Genomic and Transcriptome Analyses of a Thermophilic Bacterium Geobacillus stearothermophilus B5 Isolated from Compost Reveal Its Enzymatic Basis for Lignocellulose Degradation

Upgrade from aerated static pile to agitated bed systems promotes lignocellulose degradation in large-scale composting through enhanced microbial functional diversity

Composting presents a viable management solution for lignocellulose-rich municipal solid waste. However, our understanding about the microbial metabolic mechanisms involved in the biodegradation of lignocellulose, particularly in industrial-scale composting plants, remains limited. This study employed metaproteomics to compare the impact of upgrading from aerated static pile (ASP) to agitated bed (AB) systems on physicochemical parameters, lignocellulose biodegradation, and microbial metabolic pathways during large-scale biowaste composting process, marking the first investigation of its kind. The degradation rates of lignocellulose including cellulose, hemicellulose, and lignin were significantly higher in AB (8.21%-32.54%, 10.21%-39.41%, and 6.21%-26.78%) than those (5.72%-23.15%, 7.01%-33.26%, and 4.79%-19.76%) in ASP at three thermal stages, respectively. The AB system in comparison to ASP increased the carbohydrate-active enzymes (CAZymes) abundance and production of the three essential enzymes required for lignocellulose decomposition involving a mixture of bacteria and fungi (i.e., Actinobacteria, Bacilli, Sordariomycetes and Eurotiomycetes). Conversely, ASP primarily produced exoglucanase and β-glucosidase via fungi (i.e., Ascomycota). Moreover, AB effectively mitigated microbial stress caused by acetic acid accumulation by regulating the key enzymes involved in acetate conversion, including acetyl-coenzyme A synthetase and acetate kinase. Overall, the AB upgraded from ASP facilitated the lignocellulose degradation and fostered more diverse functional microbial communities in large-scale composting. Our findings offer a valuable scientific basis to guide the engineering feasibility and environmental sustainability for large-scale industrial composting plants for treating lignocellulose-rich waste. These findings have important implications for establishing green sustainable development models (e.g., a circular economy based on material recovery) and for achieving sustainable development goals.

Dynamic changes in bacterial communities in three species of corals during the 2017 bleaching event in subtropical Hong Kong waters

Bacteria play important roles in coral health, yet little is known about the dynamics of coral-associated bacterial communities during coral bleaching. Here, we reported the dynamic changes of bacterial communities in three scleractinian corals (Montipora peltiformis, Pavona decussata and Platygyra carnosa) during and after bleaching through amplicon sequencing. Our results revealed that the bacterial composition and dominant bacteria varied among the three coral species. The higher susceptibility of M. peltiformis to bleaching corresponded to a lower bacterial community diversity, and the dominant Synechococcus shifted in abundance during the bleaching and coral recovery phases. The resilient P. decussata and P. carnosa had higher bacterial diversity and a more similar bacterial composition between the healthy and bleached conditions. Overall, our study reveals the dynamic changes in coral-associated microbial diversity under different conditions, contributing to explaining the differential susceptibility of corals to extreme climate conditions.

Effect of Thermophilic Microbial Agents on Crude Fiber Content, Carbohydrate-Active Enzyme Genes, and Microbial Communities during Chinese Medicine Residue Composting

The objective of this study was to investigate the impact of thermophilic bacteria on crude fiber content, carbohydrate-active enzyme (CAZyme) genes, and associated microbial communities during Chinese medicine residues composting. The study examines changes over 15 days of composting with (T) and without (CK) thermophilic microbial agents. Results show that the group T compost temperature reached a maximum of 71.0 °C and remained above 70 °C for 2 days, while the group CK maximum temperature was only 60.9 °C. On Day 15, the seed germination index (GI) of group T reached 98.7%, while the group CK GI was only 56.7%. After composting, the degradation rates of cellulose, hemicellulose, and lignin in group T increased by 5.1, 22.5, and 18.5%, respectively, compared to those in group CK. Thermophilic microbial agents changed the microbial communities related to CAZymes, increasing unclassified_o_Myxococcales and Sphaerobacter abundance and reducing Acinetobacter and Sphingobacterium abundance. Thermophilic microbial agents also increased the abundance of the GT4, GT2_Glycos_transf_2, and AA3 gene families. These results show that thermophilic microbial agents can increase composting temperature, accelerate compost maturation, and promote crude fiber degradation. Therefore, they have broad application potential.

