignocellulose degradation, precursors especially amino acids and their metabolism process enhanced by the regulation of pH and Phanerochaete were the main direct factors for humic acid formation in composting. This finding helps to understand the regulating mechanism of fungal bioaugmentation to improve the maturity of agricultural waste composting.

Manure enriched with nitrogen derived from high-protein food waste in a large dining facility

Food waste (FW) from large dining facility has been a pressing environmental challenge in China recently. This study developed an innovative species-specific feeding strategy for producing pigeon meat and excellent manure from FW. Adding FW to the feed of pigeons significantly increased their feed intake and promoted their growth although the pigeons showed a strong aversion to the FW. We produced a "super manure" with exceptionally high nitrogen (N) content (mean = 10.77 % on a dry basis, 8.04-12.57 %, n = 264) by feeding slowly-growing pigeon species (Columba livia vs. and Caoge Huzhou 11) with protein-high commercial feed and FW. A significant negative relationship between the N and carbon (C) contents in the pigeon manure was found, with C depletion higher than N depletion. Furthermore, the N content in the anaerobic composting (AnC) manure was 29.16 % higher than that in the FW. Fourier transform infrared (FT-IR) analysis and stable isotopes δ13C and δ15N in the manure clearly identified the transformations of nutrients during pigeon feeding and the AnC process. This study opens a path for producing N-high manure using protein-high food waste.

Fungi play a crucial role in sustaining microbial networks and accelerating organic matter mineralization and humification during thermophilic phase of composting

Fungi play an important role in the mineralization and humification of refractory organic matter such as lignocellulose during composting. However, limited research on the ecological role of fungi in composting system hindered the development of efficient microbial agents. In this study, six groups of lab-scale composting experiments were conducted to reveal the role of fungal community in composting ecosystems by comparing them with bacterial community. The findings showed that the thermophilic phase was crucial for organic matter degradation and humic acid formation. The Richness index of the fungal community peaked at 1165 during this phase. PCoA analysis revealed a robust thermal stability in the fungal community. Despite temperature fluctuations, the community structure, predominantly governed by Pichia and Candida, remained largely unaltered. The stability of fungal community and the complexity of ecological networks were 1.26 times and 5.15 times higher than those observed in bacterial community, respectively. Fungi-bacteria interdomain interaction markedly enhanced network complexity, contributing to maintain microbial ecological functions. The core fungal species belonging to the family Saccharomycetaceae drove interdomain interaction during thermophilic phase. This study demonstrated the key role of fungi in the composting system, which would provide theoretical guidance for the development of high efficiency composting agents to strengthen the mineralization and humification of organic matter.

Biodiversity and core microbiota of key-stone ecological clusters regulate compost maturity during cow-dung-driven composting

The primary objectives of this study were to explore the community-level succession of bacteria, fungi, and protists during cow-dung-driven composting and to elucidate the contribution of the biodiversity and core microbiota of key-stone microbial clusters on compost maturity. Herein, we used high-throughput sequencing, polytrophic ecological networks, and statistical models to visualize our hypothesis. The results showed significant differences in the richness, phylogenetic diversity, and community composition of bacteria, fungi, and eukaryotes at different composting stages. The ASV191 (Sphingobacterium), ASV2243 (Galibacter), ASV206 (Galibacter), and ASV62 (Firmicutes) were the core microbiota of key-stone bacterial clusters relating to compost maturity; And the ASV356 (Chytridiomycota), ASV470 (Basidiomycota), and ASV299 (Ciliophora) were the core microbiota of key-stone eukaryotic clusters relating to compost maturity based on the data of this study. Compared with the fungal taxa, the biodiversity and core microbiota of key-stone bacterial and eukaryotic clusters contributed more to compost maturity and could largely predict the change in the compost maturity. Structural equation modeling revealed that the biodiversity of total microbial communities and the biodiversity and core microbiota of the key-stone microbial clusters in the compost directly and indirectly regulated compost maturity by influencing nutrient availability (e.g., NH4+-N and NO3--N), hemicellulose, humic acid content, and fulvic acid content, respectively. These results contribute to our understanding of the biodiversity and core microbiota of key-stone microbial clusters in compost to improve the performance and efficiency of cow-dung-driven composting.

Influence of biochar on succession of fungal communities during food waste composting

This study aims to examine the effects of biochar on fungal dynamics during food waste composting. The different dosage of wheat straw biochar from 0 to 15% (0%, 2.5%, 5%, 7.5%, 10%, and 15%) were used as an additive to composting and examined for 42 days. The results showed that Ascomycota (94.64%) and Basidiomycota (5.36%) were the most dominant phyla. The most common fungal genera were Kluyveromyces (3.76%), Candida (5.34%), Trichoderma (2.30%), Fusarium (0.46%), Mycothermus-thermophilus (5.67%), Trametes (0.46%), and Trichosporon (3.38%). The average number of operational taxonomic units were 469, with the greatest abundance seen in the 7.5% and 10% treatments. Redundancy analysis revealed that different concentrations of biochar applied treatments have significantly distinct fungal communities. Additionally, correlation analyses of fungal interactions with environmental elements, performed through a heatmap, also indicate a distinct difference among the treatments. The study clearly demonstrates that 15% of biochar has a positive impact on fungal diversity and improves the food waste composting.

Prediction of composting maturity and identification of critical parameters for green waste compost using machine learning

Ensuring the maturity of green waste compost is crucial to composting processes and quality control of compost products. However, accurate prediction of green waste compost maturity remains a challenge, as there are limited computational methods available. This study aimed to address this issue by employing four machine learning models to predict two indicators of green waste compost maturity: seed germination index (GI) and T value. The four models were compared, and the Extra Trees algorithm exhibited the highest prediction accuracy with R2 values of 0.928 for GI and 0.957 for T value. To identify the interactions between critical parameters and compost maturity, The Pearson correlation matrix and Shapley Additive exPlanations (SHAP) analysis were conducted. Furthermore, the accuracy of the models was validated through compost validation experiments. These findings highlight the potential of applying machine learning algorithms to predict green waste compost maturity and optimise process regulation.

