The succession of GH6 cellulase-producing microbial communities and temporal profile of GH6 gene abundance during vermicomposting of maize stover and cow dung

From kinetics to synergy: Elucidating the action characterization of GH5 processive endoglucanase M3-1

The economic viability of cellulose biotransformation remains constrained by high enzyme costs, with processive endoglucanases emerging as promising candidates due to their dual-function hydrolysis mechanism. However, comprehensive kinetic and synergistic analyses of these enzymes are notably limited. This study investigates the kinetic properties of GH5 processive endoglucanase (M3-1) through various kinetic models. Inverse Michaelis-Menten analysis revealed M3-1's superior substrate recognition capacity, demonstrating 95.5 % productive binding site coverage compared to 48.8 % in non-processive endoglucanases. This enhanced efficiency is attributed to M3-1's distinctive structural features, particularly its open and deep cleft configuration. Pre-steady-state kinetics identified substrate association as the rate-limiting step, providing crucial direction for enzyme engineering efforts. Synergistic studies with cellobiohydrolase (CBH) demonstrated remarkable degradation synergy (DS value up to 8.2 on filter paper) and improved substrate resistance compared to traditional EG/CBH combinations. We propose a novel bidirectional degradation mechanism for the M3-1/CBH system, operating both inside-out and outside-in. The effectiveness of M3-1/CBH combination was further enhanced by up to 320 % through the addition of nonionic surfactants and expansin. These findings advance our understanding of processive endoglucanases and their potential applications in biomass conversion.

The impact of rumen microbial composition on apparent digestibility, rumen fermentation and metabolism in Sanhe cows and Holstein cows of different parities under identical dietary conditions

Previous studies have discussed the association between serum metabolism and lactation performance among Sanhe and Holstein cows of different parities and found that the metabolic profiles of these two breeds vary differently with parity. Since the rumen is the central organ for nutrient absorption and production transformation in dairy cows, it remains unknown whether the differences observed under the same dietary conditions are related to the structure of the rumen microbiome. This study measured the apparent digestibility and rumen fermentation parameters of Sanhe cows (S1/S2/S3/S4) and Holstein cows (H1/H2/H3/H4) across four parities and generated a comprehensive rumen microbiome dataset using high-throughput sequencing technology. Significant differences in dry matter digestibility (p = 0.001) and ammonia nitrogen (p = 0.024) were observed among the S groups, with higher trends of various VFA contents in S1 (0.05 < p < 0.1). The H group showed significant differences in crude protein digestibility (p = 0.001), higher isovaleric acid content in H1 (p = 0.002), and the lowest acetate to propionate ratio (p = 0.002) in H3. Metagenomic sequencing results indicated consistency between rumen microbiome patterns and metabolic changes, with S1 distinctly different from S2/S3/S4, and H1 and H2 different from H3 and H4. The species composition of the rumen microbiome was similar between Sanhe and Holstein cows, but differences in abundance were noted. Rhizophagus , Neocallimastix, and Piromyces were more abundant in S1, H1, and H2, and pathways such as autophagy-animal, plant-pathogen interaction, and endocytosis were significantly enriched in these parities. Multiparous Sanhe cows had higher abundances of ATP-binding cassette transporters pathways. Additionally, CAZymes such as GH84 and GH37 were significantly associated with differential physiological indicators and milk traits. In conclusion, this study reveals the complex relationship between rumen microbiota and metabolic characteristics in Sanhe and Holstein cows of different parities, indicating that changes in the structure of the rumen microbiome may be key factors affecting lactation performance and metabolic differences in dairy cows.

