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

Enhanced organic degradation and microbial community cooperation by inoculating Bacillus licheniformis in low temperature composting

Microbial activity and interaction are the important driving factors in the start-up phase of food waste composting at low temperature. The aim of this study was to explore the effect of inoculating Bacillus licheniformis on the degradation of organic components and the potential microbe-driven mechanism from the aspects of organic matter degradation, enzyme activity, microbial community interaction, and microbial metabolic function. The results showed that after inoculating B. licheniformis, temperature increased to 47.8°C on day 2, and the degradation of readily degraded carbohydrates (RDC) increased by 31.2%, and the bioheat production increased by 16.5%. There was an obvious enhancement of extracellular enzymes activities after inoculation, especially amylase activity, which increased by 7.68 times on day 4. The inoculated B. licheniformis colonized in composting as key genus in the start-up phase. Modular network analysis and Mantel test indicated that inoculation drove the cooperation between microbial network modules who were responsible for various organic components (RDC, lipid, protein, and lignocellulose) degradation in the start-up phase. Metabolic function prediction suggested that carbohydrate metabolisms including starch and sucrose metabolism, glycolysis / gluconeogenesis, pyruvate metabolism, etc., were improved by increasing the abundance of related functional genes after inoculation. In conclusion, inoculating B. licheniformis accelerated organic degradation by driving the cooperation between microbial network modules and enhancing microbial metabolism in the start-up phase of composting.

Synergistic effects of chemical additives and mature compost on reducing H2S emission during kitchen waste composting

Additives could improve composting performance and reduce gaseous emission, but few studies have explored the synergistic of additives on H2S emission and compost maturity. This research aims to make an investigation about the effects of chemical additives and mature compost on H2S emission and compost maturity of kitchen waste composting. The results showed that additives increased the germination index value and H2S emission reduction over 15 days and the treatment with both chemical additives and mature compost achieved highest germination index value and H2S emission reduction (85%). Except for the treatment with only chemical additives, the total sulfur content increased during the kitchen waste composting. The proportion of effective sulfur was higher with the addition of chemical additives, compared with other groups. The relative abundance of H2S-formation bacterial (Desulfovibrio) was reduced and the relative abundance of bacterial (Pseudomonas and Paracoccus), which could convert sulfur-containing substances and H2S to sulfate was improved with additives. In the composting process with both chemical additives and mature compost, the relative abundance of Desulfovibrio was lowest, while the relative abundance of Pseudomonas and Paracoccus was highest. Taken together, the chemical additives and mature compost achieved H2S emission reduction by regulating the dynamics of microbial community.

Integrating bioprocess and metagenomics studies to enhance humic acid production from rice straw

Rice straw burning annually (millions of tons) leads to greenhouse gas emissions, and an alternative solution is producing humic acid with high added-value. This study aimed to examine the influence of a microbial consortium and other additives (chicken manure, urea, olive mill waste, zeolite, and biochar) on the composting process of rice straw and the subsequent production of humic acid. Results showed that among the fungal species, Thermoascus aurantiacus exhibited the most prominent impact in expediting maturation and improving compost quality, and Bacillus subtilis was the most abundant bacterial species based on metagenomics analysis. The highest temperature, C/N ratio reduction, and amount of humic acid production (Respectively in lab 61 °C, 54.67%, 298 g kg-1 and in pilot level 65 °C, 72.11%, 310 g kg-1) were related to treatments containing these microorganisms and other additives except urea. Consequently, T. aurantiacus and B. subtilis can be employed on an industrial scale as compost additives to further elevate quality. Functional analysis showed that the bacterial enzymes in the treatments had the highest metabolic activities, including carbohydrate and amino acid metabolism compared to the control. The maximum enzymatic activities were in the thermophilic phase in treatments which were significantly higher than that in the control. The research emphasizes the importance of identifying and incorporating enzymatically active strains that are suitable for temperature conditions, alongside the native strains in decomposing materials. This strategy significantly improves the composting process and yields high-quality humic acid during the thermophilic phase.

