Bacterial and fungal community dynamics during different stages of agro-industrial waste composting and its relationship with compost suppressiveness

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.

Effect of initial moisture content, resulting from different ratios of vegetable waste to maize straw, on compost was mediated by composting temperatures and microbial communities at low temperatures

Owing to the huge amounts and perishable character of vegetable wastes, composting is one of the best options for recycling vegetable wastes post-harvest. The initial moisture content (MC) is critical for optimizing composting process, but the effect of high MC in undehydrated vegetable wastes on composting was rarely reported. For this, the plant-scale windrows were prepared by mixing cauliflower waste and maize straw at different ratios to control initial MC of 70 % (T1-70) and 80 % (T2-80), respectively, and composted in winter. As composting progressed, substantial organic matter degradation, progressive humification, decreases in electrical conductivity and increases of pH and germination index (GI) were observed in both treatments. Nonetheless, T1-70 accelerated heating rate early during composting, prolonged high temperature period (>50 °C) by 30 d, thus increased the harmless level of composting, and significantly improved the humification of end-products compared to T2-80. Results also revealed that T1-70 activated more indigenous microbes and enhanced microbial interactions early during composting, with the fungi enriched in T1-70 playing an important role in accelerating the composting process. Remarkably, the difference in composting temperatures, humification degree, and microbial communities between the two treatments was most significant during the maturation phase. In this phase, MWH_CFBk5, Planktosalinus, Pseudopedobacter, and Luteimonas enriched in T1-70 were positively correlated with humification indices. It is suggested that the effect of initial MC, resulting from different ratios of vegetable waste to maize straw, on their composting was mediated by the composting temperature and microbial communities at low temperatures.

Enhancing C and N turnover, functional bacteria abundance, and the efficiency of biowaste conversion using Streptomyces-Bacillus inoculation

Microbial inoculation plays a significant role in promoting the efficiency of biowaste conversion. This study investigates the function of Streptomyces-Bacillus Inoculants (SBI) on carbon (C) and nitrogen (N) conversion, and microbial dynamics, during cow manure (10% and 20% addition) and corn straw co-composting. Compared to inoculant-free controls, inoculant application accelerated the compost's thermophilic stage (8 vs 15 days), and significantly increased compost total N contents (+47%) and N-reductase activities (nitrate reductase: +60%; nitrite reductase: +219%). Both bacterial and fungal community succession were significantly affected by DOC, urease, and NH4+-N, while the fungal community was also significantly affected by cellulase. The contribution rate of Cupriavidus to the physicochemical factors of compost was as high as 83.40%, but by contrast there were no significantly different contributions (∼60%) among the top 20 fungal genera. Application of SBI induced significant correlations between bacteria, compost C/N ratio, and catalase enzymes, indicative of compost maturation. We recommend SBI as a promising bio-composting additive to accelerate C and N turnover and high-quality biowaste maturation. SBI boosts organic cycling by transforming biowastes into bio-fertilizers efficiently. This highlights the potential for SBI application to improve plant growth and soil quality in multiple contexts.

Mechanism of magnetite-assisted aerobic composting on the nitrogen cycle in pig manure

Magnetite affects nitrogen cycle of pig manure (PM) biostabilisation was investigated. Various doses of magnetite (0 % (T1); 2.5 % (T2); 5 % (T3); 7.5 % (T4)) were homogeneously added into PM and wolfberry branch fillings (BF) mixture for a 50-day composting. Compared to T1, total nitrogen (TN) loss in gaseous form increased remarkably by 17.51 %, 56.31 %, and 24.91 %, respectively, in T2-T4. In particular, T3 dramatically increased the cumulative N2O emission but decreased NH3 emissions. However, T2 and T3 enhanced the total nitrogen contents by 7.24 % and 3.09 %. Structural equation models (SEM) analysis indicated that magnetite addition increased the direct and indirect pathways of N2O emission. Further analysis revealed that Ruminofilibacter and N2O emission were significantly correlated, and Pseudomonas played a vital role in nitrogen preservation. Although using 2 % magnetite as an additive could increase the TN content, the obvious increase of N2O emission should be considered in engineering practice.