Exploring strategies for kitchen waste treatment and remediation from the perspectives of microbial ecology and genomics

Nowadays, the rapid growth of population has led to a substantial increase in kitchen waste and wasted sludge. Kitchen waste is rich in organic matter, including lignocellulose. Synergistic treatment involving kitchen waste and wasted sludge can enhance treatment process. Vermicomposting can facilitate microbial activities on organic matter. Nevertheless, the underlying mechanisms remain unclear. In this study, metagenomics was used to analyze microbial functional genes in vermicomposting. Redundancy analysis found that TOC, TN and DTN adversely affect earthworm growth and reproduction. The relative abundance of Bacteroidetes and Firmicutes increased with earthworms, thereby potentially augmenting lignocellulose degradation. The predominant functional genes included amino acid, carbohydrate, and inorganic ion conversion and metabolism. Metagenomics analysis demonstrated that GH1, GH3, GH5, GH6, GH9, GH12, GH44, GH48 and GH74, GT41, GT4, GT2, and GT51 were dominant. Furthermore, there was higher abundance of carbohydrate-active enzymes in the vermicomposting, particularly during the later phases (30-45 days). Co-occurrence network revealed that Cellvibrio in the vermicomposting exhibited a relatively dense positive correlation with other microbial groups. The findings elucidated the mechanism of vermicomposting as a promising approach for managing kitchen waste and wasted sludge.

Unraveling the synergistic interplay of sulfur and wheat straw in heterotrophic-autotrophic denitrification for sustainable groundwater nitrate remediation

Nitrate pollution in groundwater is a global environmental issue that poses significant threats to human health and ecological security. This study focuses on elucidating the mechanisms of heterotrophic-autotrophic cooperative denitrification (HAD) by employing wheat straw and elemental sulfur as electron donors in varying proportions. The research initially underscores that heterotrophic denitrification (HD) accelerates the denitrification process due to its high-energy metabolism. However, as readily degradable organic matter diminished, reliance on more complex substrates such as lignocellulose posed a challenge to HD. This marks a pivotal transition towards autotrophic denitrification (AD), which, despite a slower initial rate, exhibits a more sustained denitrification performance. A low proportion of heterotrophic denitrification layer (e.g., 3:1) at the bottom facilitating efficient and sustainable denitrification. HD is capable of simultaneous removal of nitrates and nitrites, whereas AD demonstrates a higher affinity for nitrates, with nitrite accumulation reaching 100% at high influent nitrate concentrations (100 mg/L). HD not only provides the necessary alkaline environment for AD but also reduces sulfate production, whereas AD utilizes the residual organic carbon and ammonia produced by HD. The heterotrophic layer is characterized by a diverse community, whereas the autotrophic layer is predominantly composed of Thiobacillus. By delineating the interactive mechanisms and characteristics of HAD, this study highlights the importance of balancing heterotrophic and autotrophic activities for the effective remediation of groundwater nitrates.

Response of soil microbial glycoside hydrolase family 6 cellulolytic population to lignocellulosic biochar reveals biochar stability toward microbial degradation

Biochar produced from lignocellulosic biomass offers an opportunity to recycle waste into a valuable soil amendment. The application of biochar has been proposed to mitigate climate change by sequestering carbon in the soil. However, the field impact of biochar treatment on the cellulolytic microbial populations involved in the earlier steps of cellulose degradation is poorly understood. A field trial spanning three consecutive crop cycles of Zea mays was conducted in a degraded tropical Ultisol of Peninsular Malaysia. The soil was amended with two contrasting biochar made from oil palm kernel shells (pyrolyzed at 400°C) and rice husks (gasified at 800°C) with or without fertilizer supplementation. Soil samples were taken at each harvesting stage and analyzed for total organic carbon, labile active organic carbon, total cellulase, and β-glucosidase. Microbial glycoside hydrolase family 6 (GH6) cellulase genes and transcripts, involved in the early steps of cellulose degradation, were quantified from the extracted soil deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), respectively. Total organic carbon, labile active organic carbon, and β-glucosidase activity were significantly increased, while no effect on total cellulase activity was found. Both biochars stimulated the total population (DNA-derived) abundance of soil microorganisms harboring the GH6 cellulase genes. The biochar amendment did not affect the active population (RNA-derived) of the GH6 cellulolytic community, showing no significant changes in transcript expression. This indirectly corroborates the role of biochar as a potential carbon sequester in the soil.