Effect of microbial inoculum on composting efficiency in the composting process of spent mushroom substrate and chicken manure

This work aimed to investigate the microbial mechanisms for the improvement of composting efficiency driven by the compound microbial inoculum (MI) (Bacillus subtilis SL-44, Enterobacter hormaechei Rs-189 and Trichoderma reesei) during co-composting of spent mushroom substrate (SMS) and chicken manure (CM). The treatments used in the study were as follows: 1) MI (inoculation with microbial inoculum), 2) CI (inoculation with commercial microbial inoculum), and 3) CK (without inoculation). The results demonstrated that MI increased the seed germination index (GI) by 25.11%, and contents of humus, humic acid (HA) and available phosphorus (AP) were correspondingly promoted by 12.47%, 25.93% and 37.16%, respectively. The inoculation of MI increased the temperature of the thermophilic stage by 3-7 °C and achieved a cellulose degradation rate of 52.87%. 16S rRNA gene analysis indicated that Actinobacteria (11.73-61.61%), Firmicutes (9.46-65.07%), Proteobacteria (2.86-32.17%) and Chloroflexi (0.51-10.92%) were the four major phyla during the inoculation composting. Bacterial metabolic functional analysis revealed that pathways involved in amino acid and glycan biosynthesis and metabolism were boosted in the thermophilic phase. There was a positive correlation between bacterial communities and temperature, humification and phosphorus fractions. The average dry weight, fresh weight and seedling root length in the seedling substrates adding MI compost were 1.13, 1.23 and 1.06 times higher than those of the CK, respectively. This study revealed that biological inoculation could improve the composting quality and efficiency, potentially benefiting the resource utilization of agricultural waste resources.

Dynamics and functions of biomarker taxa determine substrate-specific organic waste composting

Bacteria are an influential component of diverse composting microbiomes, but their structure and underlying dynamics are poorly understood. This study analyzed the bacterial communities of 577 compost datasets globally and constructed a substrate-dependent catalog with more than 15 million non-redundant 16S rRNA gene sequences. Using a random-forest machine-learning model, 30 biomarker taxa were identified that accurately distinguish between the food, sludge and manure waste composting microbiomes (accuracy >98 %). These biomarker taxa were closely associated with carbon and nitrogen metabolic processes, during which they contributed to the predominant stochastic process and are influenced by different factors in the substrate-specific composts. This is corroborated by the community topological characteristics, which feature the biomarkers as keystone taxa maintaining the bacterial network stability. These findings provide a theoretical basis to identify and enhance the biomarker-functional bacteria for optimizing the composting performance of different organic wastes.

Exploitation of microbial activities at low pH to enhance planetary health

Awareness is growing that human health cannot be considered in isolation but is inextricably woven with the health of the environment in which we live. It is, however, under-recognized that the sustainability of human activities strongly relies on preserving the equilibrium of the microbial communities living in/on/around us. Microbial metabolic activities are instrumental for production, functionalization, processing, and preservation of food. For circular economy, microbial metabolism would be exploited to produce building blocks for the chemical industry, to achieve effective crop protection, agri-food waste revalorization, or biofuel production, as well as in bioremediation and bioaugmentation of contaminated areas. Low pH is undoubtedly a key physical-chemical parameter that needs to be considered for exploiting the powerful microbial metabolic arsenal. Deviation from optimal pH conditions has profound effects on shaping the microbial communities responsible for carrying out essential processes. Furthermore, novel strategies to combat contaminations and infections by pathogens rely on microbial-derived acidic molecules that suppress/inhibit their growth. Herein, we present the state-of-the-art of the knowledge on the impact of acidic pH in many applied areas and how this knowledge can guide us to use the immense arsenal of microbial metabolic activities for their more impactful exploitation in a Planetary Health perspective.

Co-inoculation of phosphate-solubilizing bacteria and phosphate accumulating bacteria in phosphorus-enriched composting regulates phosphorus transformation by facilitating polyphosphate formation

This study aimed to explore the impact of co-inoculating phosphate-solubilizing bacteria (PSB) and phosphate accumulating bacteria (PAB) on phosphorus forms transformation, microbial biomass phosphorus (MBP) and polyphosphate (Poly-P) accumulation, bacterial community composition in composting, using high throughput sequencing, PICRUSt 2, network analysis, structural equation model (SEM) and random forest (RF) analysis. The results demonstrated PSB-PAB co-inoculation (T1) reduced Olsen-P content (1.4 g) but had higher levels of MBP (74.2 mg/kg) and Poly-P (419 A.U.) compared to PSB-only (T0). The mantel test revealed a significantly positive correlation between bacterial diversity and both bioavailable P and MBP. Halocella was identified as a key genus related to Poly-P synthesis by network analysis. SEM and RF analysis showed that pH and bacterial community had the most influence on Poly-P synthesis, and PICRUSt 2 analysis revealed inoculation of PAB increased ppk gene abundance in T1. Thus, PSB-PAB co-inoculation provides a new idea for phosphorus management.