Effects of a novel microbial fermentation medium produced by Tremella aurantialba SCT-F3 on cigar filler leaf

Introduction

Adding a fermentation medium is an effective way to improve the quality of cigar tobacco leaves.

Methods

A novel microbial fermentation medium produced by an edible medicinal fungus, Tremella aurantialba SCT-F3 (CGMCC No.23831) was used to improve the quality of cigar filler leaves (CFLs). Changes in sensory quality, chemical components, volatile flavor compounds (VFCs), and the structure and function of microbes were investigated during the fermentation process.

Results

The sensory quality of CFLs supplemented with the T. aurantialba SCT-F3 fermentation medium significantly improved. Adding the fermentation medium increased the total alkaloid, reducing sugar, total sugar, and 12 VFCs significantly. A total of 31 microbial genera were significantly enriched, which increased the microbial community's richness and diversity. Microbial functions increased, including nucleotide biosynthesis, amino acid biosynthesis, fatty acid and lipid biosynthesis, nicotine degradation, and nicotinate degradation. During fermentation, the total alkaloid, reducing sugar, and total sugar content decreased. The richness and diversity of the microbial community decreased, whereas bacterial enzyme activity increased. At the end of fermentation, the sensory quality was excellent. The microbial structure gradually stabilized, and functional genes were low. The contents of the four Maillard reaction products and three nicotine degradation products increased significantly. 2-Ethyl-6-methylpyrazine, methylpyrazine, D,L-anatabine, β-nicotyrine, nicotinic degradation products, and total nitrogen were significantly and positively correlated with sensory quality. Methylpyrazine, D,L-anatabine, and β-nicotyrine were negatively correlated with Luteimonas, Mitochondria, Paracoccus, Stemphylium, and Stenotrophomonas.

Conclusion

This research provides not only a new microbial fermentation medium that utilizes edible and medicinal fungi to improve the quality of fermented CFLs, but also new ideas for the development and application of other edible medicinal fungi to improve the quality of cigar tobacco leaves.

Dynamics of Bacterial Diversity and Functions with Physicochemical Properties in Different Phases of Pig Manure Composting

Bacteria are key drivers in regulating ecosystem functions, and understanding the diversity and dynamic changes in bacteria in composting is very important for optimizing compost. This study investigated the structure, composition, and function of bacterial communities in alkaline pig manure compost using Miseq sequencing, PICRUSt2. The ACE and Chao1 indices of the bacterial communities in various phases were significantly different. Bacterial communities of alkaline pig compost were different from neutral and acidic swine manure compost, and there were 438 genera of common bacteria in various stages. The main bacterium was the phylum Firmicutes. There were six genera, including Romboutsia, Clostridium, Terrisporobacter, norank_f_Marinococcaceae, Saccharomonospora, and unclassified_f_Bacillaceae, that were significantly correlated (p < 0.05), or even extremely significantly correlated (p < 0.001), with the physicochemical properties. TOC, moisture, C/N, and Tem were the key factors that caused changes in bacterial communities in composting. PICRUSt2 analysis showed that there were seven functional groups: metabolism (45.02-48.07%), environmental information processing (15.25-16.00%), genetic information processing (16.97-20.02%), cellular processes (3.63-4.37%), human diseases (0.71-0.82%), organismal systems (0.66-0.77%), and unclassified (13.93-14.36%). This study will provide a reference for improving bacteria growth and reproduction conditions in pig manure composting, optimizing the process, and improving the efficiency of composting.

Comparison of bacterial and fungal communities structure and dynamics during chicken manure and pig manure composting

Composting is a sustainable and eco-friendly technology that turns animal waste into organic fertilizers. It remains unclear whether differences exist in the structure of microbial communities during different livestock manure composting. This study analyzed the dynamic change of bacterial and fungal communities, metabolic function, and trophic mode during chicken manure (CM) and pig manure (PM) composting based on 16S rRNA and ITS sequencing. Environmental factors were investigated for their impact on microbial communities. During composting, bacterial diversity decreased and then increased, while fungal diversity slightly increased and then decreased. Saccharomonospora and Aspergillus were the dominant genera and key microorganisms in CM and PM, respectively, which played crucial roles in sustaining the stability of the ecological network structure in the microbial ecology and participating in metabolism. Saccharomonospora gradually increased, while Aspergillus increased at first and then decreased. PM had better microbial community stability and more keystone taxa than CM. In CM and PM, the primary function of bacterial communities was metabolism, while saprotroph was the primary trophic mode of fungal communities. Dissolved organic carbon (DOC) was the primary factor influencing the structure and function of microbial communities in CM and PM. In addition to DOC, pH and moisture were important factors affecting the fungal communities in CM and PM, respectively. These results show that the succession of bacteria and fungi in CM and PM proceeded in a similar pattern, but there are still some differences in the dominant genus and their responses to environmental factors.

Microplastics drive microbial assembly, their interactions, and metagenomic functions in two soils with distinct pH and heavy metal availability

Microplastics (MPs) have emerged as widely existing global environmental concerns in terrestrial ecosystems. However, the mechanisms that how MPs are affecting soil microbes and their metagenomic functioning is currently uncertain. Herein, we investigated the response mechanisms of bacterial and fungal communities as well as the metagenomic functions to the addition of MPs in two soils with distinct pH and heavy metals. In this study, the acidic soil (Xintong) and the neutral soil (Huanshan) contaminated by heavy metals were incubated with Polyvinyl Chloride (PVC) MPs at ratios of 2.5% and 5% on 60 and 120 days. We aimed to evaluate the responding, assembly, and interactions of the metagenomic taxonomy and function. Results showed that only in the acidic soil, PVC MPs significantly increased soil pH and decreased CaCl₂-extractable heavy metals, and also reduced bacterial alpha diversity and interaction networks. The relative proportions of Proteobacteria and Bacteroidota in bacteria, and Mortierellomycota in fungi, were increased, but Chloroflexi and Acidobacteriota in bacteria, Ascomycota and Basidiomycota in fungi, were significantly decreased by PVC MPs. Metagenomic functions related to C cycling were repressed but the nutrient cycles were enriched with PVC MPs. In conclusion, our study suggests that the addition of PVC MPs could shift soil microbial community and metagenomic functioning, as well as increasing soil pH and reduced heavy metal availability.