Exploring carbon conversion and balance with magnetite-amended during pig manure composting

This study was designed to explore the magnetite in maturation and humification during pig manure (PM) and wolfberry branch fillings (BF) composting. Different proportions of magnetite (T1, 0%; T2, 2.5%; T3, 5%; T4, 7.5%;) were blended with PM for 50 days of composting. The findings indicated magnetite amendment has no influence on the maturity, and the 5% ratio significantly promoted humic acid (HA) formation and fulvic acid (FA) decomposition compared to other treatments. Compared to T1, magnetite addition significantly increased CO2 and CH4 emissions by 106.39%-191.69% and 6.88-13.72 times. The further analysis suggested that magnetite improved Ruminofilibacter activity were significantly positively associated with HA, and C emissions. The further PICRUSt 2 analysis showed membrane transport may enhance environmental information processing by magnetite. Overall, these results demonstrated higher organic matter (OM) degradation and HA formation with an additional increase in microbial activity highlighted advantages of using magnetite during PM composting.

Comparison of bioaerosol release characteristics between windrow and trough sludge composting plants: Concentration distribution, community evolution, bioaerosolization behaviour, and exposure risk

Windrow and trough composting are two mainstream composting methods, but the effect of composting methods on bioaerosol release from sludge composting plants is unclear. The study compared the bioaerosol release characteristics and exposure risks between the two composting methods. The results showed that the bacterial aerosol concentrations in the windrow composting plant ranged from 14,196 to 24,549 CFU/m3, while the fungal aerosol concentrations in the trough composting plant reached 5874 to 9284 CFU/m3; there were differences in the microbial community structures between the two sludge composting plants, and the composting method had a greater effect on bacterial community evolution than on fungal community evolution. The biochemical phase was the primary source of the bioaerosolization behaviour of the microbial bioaerosols. In the windrow and trough composting plants, the bacterial bioaerosolization index ranged from 1.00 to 999.28 and from 1.44 to 24.57, and the fungal bioaerosolization index ranged from 1.38 to 1.59 and from 0.34 to 7.72, respectively. Bacteria preferentially aerosolized mainly in the mesophilic stage, while the peak of the fungal bioaerosolization index appeared in the thermophilic stage. The total non-carcinogenic risks for bacterial aerosols were 3.4 and 2.4, while those for fungi were 1.0 and 3.2 in the trough and windrow sludge composting plants, respectively. Respiration is the main exposure pathway for bioaerosols. It is necessary to develop different bioaerosol protection measures for different sludge composting methods. The results of this study provided basic data and theoretical guidance for reducing the potential risk of bioaerosols in sludge composting plants.

Evaluating the potential of biodegradation of swine manure through rotary drum composting utilizing different bulking agents

The rapid expansion of the pig industry and the concurrent increase in pig units have posed a significant waste management challenge, particularly in the form of piggery waste. In this study, the potential of three different bulking agents (sawdust, dry leaves, and rice straw) for the biodegradation of piggery waste was evaluated through rotary drum composting (RDC). Following the composting time of 20 days, evaluations of macro and micronutrient concentrations and the C/N ratio revealed stable, matured compost that could be used in farming. However, the saw dust amended RDC (RDC1) outperformed among the studied trails; the total nitrogen content of 1.54%, total phosphorus of 7.68 g kg-1, and total potassium of 23.45 g kg-1 demonstrated the bioproduct produced through RDC1 resulted in superior-quality end product achieved in only 20 days in comparison with other bulking agents studied. Further, the outcomes of the study can serve the swine livestock sector through effective bioconversion of the waste.