Quorum sensing in different subcommunities becomes the key factor affecting the humification of the aerobic composting system with sauerkraut fermentation wastewater

Aerobic composting is an effective and harmless method to treat Sauerkraut fermentation wastewater (SFW). Given the limited understanding of the effect of quorum sensing (QS) on humification in subcommunities under acidic environments, a large-scale analysis was conducted to identify features that impact the response of QS to humification in different subcommunities. The results showed that the addition of SFW directly affected humification in subcommunities A and C, and the abundances of functional genes related to carbon fixation and carbon degradation were significantly increased at 7 and 15 d, respectively. In addition, subcommunity B indirectly affected humus production but regulated carbon metabolic pathways such as glycolysis/gluconeogenesis and pentose phosphate by QS with subcommunities B. These findings provide a novel perspective for analysing the regulation of humification in aerobic composting and suggest that composting has potential applications in organic wastewater treatment.

Comparing bacterial dynamics for the conversion of organics and humus components during manure composting from different sources

The study aimed to compare the differences in organic fractions transformation, humus components and bacterial community dynamics during manure composting from different sources, and to identify the key biotic and abiotic factors driving the humification process. Five types of manure [pig manure (PM), cow dung (CD), sheep manure (SM), chicken manure (CM), and duck manure (DM)] were used as raw materials for 30 days composting. The results showed the obvious difference of organic fractions decomposition with more cellulose degradation in CD and SM composting and more hemicellulose degradation in PM and CM composting. Composting of PM and CD contained significantly higher humus fractions than the other composts. Fluorescence spectra indicated that SM composting tended to form structurally stable humic acid fractions, while CM and DM tended to form structurally complex fulvic acid fractions. Pearson correlation analysis showed that humification process of composts in category A (PM, CD) with higher humification degree than category B (SM, CM, and DM) was positively correlated with lignin and hemicellulose degradation. Bioinformatics analysis found that Lysinibacillus promoted the degradation of hemicellulose and the conversion of fulvic to humic acid in the composts of category A, and in category B, Thermobifida, Lactobacillus, and Ureibacillus were key genera for humic acid formation. Network analysis indicated that bacterial interaction patterns had obvious differences in composting with different humus and humification levels.

Microbial Risks Caused by Livestock Excrement: Current Research Status and Prospects

Livestock excrement is a major pollutant yielded from husbandry and it has been constantly imported into various related environments. Livestock excrement comprises a variety of microorganisms including certain units with health risks and these microorganisms are transferred synchronically during the management and utilization processes of livestock excrement. The livestock excrement microbiome is extensively affecting the microbiome of humans and the relevant environments and it could be altered by related environmental factors as well. The zoonotic microorganisms, extremely zoonotic pathogens, and antibiotic-resistant microorganisms are posing threats to human health and environmental safety. In this review, we highlight the main feature of the microbiome of livestock excrement and elucidate the composition and structure of the repertoire of microbes, how these microbes transfer from different spots, and they then affect the microbiomes of related habitants as a whole. Overall, the environmental problems caused by the microbiome of livestock excrement and the potential risks it may cause are summarized from the microbial perspective and the strategies for prediction, prevention, and management are discussed so as to provide a reference for further studies regarding potential microbial risks of livestock excrement microbes.

Assessing the climate change mitigation potential from food waste composting

Food waste is a dominant organic constituent of landfills, and a large global source of greenhouse gases. Composting food waste presents a potential opportunity for emissions reduction, but data on whole pile, commercial-scale emissions and the associated biogeochemical drivers are lacking. We used a non-invasive micrometeorological mass balance approach optimized for three-dimensional commercial-scale windrow compost piles to measure methane (CH₄), nitrous oxide (N₂O), and carbon dioxide (CO₂) emissions continuously during food waste composting. Greenhouse gas flux measurements were complemented with continuous oxygen (O₂) and temperature sensors and intensive sampling for biogeochemical processes. Emission factors (EF) ranged from 6.6 to 8.8 kg CH₄-C/Mg wet food waste and were driven primarily by low redox and watering events. Composting resulted in low N₂O emissions (0.01 kg N₂O-N/Mg wet food waste). The overall EF value (CH₄ + N₂O) for food waste composting was 926 kgCO₂e/Mg of dry food waste. Composting emissions were 38-84% lower than equivalent landfilling fluxes with a potential net minimum savings of 1.4 MMT CO₂e for California by year 2025. Our results suggest that food waste composting can help mitigate emissions. Increased turning during the thermophilic phase and less watering overall could potentially further lower emissions.