Succession of Fungal Community during Outdoor Deterioration of Round Bamboo

Bamboo's mechanical and aesthetic properties are significantly influenced by fungi. However, few studies have been conducted to investigate the structure and dynamics of fungal communities in bamboo during its natural deterioration. In this study, fungal community succession and characteristic variations of round bamboo in roofed and unroofed environments over a period of 13 weeks of deterioration were deciphered using high-throughput sequencing and multiple characterization methods. A total of 459 fungal Operational Taxonomic Units (OTUs) from eight phyla were identified. The fungal community's richness of roofed bamboo samples showed an increasing trend, whereas that of unroofed bamboo samples presented a declining trend during deterioration. Ascomycota and Basidiomycota were the dominant phyla throughout the deterioration process in two different environments: Basidiomycota was found to be an early colonizer of unroofed bamboo samples. Principal Coordinates Analysis (PCoA) analysis suggested that the deterioration time had a greater impact on fungal community variation compared to the exposure conditions. Redundancy analysis (RDA) further revealed that temperature was a major environmental factor that contributed to the variation in fungal communities. Additionally, the bamboo epidermis presented a descending total amount of cell wall components in both roofed and unroofed conditions. The correlation analysis between the fungal community and relative abundance of three major cell wall components elucidated that Cladosporium was negatively correlated with hemicellulose in roofed samples, whereas they presented a positive correlation with hemicellulose and a negative correlation with lignin in unroofed samples. Furthermore, the contact angle decreased during the deterioration process in the roofed as well as unroofed samples, which could arise from the degradation of lignin. Our findings provide novel insights into the fungal community succession on round bamboo during its natural deterioration and give useful information for round bamboo protection.

Compost with spent mushroom substrate and chicken manure enhances rice seedling quality and reduces soil-borne pathogens

Using cultivated soils for rice seedlings can reduce the sustainability of arable land and thus giving negative impacts to food production. As a substitute, spent mushroom compost (SMC), which has high water-holding capacity and nutrient content, shows great potentials. To determine the impacts of the proportion of SMC and paddy soil on seedling quality, rhizosphere microbial characteristics, and fungal pathogens in rice seedling substrates, we conducted a 21-day pot experiment for rice seedling under five treatments: CK, 100% paddy soil; R1, 20% SMC and 80% paddy soil; R2, 50% SMC and 50% paddy soil; R3, 80% SMC and 20% paddy soil; and R4, 100% SMC. The results showed that incorporating SMC into the substrate, especially at 50% volume (R2), increased seedling growth and vitality at the seedling growth stage without external fertilization. Moreover, the SMC amendment increased microbial activity and promoted rice seedling recruitment of plant growth-promoting rhizobacteria (PGPR) and fungi (PGPF). In addition, using SMC significantly reduced the abundance of pathogenic fungi, especially Magnaporthe grisea. Overall, the multi-faceted benefits exhibit the strong possibilities of using SMC in sustainable rice productions.

Evolution of fungal and non-fungal eukaryotic communities in response to thermophilic co-composting of various nitrogen-rich green feedstocks

Thermophilic composting is a promising soil and waste management approach involving diverse micro and macro-organisms, including eukaryotes. Due to sub-optimal amounts of nutrients in manure, supplemental feedstock materials such as Lantana camara, and Tithonia diversifolia twigs are used in composting. These materials have, however, been reported to have antimicrobial activity in in-vitro experiments. Furthermore, the phytochemical analysis has shown differences in their complexities, thus possibly requiring various periods to break down. Therefore, it is necessary to understand these materials' influence on the biological and physical-chemical stability of compost. Most compost microbiome studies have been bacterial-centric, leaving out eukaryotes despite their critical role in the environment. Here, the influence of different green feedstock on the fungal and non-fungal eukaryotic community structure in a thermophilic compost environment was examined. Total community fungal and non-fungal eukaryotic DNA was recovered from triplicate compost samples of four experimental regimes. Sequencing for fungal ITS and non-fungal eukaryotes; 18S rDNA was done under the Illumina Miseq platform, and bioinformatics analysis was done using Divisive Amplicon Denoising Algorithm version 2 workflow in R version 4.1. Samples of mixed compost and composting day 84 recorded significantly (P<0.05) higher overall fungal populations, while Lantana-based compost and composting day 84 revealed the highest fungal community diversity. Non-fungal eukaryotic richness was significantly (P< 0.05) more abundant in Tithonia-based compost and composting day 21. The most diverse non-fungal eukaryotic biome was in the Tithonia-based compost and composting day 84. Sordariomycetes and Holozoa were the most contributors to the fungal and non-fungal community interactions in the compost environment, respectively. The findings of this study unravel the inherent influence of diverse composting materials and days on the eukaryotic community structure and compost's biological and chemical stability.

Spatial distribution of bacterial resistance towards antibiotics of rural sanitation system in China and its potential link with diseases incidence

Chinese government is vigorously promoting toilet renovation in rural areas to reduce the risk of human feces exposure, which would cause infectious diseases, especially antibiotic resistance genes (ARGs) and pathogens. However, the distribution of ARGs in human feces from different regions of China remained ill-defined. It is not yet known how the survival of ARGs after toilet treatment is associated with the regional infection rates. Here, we investigated the prevalence of ARGs in human feces in rural areas of China and their potential relationship with infectious diseases for the first large-scale. The results showed that there were still high ARGs residues in human feces after rural toilet treatment, especially tetM-01 and ermB with average relative abundance as high as 1.21 × 10^-1 (Eastern) and 1.56 × 10^-1 (Northern), respectively. At a large regional scale, the significant differences in human feces resistomes were mainly shaped by the toilet types, TN, NH₃-N, and the bacterial community. A critical finding was that toilets still cannot effectively decrease the pathogenicity risk in human feces. The significant positive relationship (P<0.05) between infectious diseases and ARGs can infer that ARGs in human feces exposure might be a critical path for enhancing the incidence of diseases, as these ARGs hinder the effectiveness of antibiotics.