Role of Fungi in Imparting General Disease Suppressiveness in Soil from Organic Field

Soil microbial communities are key players responsible for imparting suppressive potential to the soil against soil-borne phytopathogens. Fungi have an immense potential to inhibit soil-borne phytopathogens, but the fungal counterpart has been less explored in this context. We assessed the composition of fungal communities in soil under long-term organic and conventional farming practice, and control soil. The disease-suppressive potential of organic field was already established. A comparative analysis of the disease suppressiveness contributed by the fungal component of soil from conventional and organic farms was assessed using dual culture assays. The quantification of biocontrol markers and total fungi was done; the characterization of fungal community was carried out using ITS-based amplicon sequencing. Soil from organic field exhibited higher disease-suppressive potential than that from conventional farming, against the pathogens selected for the study. Higher levels of hydrolytic enzymes such as chitinase and cellulase, and siderophore production were observed in soil from the organic field compared to the conventional field. Differences in community composition were observed under conventional and organic farming, with soil from organic field exhibiting specific enrichment of key biocontrol fungal genera. The fungal alpha diversity was lower in soil from the organic field compared to the conventional field. Our results highlight the role of fungi in contributing to general disease-suppressive ability of the soil against phytopathogens. The identification of fungal taxa specifically associated with organic farming can aid in understanding the mechanism of disease suppression under such a practice, and can be exploited to induce general disease suppressiveness in otherwise conducive soil.

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.

Bacterial community dynamics and co-occurrence network patterns during different stages of biochar-driven composting

Bacterial communities were dynamically tracked at four stages of biochar-driven sheep manure pile composting, and the co-occurrence networks with keystone taxa were established. The succession of bacterial community obvious varied during the composting process, Proteobacteria predominant in initial stage (39%) then shifted into Firmicutes in thermophilic (41%) and mesophilic (27%) stages, finally the maturation stage dominant by Bacteroidota (26%). Visualizations of bacterial co-occurrence networks demonstrate more cooperative mutualism and complex interactions in the thermophilic and mesophilic phases. Noticeably, the 7.5 and 10% biochar amended composts shown highest connections (736 and 663 total links) and positive cooperation (97.37 and 97.13% positive link) as well as higher closeness centrality and betweenness centrality of keystone taxa. Overall, appropriate biochar addition alters bacterial community succession and strengthens connection between keystone taxa and other bacteria, with 7.5 and 10% biochar amended composts has intense mutualistic symbiosis among bacterial communities.

Effect of moisture content, aeration rate, and C/N on maturity and gaseous emissions during kitchen waste rapid composting

To determine factors affecting compost maturity and gaseous emissions during the rapid composting of kitchen waste, an orthogonal test was conducted with three factors: moisture content (MC) (55%, 60%, 65%), aeration rate (AR) (0.3,0.6 and 0.9 L·kg^-1DM·min^-1) and C/N ratio (21, 24, 27). The results showed that the importance of factors affecting compost maturity was: C/N > AR > MC, optimal conditions were: C/N of 24, AR of 0.3 L·kg^-1DM·min^-1and MC of 65%. For gaseous emissions, the sequence of essential factors affecting NH₃ emissions was: C/N > MC > AR, and the optimal parameters for NH₃ reduction were: C/N of 27, MC of 65%, and AR of L·kg^-1DM·min^-1. The important factors affecting N₂O and H₂S emissions are both: MC > C/N > AR, while their best parameters were different. The optimal parameters for N₂O emission reduction were MC of 60%, AR of 0.3 L·kg^-1DM·min^-1 and C/N of 24, while these for H₂S were MC of 55%, AR of 0.3 L·kg^-1DM·min^-1 and C/N of 21. The C/N mainly affected the compost maturity and AR further affected the maturity and pollutant gas emissions by influencing the temperature and O₂ content. Considering comprehensively the maturity and gaseous reduction, the optimal control parameters were: MC of 60%-65%, AR of L·kg^-1DM·min^-1, and C/N of 24-27.