Effect of inoculating thermophilic bacterial consortia on compost efficiency and quality

The objective of this study was to investigate the potential effects of thermophilic bacterial consortia on compost efficiency and quality. The application of bacterial consortia resulted in an earlier onset of the thermophilic period (THP), an increased upper temperature limit, and an extended duration of the THP by 3-5 days compared to the control group (CK). Microbial inoculation significantly improved the efficiency of organic matter degradation, as well as the content of water-soluble nitrogen (WSN) and humic acid-carbon (HAC). In the case of consortium Ⅱ inoculation (T2), the activities of cellobiohydrolase, β-glucosidase, and protease were increased by 81.81 %, 70.13 %, and 74.09 % at the THP respectively compared to CK. During the maturation stage, T2 also exhibited the highest PV, n/PIII, n value (1.33) and HAC content (39.53 mg·g-1), indicating that inoculation of consortium Ⅱ effectively promoted substrate maturity and product quality. Moreover, this inoculation effectively optimized the bacterial communities, particularly the growth of Planococcus, Chelatococcus, and Chelativorans during the composting, which were involved in carbon and nitrogen conversion or HAC synthesis. Carbohydrate and amino acid metabolism, and membrane transport were predominant in the consortia-inoculated samples, with an increased gene abundance, suggesting that inoculation contributed to promoting the biodegradation of lignocellulose and the exchange of favorable factors. In conclusion, this study demonstrates that inoculating thermophilic bacterial consortia has a positive impact on enhancing the resource utilization efficiency of agricultural waste and improving the quality of compost products.

Identification of driving factors of lignocellulose degrading enzyme genes in different microbial communities during rice straw composting

The study aims to clarify the driving factors of lignocellulose degrading enzyme genes abundance during rice straw composting. Lignocellulose degrading strains b4 (Bacillus subtilis), z1 (Aspergillus fumigatus) were inoculated into pure culture, respectively. Meanwhile, three rice straw composting groups were set up, named CK (control), B4 (inoculating b4) and Z1 (inoculating z1). Results confirmed the composition of functional genes related to lignocellulose metabolism for strains. Lignocellulose degrading enzyme genes abundance was up-regulated by inoculation, which promoted the decomposition of lignocellulose. Modular microorganisms, such as Actinobacteria, Proteobacteria, Ascomycetes and Basidiomycetes, were identified as driving factors that affected lignocellulose degrading enzyme genes abundance. pH, organic matter and soluble sugar content affected lignocellulose degrading enzyme genes abundance by affecting modular microorganisms. In addition, a potential priming effect was put forward based on the driving factors. This study provided theoretical guidance for regulating the abundance of lignocellulose degrading enzyme genes to promote lignocellulose degradation.

Effects of carbamazepine on gut microbiota, ARGs and intestinal health in zebrafish