Effects of micro-positive pressure environment on nitrogen conservation and humification enhancement during functional membrane-covered aerobic composting

Aerobic composting is a humification process accompanied by nitrogen loss. This study is the first research systematically investigating and elucidating the mechanism by which functional membrane-covered aerobic composting (FMCAC) reduces nitrogen loss and enhances humification. The variations in bioavailable organic nitrogen (BON) and humic substances (HSs) in different composting systems were quantitatively studied, and the functional succession patterns of fungal groups were determined by high-throughput sequencing and FUNGuild. The FMCAC improved oxygen utilization and pile temperature, increased BON by 29.95 %, reduced nitrogen loss by 34.00 %, and enhanced humification by 26.09 %. Meanwhile, the FMCAC increased the competitive advantage of undefined saprotroph and significantly reduced potential pathogenic fungi (<0.10 %). Structural equation modeling indicated that undefined saprotroph facilitated the humification process by increasing the production of BON and storing BON in stable humic acid. Overall, the FMCAC increased the safety, stability, and quality of the final compost product.

Effects of functional membrane coverings on carbon and nitrogen evolution during aerobic composting: Insight into the succession of bacterial and fungal communities

Carbon and nitrogen evolution and bacteria and fungi succession in two functional membrane-covered aerobic composting (FMCAC) systems and a conventional aerobic composting system were investigated. The micro-positive pressure in each FMCAC system altered the composting microenvironment, significantly increased the oxygen uptake rates of microbes (p < 0.05), and increased the abundance of cellulose- and hemicellulose-degrading microorganisms. Bacteria and fungi together influenced the conversion between carbon and nitrogen forms. FMCAC made the systems less anaerobic and decreased CH₄ production and emissions by 22.16 %-23.37 % and N₂O production and emissions by 41.34 %-45.37 % but increased organic matter degradation and NH₃ production and emissions by 16.91 %-90.13 %. FMCAC decreased carbon losses, nitrogen losses, and the global warming potential by 7.97 %-11.24 %, 15.43 %-34.00 %, and 39.45 %-42.16 %, respectively. The functional membrane properties (pore size distribution and air permeability) affected fermentation process and gaseous emissions. A comprehensive assessment indicated that FMCAC has excellent prospects for application.

Community succession of microbial populations related to CNPS biological transformations regulates product maturity during cow-manure-driven composting

The main objective of present study was to understand the community succession of microbial populations related to carbon-nitrogen-phosphorus-sulfur (CNPS) biogeochemical cycles during cow-manure-driven composting and their correlation with product maturity. The abundance of microbial populations associated with C degradation, nitrification, cellular-P transport, inorganic-P dissolution, and organic-P mineralization decreased gradually with composting but increased at the maturation phase. The abundance of populations related to N-fixation, nitrate-reduction, and ammonification increased during the mesophilic stage and decreased during the thermophilic and maturation stages. The abundance of populations related to C fixation and denitrification increased with composting; however, the latter tended to decrease at the maturation stage. Populations related to organic-P mineralization were the key manipulators regulating compost maturity, followed by those related to denitrification and nitrification; those populations were mediated by inorganic N and available P content. This study highlighted the consequence of microbe-driven P mineralization in improving composting efficiency and product quality.

Dynamic changes in fecal microbiota in donkey foals during weaning: From pre-weaning to post-weaning

Introduction

A better understanding of the microbiota community in donkey foals during the weaning transition is a prerequisite to optimize gut function and improve feed efficiency. The objective of the present study was to investigate the dynamic changes in fecal microbiota in donkey foals from pre-to post-weaning period.

Methods

A total of 27 fecal samples of donkey foals were collected in the rectum before morning feeding at pre-weaning (30 days of age, PreW group, n = 9), dur-weaning (100 days of age, DurW group, n = 9) and post-weaning (170 days of age, PostW group, n = 9) period. The 16S rRNA amplicon sequencing were employed to indicate the microbial changes during the weaning period.

Results

In the present study, the cessation of breastfeeding gradually and weaning onto plant-based feeds increased the microbial diversity and richness, with a higher Shannon, Ace, Chao and Sobs index in DurW and PostW than in PreW (p < 0.05). The predominant bacterial phyla in donkey foal feces were Firmicutes (>50.5%) and Bacteroidota (>29.5%), and the predominant anaerobic fungi and archaea were Neocallimastigomycota and Euryarchaeota. The cellulolytic related bacteria including phylum Firmicutes, Spirochaetota and Fibrobacterota and genus norank_f_F082, Treponema, NK4A214_group, Lachnospiraceae_AC2044_group and Streptococcus were increased from pre-to post-weaning donkey foals (p < 0.05). Meanwhile, the functions related to the fatty acid biosynthesis, carbohydrate metabolism and amino acid biosynthesis were significantly enriched in the fecal microbiome in the DurW and PostW donkeys. Furthermore, the present study provided the first direct evidence that the initial colonization and establishment of anaerobic fungi and archaea in donkey foals began prior to weaning. The relative abundance of Orpinomyces were the highest in DurW donkey foals among the three groups (p < 0.01). In terms of archaea, the abundance of Methanobrevibacter were higher in PreW than in DurW and PostW (p < 0.01), but the abundance of Methanocorpusculum were significantly increased in DurW and PostW compared to PreW donkey foals (p < 0.01).

Discussion

Altogether, the current study contributes to a comprehensive understanding of the development of the microbiota community in donkey foals from pre-to post-weaning period, which may eventually result in an improvement of the digestion and feed efficiency in donkeys.