Impacts of composting duration on physicochemical properties and microbial communities during short-term composting for the substrate for oyster mushrooms

A short-term composting process to prepare substrate is an effective way to cultivate oyster mushrooms (Pleurotus spp.), which can increase the yield of mushrooms and lower the rate of contamination in non-industrialized cultivation. Moreover, it is different from the traditional composting processes for fertilizers and lacks systematic study, such as microbial succession and compost quality. In this study, a series of different tests of composting duration (0, 2, 4 and 5 d) were performed. A composting duration of 4-5 d over 58 °C was suitable for mushroom cultivation based on the biological efficiency (BE) range of 69.76-73.41 % and the contamination rate of 0 %. The content of total carbon (TC) continuously decreased during composting, while the content of total nitrogen (TN) reacted in an opposite matter. The final TN and C/N ratios were 1.89 % and 28/1, respectively, which fell well within the optimal range of nutritional requirements for oyster mushroom cultivation. The composting bacteria were more diverse than the fungal species. Caldibacillus, Thermobispora, Thermopolyspora, Thermobacillus and Ureibacillus were the predominant bacterial genera during the thermophilic stage. Co-occurrence patterns of microbial communities and physicochemical properties were performed using a network analysis, which indicated that bacteria can play more efficient roles than fungi in the degradation of organic matter. The structural equation model showed that composting duration significantly affected bacterial diversity, lignocellulose degradation rates, and BE. The correlations between bioinformatics parameters with composting characters and agronomic traits were determined by the Mantel test and showed that the induction of bacterial diversity over time rapidly activated carbon metabolism during short-term composting. This study provides a new idea of agro-waste composting for mushroom cultivation.

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.

Straw waste promotes microbial functional diversity and lignocellulose degradation during the aerobic process of pig manure in an ectopic fermentation system via metagenomic analysis

This study compares the physicochemical properties, lignocellulose degradation, microbial community composition, and carbohydrate-active enzymes (CAZymes) in ectopic fermentation systems (EFS) of pig manure mixed with either conventional padding (C) or straw waste (A). The degradation rates of cellulose, hemicellulose, and lignin were found to be significantly higher in A (27.72%, 22.72%, and 18.80%, respectively) than in C (21.05%, 16.17%, and 11.69%, respectively) owing to the activities of lignocellulolytic enzymes. Metagenomics revealed that straw addition had a stronger effect on the bacterial community succession than fungi. The abundances of Sphingobacterium, Pseudomonas, and CAZymes were higher in A than in C, as well as the auxiliary activity enzymes, which are crucial for lignocellulose degradation. Redundancy analysis indicates a positive correlation between lignocellulose degradation and Sphingobacterium, Pseudomonas, Bacillus, and Actinobacteria contents. A structural equation model was applied to further verify that the increased microbial functional diversity was the primary driver of lignocellulosic degradation, which could be effectively regulated by the enhanced temperature with straw addition. Replacing traditional padding with straw can thus accelerate lignocellulosic degradation, promote microbial functional diversity, and improve the EFS efficiency.

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.

Insights into the effect of iron-carbon particle amendment on food waste composting: Physicochemical properties and the microbial community

The effects of iron-carbon (Fe-C) particle amendment on organic matter degradation, product quality and functional microbial community in food waste composting were investigated. Fe-C particles (10%) were added to the material and composted for 32 days in a lab-scale composting system. The results suggested that Fe-C particle enhanced organic matter degradation by 12.3%, particularly lignocellulose, leading to a greater humification process (increased by 15.5%). In addition, NO₃^--N generation was enhanced (15.9%) by nitrification with more active ammonia monooxygenase and nitrite oxidoreductase activities in the cooling and maturity periods. Fe-C particles not only significantly increased the relative abundances of Bacillus and Aspergillus for organic matter decomposition, but also decreased the relative abundances of acid-producing bacteria. RDA analysis demonstrated that the bacterial community was significantly influenced by dissolved organic matter, C/N, NO₃^--N, humic acid, volatile fatty acids and pH, while electrical conductivity was the key factor affecting the fungal community.