Response characteristics of Flax retting liquid addition during chicken manure composting: Focusing on core bacteria in organic carbon mineralization and humification

To explore the applicability of flax retting liquid (FRL) addition, the physicochemical properties, microbial community structure and function, carbon conversion and humus (HS) formation were assessed during chicken manure (CM) aerobic composting. Compared with the control group, the addition of FRL increased the temperature at thermophilic phase, while the microbial mass carbon content (MBC) in SCF and FRH groups raised to 96.1±0.25 g/Kg and 93.33±0.27 g/Kg, respectively. Similarly, FRL also improved the concent of humic acid (HA) to 38.44±0.85 g/Kg, 33.06±0.8 g/Kg, respcetively. However, fulvic acid (FA) decreased to 30.02±0.55g/Kg, 31.4±0.43 g/Kg, respectively and further reduced CO₂ emissions. FRL influenced the relative abundance of Firmicutes at thermophilic phase and Ornithinimicrobium at maturity phase. Additionally, FRL strengthen the association among flora and reduce the number of bacteria, which was negative correlated with HA and positive with CO₂ during composting. These findings offer powerful technological support for improving agricultural waste recycling.

Composting pig manure with nano-zero-valent iron amendment: Insights into the carbon cycle and balance

The effectiveness of nano-zero-valent-iron (NZVI) addition during composting of pig manure (PM) was investigated. Different dosages of NZVI were mixed with PM substrate during a 50 days composting process. The results revealed that the higher share of NZVI addition, the higher OM degradation rate is. On contrary, it was observed that the higher share of NZVI addition, the lower the fulvic acid and the humin degradation rate is. Meanwhile, NZVI amendment increased the CO₂ and CH₄ emissions by 29-47 % and 53-57 %, respectively. The in-depth analysis showed that NZVI addition increased the activity of Sphaerobacter and Luteimonas, which eventually led to the degradation of hard-to-degrade OM faster. Additionally, NZVI was found to increase the filtration of microorganisms, reducing the toxicity and hygiene of compost products. No significant improvement in humic substance enhancement was observed during composting with NZVI addition but improved OM degradation.

Effects of chemical additives and mature compost on reducing nitrogen loss during food waste composting

This study is aimed at adding different types of mature compost and sulfur powder, as additives into food waste composting to investigate the effect on nitrogen loss and compost maturity. The composting experiment used the in-vessel composting method and was conducted continuously for 15 days. High-throughput sequencing was used to analyze the bacterial community during composting. Results showed that the secondary fermentation mature compost mixed with sulfur powder group had the most reduction of ammonia emission (56%) and the primary fermentation mature compost amendments were the most effective for nitrous oxide emission reduction (37%). The temperature, pH, and nitrogen forms of transformation of the pile significantly affect the nitrogen loss during composting. Firmicutes helped to promote the rapid warming of the pile, and Actinobacteria and Proteobacteria played an important role in decomposition of organic matter. Thermobifida and Ureibacillus had a main contribution to the rapid degradation of organic matter in the process of composting. The relative abundance of nitrogen-fixing bacteria was higher, and the relative abundance of predominantly ammonifying and denitrifying bacteria was lower than the control group, with the addition of different additives.

Impact of aeration rate on phosphorus conversion and bacterial community dynamics in phosphorus-enriched composting

This study was to investigate the effects of different aeration rates on phosphorus (P) conversion and bacterial community dynamics in P-enriched composting by 16S rRNA gene sequencing, sequential P fractionation, network analysis and structural equation model (SEM). Results indicated that Olsen P content increased by 138 %, 150 %, 121 % after composting with aeration rate (L kg-1 DM min-1) at 0.2 (AR0.2), 0.4 (AR0.4) and 0.6 (AR0.6). AR0.4 was more conducive to enhance P solubilization efficacy and available P accumulation. Redundancy analysis indicated Lactobacillus, Spartobacteria and Pseudomonas were key bacteria associated with HCl-Pi especially in AR0.2 and AR0.4. Network analysis showed that increased aeration rate enhanced the connection and function homoplasy among modules and AR0.4 had more orderly community organization for key bacteria to solubilize P in directly and indirectly biotic way. SEM suggested indirectly biotic P-solubilization had more contribution than directly biotic way mainly by phosphate-solubilizing bacteria.