Dissolved organic matter evolution can reflect the maturity of compost: Insight into common composting technology and material composition

Dissolved organic matter (DOM) can clearly reflect composting components changes, thus it is supposed to indicate the humification process during composting. To demonstrate this, three compost mixtures and two techniques were arranged. DOM evolution was detected by three spectral techniques. X-ray diffraction (XRD) showed that the crystal structure substances decreased gradually during the composting, including cellulose, struvite, sylvine, quartz, and calcite; Specifically, the struvite was found, which was conducive to the fixation of nitrogen and phosphorus. Fourier transform infrared spectroscopy (FTIR) and three-dimensional fluorescence spectroscopy (3D-EEM) further showed that pig manure-based mixtures, added cabbage, and windrow composting are beneficial to sugar, protein, fulvic acid, and soluble microbial by-products decompose and humic acids produce. This process was closely related to the change of physical-chemical parameters (temperature; pH; moisture content; and NH₄⁺-N content) and maturity index (C/N ratio, E₄/E₆ and GI). Therefore, DOM evolution could quickly reflect the maturity process of compost. In subsequent research, the quantitative analysis of DOM components can be considered to modify DOM spectral parameters, or to build a model, so as to achieve rapid evaluation of compost maturity.

Insight into the dynamic microbial community and core bacteria in composting from different sources by advanced bioinformatics methods

Microbial communities are important for high composting efficiency and good quality composts. This study was conducted to compare the changes of physicochemical and bacterial characteristics in composting from different raw materials, including chicken manure (CM), duck manure (DM), sheep manure (SM), food waste (FW), and vegetable waste (VW). The role and interactions of core bacteria and their contribution to maturity in diverse composts were analyzed by advanced bioinformatics methods combined sequencing with co-occurrence network and structural equation modeling (SEM). Results indicated that there were obviously different bacterial composition and diversity in composting from diverse sources. FW had a low pH and different physiochemical characteristics compared to other composts but they all achieved similar maturity products. Redundancy analysis suggested total organic carbon, phosphorus, and temperature governed the composition of microbial species but key factors were different in diverse composts. Network analysis showed completely different interactions of core bacterial community from diverse composts but Thermobifida was the ubiquitous core bacteria in composting bacterial network. Sphaerobacter and Lactobacillus as core genus were presented in the starting mesophilic and thermophilic phases of composting from manure (CM, DM, SM) and municipal solid waste (FW, VW), respectively. SEM indicated core bacteria had the positive, direct, and the biggest (> 80%) effects on composting maturity. Therefore, this study presents theoretical basis to identify and enhance the core bacteria for improving full-scale composting efficiency facing more and more organic wastes.

Humification improvement by optimizing particle size of bulking agent and relevant mechanisms during swine manure composting

For purpose of clarifying the impact on particle size of bulking agents on humification and relevant mechanisms, different length (<2 cm, 2 cm, 5 cm, 10 cm) of branch and straw were blended with swine manure individually for 100 days aerobic composting. Results demonstrated that, 2 cm and 5 cm of branch and straw promoted the highest degradation of DOC by 41.49 % and 58.42 %, and increased the humic substances by 23.81 % and 55.82 % in maturity stage, respectively, compared with other treatments. As shown in microbial consequence, the maximum relative abundance of humus funguses increased by 99.55 % and 99.92 % at phylum, and 98.95 % and 99.24 % at genus in 2 cm and 5 cm of branch and straw treatment, thus verifying the result in variation of humus content. In a word, particle size could result in obvious impact on humification, and the optimized size were about 2 cm and 5 cm of branch and straw.

Inoculating indoleacetic acid bacteria promotes the enrichment of halotolerant bacteria during secondary fermentation of composting

The secondary fermentation stage is critical for stabilizing composting products and producing various secondary metabolites. However, the low metabolic rate of mesophilic bacteria is regarded as the rate-limiting stage in composting process. In present study, two indoleacetic acid (IAA)-producing bacteria (Bacillus safensis 33C and Corynebacterium stationis subsp. safensis 29B) were inoculated to strengthen the secondary fermentation stage to improve the plant-growth promoting potential of composting products. The results showed that the addition of IAA-producing bacteria promoted the assimilation of soluble salt, the condensation and aromatization of humus, and the accumulation of dissolved organic nitrogen (DON) and dissolved organic carbon (DOC). The bioaugmentation strategy also enabled faster microbial community succession during the medium-late phase of secondary fermentation. However, the colonization of Bacillus and Corynebacterium could not explain the disproportionate increase of IAA yield, which reached up to 5.6 times compared to the control group. Deeper analysis combined with physicochemical properties and microbial community structure suggested that IAA-producing bacteria might induce the increase of salinity, which enriched halotolerant bacteria capable of producing IAA, such as Halomonas, Brachybacterium and Flavobacterium. In addition, the results also proved that it was necessary to shorten secondary fermentation time to avoid IAA degradation without affecting composting maturity. In summary, enhancing secondary fermentation of composting via adding proper IAA-producing bacteria is an efficient strategy for upgrading the quality of organic fertilizer.

Evaluating differences in humic substances formation based on the shikimic acid pathway during different materials composting

This study aimed to evaluate differences in humic substance (HS) formation based on the shikimic acid pathway (SAP) during five different materials composting. The results showed that compared with other three materials, gallic acid, protocatechuic acid and shikimic acid of the SAP products in lawn waste (LW) and garden waste (GW) compost decreased significantly. Furthermore, as important indicators for evaluating humification, humic acid and degree of polymerization increased by 39.4%, 79.5% and 21.8%, 87.9% in LW and GW, respectively. Correlation analysis showed that SAP products were strongly correlated with HS fractions in LW and GW. Meanwhile, network analysis indicated that more core bacteria associated with both SAP products and HS were identified in LW and GW. Finally, the structural equation model proved that SAP had more significant contribution to humification improvement in LW and GW. These findings provided theoretical foundation and feasible actions to improve compost quality by the SAP.