β-Glucosidase-producing microbial community in composting: Response to different carbon metabolic pressure influenced by biochar

Poor management of agricultural waste will cause a lot of environment pollution and the composting process is one of the most effective measures for resource reuse of agricultural waste. β-Glucosidase-producing microbial communities play a vital role in cellulose degradation during composting and regulate cellulase production via differentially expressed glucose/non-glucose tolerant β-glucosidase genes. Biochar is widely used as an amendment in compost to accelerate cellulose degradation during composting. However, Biochar-mediated impacts on β-glucosidase-producing microbial communities in compost are unclear. Here, different carbon metabolism pressures were set in natural and biochar compost to elucidate the regulation mechanism and interaction of the β-glucosidase microbial community. Results showed that the addition of biochar decreased the transcription of β-glucosidase genes and led to a reduction of β-glucosidase activity. Micromonospora and Cellulosimicrobium were the predominant functional communities determining cellulose degradation during biochar compost. Biochar addition strengthened the response of the functional microbial community to carbon metabolism pressure. And adding biochar altered the key β-glucosidase-producing microbial communities, influencing cellulase and the interaction between these communities to respond to the different carbon metabolic pressure of compost. Biochar also shifted the co-occurrence network of β-glucosidase-producing microbial community by changing the keystone species. Furthermore, co-occurrence network analysis revealed that high glucose decreased the complexity and stability of the functional microbial network. Most functional microorganisms from Streptomyces produce non-glucose tolerant β-glucosidase, which were the key bacterial communities affecting β-glucosidase activity in the non-glucose treatment. This study provides new insights into the response of functional microbial communities and the regulation of enzyme production during the transformation of cellulosic biomass.

The temporal profile of GH1 gene abundance and the shift in GH1 cellulase-producing microbial communities during vermicomposting of corn stover and cow dung

Vermicomposting is a promising method for corn stover management to achieve bioresource recovery and environmental protection. Most β-glucosidases, which limit the cellulose degradation rate during vermicomposting of corn stover, belong to glycoside hydrolase family 1 (GH1). This study was conducted with different earthworm densities to quantify the GH1 gene abundance and investigate the evolution of GH1 cellulase-producing microbial communities using qPCR and pyrosequencing. The results showed that β-glucosidase activity, GH1 gene abundance, TOC, and microbial communities carrying the GH1 gene were affected by processing time and earthworm density. After introducing earthworms, β-glucosidase activity increased to 1.90-2.13 U/g from 0.54 U/g. The GH1 gene abundance of treatments with earthworms (5.82E+09-6.70E+09 copies/g) was significantly higher than that of treatments without earthworms (2.48E+09 copies/g) on Day 45. Earthworms increased the richness of microbial communities. The relative abundances of Sphingobium and Dyadobacter, which are dominant genera harboring the GH1 gene, were increased by earthworms to peak values of 23.90% and 11.20%, respectively. Correlation analysis showed that Sphingobium, Dyadobacter, Trichoderma, and Starkeya were positively associated with β-glucosidases. This work sheds new light on the mechanism of cellulose degradation during vermicomposting at the molecular level.

Turning earthworms into moonworms: Earthworms colonization of lunar regolith as a bioengineering approach supporting future crop growth in space

The earthworms beneficial effects on soils may be promising to improve lunar soil fertility, enabling the use of local substrates for space farming. Herein, we investigated the effects of the lunar regolith simulant (LHS-1) at different concentrations in cow manure mixtures on the survival and fitness of Eisenia fetida. During 14 and 60-day experiments, although E. fetida showed an increased mortality with LHS-1 alone, most of the population survived. More numerous tunnels were observed when exposed to the higher concentrations of LHS-1 (poor in nutrients for earthworms). This may be related to an increased mobility for food search. The cocoons production was not affected by different substrate treatments, except for the highest concentration of LHS-1. No effects of different LHS-1 concentrations on the amount of ingested substrate were recorded. This study shows that E. fetida can potentially colonize lunar regolith representing a future valuable biological tool for supporting crops growth on the Moon.