Performance evaluation of a novel two-stage biodegradation technique through management of toxic lignocellulosic terrestrial weeds

The present study investigates the biodegradation of two potentially toxic terrestrial weeds Parthenium hysterophorus and Lantana camara, implementing a novel two-stage biodegradation technique; Rotary drum composting followed by vermicomposting (RV). The RV approach was refined for a 7-day thermophilic degradation in an in-vessel rotary drum composter, followed by a 20-day mesophilic degradation utilizing Eisenia fetida and Eudrilus eugeniae vermi-monocultures. However, rotary drum composting (RDC) was performed for both the weeds (for 27 days), facilitating only initial thermophilic degradation to compare the efficacy of the RV technique. Lignocelluloses analysis revealed that cellulose degradation doubled during RV technique, indicating efficient biodegradation in reactors administered with E. fetida vermiculture compared to RDC (19.60 to 42.80% and 26.80 to 66.50% in P. hysterophorus and L. camara feedstocks). Further, these results also correlated with the X-Ray diffractograms of all trials showing the degradation of crystalline cellulose at 2θ: 20-50° for RV. Moreover, to ensure product safety, the analyzed total heavy metals content also unveiled the advantage of RV over RDC as validated by the accumulation of higher concentrations of zinc (45% and 33% in P. hysterophorus and L. camara feedstocks) and lead (55% and 45% in P. hysterophorus and L. camara feedstocks) in reactors with E. fetida. The material's seed germination index increased to 80% in the final product of all trials in the RV technique, indicating the diminishing of the phytotoxic nature. Subsequently, pot studies also indicated that the RV technique was coherent in managing noxious weeds.

Safety Level of Microorganism-Bearing Products Applied in Soil-Plant Systems

The indiscriminate use of chemical fertilizers adversely affects ecological health and soil microbiota provoking loss of soil fertility and greater pathogen and pest presence in soil-plant systems, which further reduce the quality of food and human health. Therefore, the sustainability, circular economy, environmental safety of agricultural production, and health concerns made possible the practical realization of eco-friendly biotechnological approaches like organic matter amendments, biofertilizers, biopesticides, and reuse of agro-industrial wastes by applying novel and traditional methods and processes. However, the advancement in the field of Biotechnology/Agriculture is related to the safety of these microorganism-bearing products. While the existing regulations in this field are well-known and are applied in the preparation and application of waste organic matter and microbial inoculants, more attention should be paid to gene transfer, antibiotic resistance, contamination of the workers and environment in farms and biotech-plants, and microbiome changes. These risks should be carefully assessed, and new analytical tools and regulations should be applied to ensure safe and high-quality food and a healthy environment for people working in the field of bio-based soil amendments.

Solid digestate biochar amendment on pig manure composting: Nitrogen cycle and balance

Effect of solid digestate biochar (DB) on nitrogen cycle and balance was evaluated during composting by adding DB into mixtures of pig manure and Lycium chinensis branch filings. Results indicated that DB addition improved composting microenvironment and increased the total N content of the final product. Furthermore, N balance calculation indicated that the NH₃ and N₂O emissions accounted for 72.14%-81.39% and 0.49%-2.37% of the total N loss without DB addition, respectively. After using DB, the N reductions in the form of NH₃ and N₂O reduced from 10.78% to < 5.73% and from 0.34% to < 0.041% of total N, respectively. Addition of DB affected N fixation with 92.32%-93.67% of total N fixed in the compost than that of the T1 treatment (85.63%). DB amendment enhanced the aerobic bacterial communities and hindered anaerobic bacterial growth, thus benefiting the NH₃ and N₂O emission mitigation and N conservation.