Emission of volatile sulphur compounds during swine manure composting: Source identification, odour mitigation and assessment

This study aimed to identify the sources of volatile sulphur compounds (VSCs) and evaluate their mitigation by ferric oxide (Fe₂O₃) during swine manure composting. Four chemicals, including l-cysteine, l-methionine, sodium sulphite, and sodium sulphate, were further added to simulate organic and inorganic sulphur-containing substances in swine manure to track VSC sources during composting. Results show that sulphur simulants induced the emission of six common VSCs, including methyl sulphide (Me₂S), dimethyl sulphide (Me₂SS), carbonyl sulphide (COS), carbon disulphide (CS₂), methyl mercaptan (MeSH), and ethyl mercaptan (EtSH), during swine manure composting. Of them, COS, CS₂, MeSH and Me₂SS were predominantly contributed by the biodegradation of methionine and cysteine, while Me₂S and EtSH were dominated by the reduction of sulphite and sulphate. Further Fe₂O₃ addition at 1.5 % of total wet weight of composting materials immobilized elemental sulphur and inhibited sulphate reduction to reduce the emission of VSCs by 46.7-80.9 %. Furthermore, odour assessment indicated that adding Fe₂O₃ into composting piles significantly reduced the odour intensity level to below 4, the odour value of VSCs by 47.1-81.3 %, and thus the non-carcinogenic risk by 68.4 %.

Variation in community structure and network characteristics of spent mushroom substrate (SMS) compost microbiota driven by time and environmental conditions

Global mushroom production is growing rapidly, raising concerns about polluting effects of spent mushroom substrate (SMS) and interest in uses in composts. In this study, SMS composting trials and high-throughput sequencing were carried out to investigate to better understand how the structure, co-occurrence patterns, and functioning of bacterial and fungal communities vary through compost time and across environmental conditions. The results suggested that both bacterial and fungal microbiota displayed significant variation in community composition across different composting stages. Enzyme activity levels showed both directional and fluctuating changes during composting, and the activity dynamics of carboxymethyl cellulase, polyphenol oxidase, laccase, and catalase correlated significantly with the succession of microbial community composition. The co-occurrence networks are "small-world" and modularized and the topological properties of each subnetwork were significantly influenced by the environmental factors. Finally, seed germination and seedling experiments were performed to verify the biosafety and effectiveness of the final composting products.

Deciphering the effect of exogenous lignocellulases addition on the composting efficiency and microbial communities

This study aimed to reveal the potential effects of exogenous lignocellulases addition on the composting efficiency and microbial communities. The lignocellulases addition at the mesophilic phase (MEP) greatly expedited the substrate conversion and the rise of temperature at the initial stage, driving the early arrival of thermophilic phase (THP), caused by the positive effects of Sphingobacterium and Brevundimonas. When being added at the THP, the potential functions and interactions of microbial communities were stimulated, especially for Thermobispora and Mycothermus, which prolonged the duration of the THP and expedited the humic acid formation. Simultaneous addition (MEP and THP) significantly altered the microbial community succession and activated the microbes that contributed to the lignocellulases secretion, exhibiting the highest cellobiohydrolase (36.19 ± 3.25 U· g^-1 dw) and xylanase (47.51 ± 3.32 U·g^-1 dw) activity at the THP. These findings provide new strategies that can be effectively utilized to improve the efficiency and quality of 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.

Fungal community enhanced humification and influenced by heavy metals in industrial-scale hyperthermophilic composting of municipal sludge

The succession of fungal community and effects of heavy metals on fungi during industrial-scale hyperthermophilic composting of municipal sludge remain unclear. Results showed hyperthermophilic composting enhanced decomposition and humification of municipal sludge in the short terms, while heavy metal concentrations and speciation had no significant change with high copper and zinc levels (101-122 and 292-337 mg/kg, respectively) in compost samples. The fungal community and its ecological assembly displayed dynamic change during hyperthermophilic composting. Some thermophilic-resistant fungi, such as phylum Ascomycota and genera Candida, Aspergillus, Thermomyces and Petriella dominated in hyperthermophilic phase. Heavy metals served important effects on fungal community structure and functions during composting. Some fungal drivers (e.g., Thermomyces, Petriella and Schizophyllum) and keystone fungi (e.g., Candida and Pichia) might be thermophilic- and heavy metal-resistant fungi which played important roles in decomposition and humification of municipal sludge. This study reveals fungal community accelerating humification and its influencing factors during composting.

Dynamic description of temporal changes of gut microbiota in broilers

The diversity of bacteria and fungi in the gut microbiota of commercial broilers that raised in cages from hatch to the end of the production cycle were examined by an analysis of 3,592 and 3,899 amplicon sequence variants (ASVs), respectively. More than 90% sequences in bacterial communities were related to Firmicutes and Proteobacteria. More than 90% sequences in fungal communities were related to Ascomycota, Basidiomycota, and Glomeromycota. A statistical analysis of the microbiota composition succession showed that age was one of the main factors affecting the intestinal microbial communities of broilers. The increasingly complex community succession of transient microbiota occurred along with an increase of age. This dynamic change was observed to be similar between bacteria and fungi. The gut microbiota had a special structure in the first 3 d after birth of broiler. The microbiota structure was quite stable in the period of rapid skeletal growth (d 14–21), and then changed significantly in the period of rapid gaining weight (d 35–42), thus indicating the composition of gut microbiota in broilers had unique structures at different developmental stages. We observed that several bacteria and fungi occupied key functions in the gut microbiota of broilers, suggesting that the gut homeostasis of broilers might be affected by losses of bacteria and fungi via altering interactions between microbiota. This study aimed to provide a data basis for manipulating the microbiota at different developmental stages, in order to improve production and the intestinal health of broilers.

Full-Scale of a Compost Process Using Swine Manure, Human Feces, and Rice Straw as Feedstock

Regarding the composting of rural waste, numerous studies either addressed the composting of a single waste component or were conducted at a laboratory/pilot scale. However, far less is known about the mixed composting effect of multi-component rural waste on a large scale. Here, we examined nutrient transformation, maturity degree of decomposition, and succession of microbial communities in large-scale (1,000 kg mixed waste) compost of multi-component wastes previously optimized by response models. The results showed that multi-component compost can achieve the requirement of maturity and exhibit a higher nutritional value in actual compost. It is worth noting that the mixed compost effectively removed pathogenic fungi, in which almost no pathogenic fungi were detected, and only two pathogenic bacteria regrown in the cooling and maturation stages. Structural equation models revealed that the maturity (germination index and the ratio of ammonium to nitrate) of the product was directly influenced by compost properties (electrical conductivity, pH, total organic carbon, moisture, temperature, and total nitrogen) compared with enzymes (cellulase, urease, and polyphenol oxidase) and microbial communities. Moreover, higher contents of total phosphorus, nitrate-nitrogen, and total potassium were conducive to improving compost maturity, whereas relatively lower values of moisture and pH were more advantageous. In addition, compost properties manifested a remarkable indirect effect on maturity by affecting the fungal community (Penicillium and Mycothermus). Collectively, this evidence implies that mixed compost of multi-component rural waste is feasible, and its efficacy can be applied in practical applications. This study provides a solution for the comprehensive treatment and utilization of rural waste.