Different ratios of Canna indica and maize-vermicompost as biofertilizers to improve soil fertility and plant growth: A case study from southwest China

Vermicomposting is recommended as an eco-friendly technology for an organic amendment to avoid the excessive use of inorganic fertilizers, which are causing environmental pollution. Here, this study evaluated soil fertility and plant growth after vermicompost amendment using reclaimed wetland plants and manure. A pot experiment was conducted to assess the seven treatments for nutrient recovery and plant growth: a control group without any fertilization (CK); four groups with vermicompost prepared from different ratios of ecological wetland plant residues, maize, and pig manure (V1, 4:6; V2, 5:5; V3, 6:6; and V4, 7:3); one group with only Canna indica (V5, Ci), and a group with synthetic fertilizers (NPK). The results showed the remarkable impacts of Ci-vermicompost and different ratios of organic fertilizer on soil fertility and plant height (28.8%) as major outcomes. In addition, vermicompost substantially increased soil total nitrogen (60.5%), soil organic matter (60.9%) including dissolved organic carbon (52.2%), and shoot biomass (V4, three-fold increase) compared with NPK and CK. Overall, the findings of this study suggest that vermicomposting combined with wetland plants is a feasible method for organic amendments and offers an innovative approach for recycling ecological waste to produce nutrient-rich organic fertilizers, reduce environmental damage, and improve crop production.

Metagenomic analysis reveals the microbial degradation mechanism during kitchen waste biodrying

Biodrying is a treatment to remove moisture using bio-heat generated during organic degradation. Organic matter degradation and microbial metabolism were studied during the whole kitchen waste biodrying, using metagenomic analysis. After the 25-day biodrying process, carbohydrate, protein and lipid contents decreased by 83.7%, 27.8% and 79.3%, respectively, and their degradation efficiencies increased after the thermophilic phase. Lipase activity exceeded 10 mmol d^-1 g^-1 throughout biodrying. Cellulase and lipase activities recovered by 2.21% and 5.77%, respectively, after the thermophilic phase, while the protease activity had a maximum increment of 347%. Metabolic analysis revealed that carbohydrate, amino acid and lipid metabolism was possibly inhibited by the high temperature, but the relative abundances of related predicted functions recovered by more than 0.9%, 7% and 11%, respectively, by the end of biodrying. Protein function prediction suggests that β-oxidation, fatty acid biosynthesis, and the degradation of cellulose and chitin were possibly enhanced during the thermophilic phase. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that leucine, isoleucine and lysine could ultimately degraded to acetyl-CoA. Weissella, Aeribacillus and Bacillus were the genera with the most enriched functional genes during the whole biodrying process. These findings help elucidate the microbial degradation processes during biodrying, which provides further scientific support for improving the application of biodrying products.

Role of multistage inoculation on the co-composting of food waste and biogas residue

Effect of diverse Lactobacillus amylophilus, Geobacillus thermoleovorans, and Bacillus subtilis inoculation patterns on the co-composting performance of food waste and biogas residue was explored. Experimental results revealed that, compared to the single-stage inoculation and non-inoculation groups, the multistage inoculation pattern prolonged the thermophilic period during composting, consequently improving organic matter decomposition and humification [with a high germination index (120.9%)]. In addition, it could promote the development of humic substances [with a high humus index (4.3) and biological index (1.4)] and lower emissions of carbon dioxide (CO₂), methane (CH₄), and ammonia (NH₃). Additionally, it could improve the microbial variety and the amounts of functional bacteria (i.e., Chloroflexi) in compost, which might be advantageous for the decomposition of refractory organic materials and plant growth. Therefore, the multistage inoculation pattern is recommended for organic waste composting in terms of its gas emissions, compost quality and efficacy benefits.