Carbamazepine (CBZ) in the aquatic environment is recognized as a potential threat to aquatic organisms and public health. However, the response of organism intestinal health, resistome, microbiota, and their relationship after CBZ exposure has been rarely reported. This study aimed to explore the impacts of CBZ on gut microbiota, antibiotic resistance genes (ARGs) and the expression of intestinal health related genes as well as their interaction using the zebrafish model. 16 S ribosomal RNA sequencing indicated CBZ altered the composition of gut microbiota. Using high-throughput quantitative polymerase chain reaction (HT-qPCR), we found the number and abundance of ARGs were impacted by CBZ levels and exposure duration. We also observed the upregulated expression of the pro-inflammatory gene IL6 and downregulated expression of toll-like receptor gene TLR2 and intestinal barrier gene TJP2a at different exposure times. Correlation analyses revealed that Geobacillus, Rhodococcus, Ralstonia, Delftia, Luteolibacter and Escherichia-Shigella might be the main bacterial genera carrying ARGs. Meanwhile, Cetobacterium and Aeromonas could be the dominant bacteria affecting intestinal health related genes. Our results could contribute to understanding the health risks of CBZ to the intestinal microecology of aquatic animals.

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.

Deciphering the dominant components and functions of bacterial communities for lignocellulose degradation at the composting thermophilic phase

The decomposition and transformation of organic matters during composting process are performed by various microorganisms. However, the bacterial communities and their functions usually vary with composting materials. Here the dominant bacterial genera and their functions were identified at the thermophilic phase during composting of mulberry branches with silkworm excrement (MSE), pig manure (MPM) and cow manure (MCD). The activities of β-glucosidase and endoglucanase were highest for MCD (1.31 and 17.15 µg g^-1 min^-1) and lowest for MPM (0.92 and 14.22 µg g^-1 min^-1). Random Forest model and correlation analysis revealed that Stenotrophomonas, Bacillus, and Sinibacillus were the dominant bacterial genera involved in lignocellulose degradation regardless of composting materials. Carbohydrate metabolism, amino acid metabolism, and DNA replication and repair were primary functions of the bacterial communities for the three types of composting. The quantification of lignocellulose degradation genes further verified the dominant functions of the bacterial communities.

Food waste composting based on patented compost bins: Carbon dioxide and nitrous oxide emissions and the denitrifying community analysis

Mature compost and rice bran were used as bulking agents to perform Food Waste Rapid Composting (FWRC) in a patented composting bin. The characteristics of CO₂ and N₂O emission and the denitrifying community were investigated. The release of CO₂ and N₂O concentrated in the early composting stage and reduced greatly after 28 h, and the N₂O emission peak of the treatment with mature compost was 8.5 times higher than that of rice bran. The high N₂O generation resulted from massive denitrifying bacteria and NO_x^--N in the composting material. The relative abundances of denitrifiers, correspondingly genes of narG and nirK were much higher in the treatment with mature compost, which contributed to the N₂O emission. Moreover, the correlation matrices revealed that N₂O fluxes correlated well with moisture, pH, temperature, and the abundances of nirK and nosZ genes during FWRC.

Safety Evaluation and Whole Genome Sequencing of Aspergillus japonicas PJ01 Reveal Its Potential to Degrade Citrus Segments in Juice Processing

Aspergillus japonicas PJ01 (A. japonicas PJ01) is a strain isolated from the rotten branches. In previ-ous studies, it was shown that it can produce complex enzymes to degrade polysaccharide com-ponents. In this study, we evaluated the safety of its crude enzyme solution. Acute oral toxicity, subchronic toxicity, micronucleus and sperm malformation tests all validated the high biologi-cal safety for the crude enzymes. Secondly, we carried out the citrus segment degradation ex-periment of crude enzyme solution. Compared with the control group, the crude enzyme solu-tion of A. japonicas PJ01 can completely degrade the segments in 50 min, which provides the basis for enzymatic peeling during juice processing. The whole genome sequencing showed that the genome of A. japonicus PJ01 has a GC content of 51.37% with a size of 36204647 bp, and encoded 10070 genes. GO, COG, KEGG and CAZy databases were used in gene annotation analyses. Pathway enrichment showed many genes related to carbohydrate metabolism, rich in genes re-lated to pectinase, xylanase and carboxylcellulase. Therefore, the complex enzyme produced by A. japonicus PJ01 can be used in gizzard juice processing to achieve efficient enzymatic decapsu-lation.