Effects of thermophiles inoculation on the efficiency and maturity of rice straw composting

The present study investigated the effects of separately or simultaneously inoculating thermophilic fungus Aspergillus fumigatus Z5 and bacterium Geobacillus stearothermophilus B5 on lignocellulose degradation, enzyme activities and humification during rice straw composting. The results indicated that inoculation of Z5 accelerated the rise of temperature in the mesophilic phase, and the degradation degree of cellulose and hemicellulose was increased by 25.3% and 20.7%, respectively, due to the higher activities of lignocellulolytic enzymes. Inoculation of B5 increased 5-7 °C of the compost temperature in the thermophilic phase, and also prolonged the duration from 33 to 41 days. Inoculated simultaneously, the secreted hydrolases of Z5 generated more nutrition and promoted the growth of B5. B5 maintained and increased the compost temperature, thus presenting a better hydrolysis environment for extracellular hydrolases. Thermophilic inoculation altered the main physicochemical factors and improved efficiency and maturity in rice straw composting.

Effects of Co-application of Cadmium-Immobilizing Bacteria and Organic Fertilizers on Houttuynia cordata and Microbial Communities in a Cadmium-Contaminated Field

Cadmium pollution is a serious threat to the soil environment. The application of bio-based fertilizers in combination with beneficial microbial agents is a sustainable approach to solving Cd pollution in farm soil. The present study investigated the effects of co-application of a Cd-immobilizing bacterial agent and two fermented organic fertilizers (fermentative edible fungi residue; fermentative cow dung) on Houttuynia cordata and its microbial communities in a Cd-polluted field. It showed that both the application of the Cd-immobilizing bacterial agent alone and the combined application of bio-based soil amendments and the bacterial agent effectively reduced >20% of the uptake of Cd by the plant. Soil nitrogen level was significantly raised after the combined fertilization. The multivariate diversity analysis and co-occurrence network algorithm showed that a significant shift of microbial communities took place, in which the microbial populations tended to be homogeneous with reduced microbial richness and increased diversity after the co-application. The treatment of fermentative cow dung with the addition of the bacterial agent showed a significant increase in the microbial community dissimilarity (R = 0.996, p = 0.001) compared to that treated with cow dung alone. The co-application of the bacterial agent with both organic fertilizers significantly increased the abundance of Actinobacteria and Bacteroidetes. The FAPROTAX soil functional analysis revealed that the introduction of the microbial agent could potentially suppress human pathogenic microorganisms in the field fertilized with edible fungi residue. It also showed that the microbial agent can reduce the nitrite oxidation function in the soil when applied alone or with the organic fertilizers. Our study thus highlights the beneficial effects of the Cd-immobilizing bacterial inoculant on H. cordata and provides a better understanding of the microbial changes induced by the combined fertilization using the microbial agent and organic soil amendments in a Cd-contaminated field.

Microecological insight to fungal structure and key fungal communities regulating nitrogen transformation based on spatial heterogeneity during cow manure composting by multi-angle and multi-aspect analyses

Composting is the mainstream technology for the treatment of agricultural solid waste, but limited efforts were made to investigate fungal composition and its contributions to nitrogen transformation in different depths of compost. In this study, spatial distributions of fungi were analyzed using high throughput sequencing by multi-angle analyses, and the key fungal communities determining nitrogen transformation were quantified and identified by multi-aspect analyses during cow manure composting. Multi-angle analyses showed that fungal structure, biomarkers and trophic mode composition varied in different layers, revealing that spatial heterogeneity is the distinctive attribute of composting system. Ascomycota and Basidiomycota were dominant phyla during composting, the two phyla peaked in top and bottom layer respectively. At mesophilic stage, Tremellales, and unclassified Ascomycota (order) were biomarkers in top and middle layer respectively, and so were Remersonia, Pyrenochaetopsis, and Wallemia in bottom layer by LEfSe analysis. Based on multi-aspect analyses, Unclassified Dothideomycetes mainly affected NH4+-N transformation both in top (1.2816***) and middle layers (1.1726*). Trichocladium asperum (0.9536***) and Zopfiella (-0.9484***) mainly affected TN transformation in top layer. Guehomyces pullulans (-0.9684**) and Preussia (-1.0508**) regulated NO3--N transformation in middle layer. Thermomyces lanuginosus (0.7127***) and Typhula sp. UW973129 (0.7298***) were the key species promoting TN and C/N transformation in bottom layer, respectively. Interestingly, different fungal communities showed a complex network interaction driving nitrogen transformation, and the abundance of microbial community could be conducive to characterizing nitrogen transformation in the vertical space of composting.

Biochar regulates bacterial-fungal diversity and associated enzymatic activity during sheep manure composting

Aimed to evaluate the coexistence of bacterial and fungal diversity and their correlation with enzymatic activity in response to biochar. This study performed aerobic composting based on typical agricultural wastes of sheep manure with additive apple tree branch biochar at distinct concentration (0, 2.5, 5, 7.5, 10 and 12.5% corresponding from T1 to T6). The result demonstrated that appropriate amendment of biochar enriched bacterial diversity (1646-1686 OTUs) but interestingly decreased fungal diversity (542-630 OTUs) compared to control (1444 and 682 OTUs). Biochar addition enhanced all enzymatic activities and its correlation with bacterial was more complex than fungal community (786 and 359 connect edges). The dominant microbes comprised of Firmicutes (45.2-35.2%), Proteobacteria (14.0-17.5%), Basidiomycota (32.4-49.5%) and Ascomycota (11.3-37.5%) among all the treatments. Overall, biochar regulates the composting microenvironment by influencing the microbial diversity and associated enzymatic activities.

Effects of microplastics on humification and fungal community during cow manure composting

The effect of microplastics (MPs) on the biological treatment of organic waste has been extensively studied, but little is known about the influence of different MPs on composting humification and the fungal community. In this study, PE, PVC, and PHA MPs were individually mixed with cow dung and sawdust and then composted. The results showed that different MPs had various influences on humification, and the humic acid to fulvic acid ratio of all MP-added treatments (0.44-0.83) was lower than that of the control (0.91). During the composting process, Ascomycota (26.32-89.14%) and Basidiomycota (0.47-4.78%) are the dominant phyla in all treatments and all microplastics decreased the diversity and richness of the fungal community at the thermophilic stage of composting. Exposure to MPs had an obvious effect on the fungal community at the genus level, and the addition of PHA and PE MPs increased the relative abundance of phytopathogenic fungi. LEfSe and network analysis indicated that MPs reduced the number of biomarkers and led to a simpler and more unstable fungal community structure compared to the control. This study has important implications for assessing microplastic pollution and organic waste disposal.

Research trend analysis of composting based on Web of Science database

Bibliometric analysis was used in this study for the quantitative evaluation of current research trends on composting. The research articles indexed from the Science Citation Index-Expanded in Web of Science database published from 2000 to 2019 were investigated. The USA, China and Spain were the top three countries considering the number of papers. Amongst the research institutes, CSIC of Spain, Chinese Academy of Sciences and Agriculture & Agri-Food Canada ranked the top three in total publication amount. Journals that published a significant number of literature regarding topics of composting included Environmental Sciences & Ecology, Agriculture and Engineering. In terms of research content, keywords such as heavy metal, heavy metal and biodegradation appeared frequently. In addition, the analysis of keywords revealed the following research hotspots in future studies: investigation of heavy metal passivator, optimisation of composting conditioner, development of all kinds of microorganisms, rational management of the composting process and improvement of solid waste life cycle assessment. To some extent, it helps to understand the current global status and trends of the related research.

Downward aeration promotes static composting by affecting mineralization and humification

A composting experiment with sewage sludge and green waste was conducted to explore the effects of aeration directions (i.e., upward and downward) on static composting systems. The compost properties, including humification indexes and organic matter loss rate, and microbial diversity during the composting, were determined. Results showed that the downward aeration promoted the homogenization of temperature and moisture of the static composting system, thereby stimulating microbial metabolism and accelerating mineralization and humification. Microbial community profiles significantly changed among the composting phases. The humification dynamics were significantly correlated with the relative abundance of multiple microbial functional groups. However, no significant effects of aeration direction on the microbial community profiles were observed. The findings indicate that downward aeration is promising to improve the quality of static compost production, by stimulating microbial metabolism rather than altering microbial community profiles.

δ-MnO2 changed the structure of humic-like acid during co-composting of chicken manure and rice straw

Improving the structure and quantity of humus is important to reduce agriculture organic waste by composting. The present study was aimed to assess the role of δ-MnO₂ on humus fractions formation during co-composting of chicken manure and rice straw. Two tests (control group (CK), the addition of δ-MnO₂ (M)) were carried out. The results showed that organic matter content decreased by 34% and 29% at M and CK, suggesting the process of organic waste disposal was accelerated by adding δ-MnO₂. The structures and quantity of fulvic acid (FA) and humic acid (HA) (as the main fractions of humus) were investigated. The δ-MnO₂ had no significant effect on improving the concentration of FA and HA (p > 0.05). However, the addition of δ-MnO₂ caused different effects on the FA and HA structure. The humification degree of FA improved, while bioavailability of HA increased through adding δ-MnO₂. The addition of δ-MnO₂ rephased the bacterial community structure, slowing down the succession rate of the bacterial community in M composting. After adding δ-MnO_2, the structural equation modeling results showed that environmental factors could directly drive changes in FA and HA by modulating the bacterial community. Furthermore, the role of FA and HA in the soil amendment was also demonstrated. Therefore, the addition of MnO₂ might be promising for agriculture organic waste treatment and environmental repair during composting.

Effects of Co-application of Cadmium-Immobilizing Bacteria and Organic Fertilizers on Houttuynia cordata and Microbial Communities in a Cadmium-Contaminated Field

Cadmium pollution is a serious threat to the soil environment. The application of bio-based fertilizers in combination with beneficial microbial agents is a sustainable approach to solving Cd pollution in farm soil. The present study investigated the effects of co-application of a Cd-immobilizing bacterial agent and two fermented organic fertilizers (fermentative edible fungi residue; fermentative cow dung) on Houttuynia cordata and its microbial communities in a Cd-polluted field. It showed that both the application of the Cd-immobilizing bacterial agent alone and the combined application of bio-based soil amendments and the bacterial agent effectively reduced >20% of the uptake of Cd by the plant. Soil nitrogen level was significantly raised after the combined fertilization. The multivariate diversity analysis and co-occurrence network algorithm showed that a significant shift of microbial communities took place, in which the microbial populations tended to be homogeneous with reduced microbial richness and increased diversity after the co-application. The treatment of fermentative cow dung with the addition of the bacterial agent showed a significant increase in the microbial community dissimilarity (R = 0.996, p = 0.001) compared to that treated with cow dung alone. The co-application of the bacterial agent with both organic fertilizers significantly increased the abundance of Actinobacteria and Bacteroidetes. The FAPROTAX soil functional analysis revealed that the introduction of the microbial agent could potentially suppress human pathogenic microorganisms in the field fertilized with edible fungi residue. It also showed that the microbial agent can reduce the nitrite oxidation function in the soil when applied alone or with the organic fertilizers. Our study thus highlights the beneficial effects of the Cd-immobilizing bacterial inoculant on H. cordata and provides a better understanding of the microbial changes induced by the combined fertilization using the microbial agent and organic soil amendments in a Cd-contaminated field.