Molecular understanding of autotrophic CO2-fixing bacterial communities in composting based on RuBisCO genes analysis

Reducing carbon and nitrogen loss by shortening the composting duration based on seed germination index (SCD@GI): Feasibilities and challenges

Addressing carbon (C) and nitrogen (N) losses through composting has emerged as a critical environmental challenge recently, and how to mitigate these losses has been a hot topic across the world. As the emissions of carbonaceous and nitrogenous gases were closely correlated with the composting process, the feasibility of composting duration shortening on C and N loss needs to be explored. Therefore, the goal of this paper is to find evidence-based approaches to reduce composting duration, utilizing the seed germination index as a metric (SCD@GI), for assessing its efficiency on C and N loss reductions as well as compost quality. Our findings reveal that the terminal seed germination index (GI) frequently surpassed the necessary benchmarks, with a significant portion of trials achieving the necessary GI within 60 % of the standard duration. Notably, an SCD@GI of 80 % resulted in a reduction of CO2 and NH3 by 21.4 % and 21.9 %, respectively, surpassing the effectiveness of the majority of current mitigation strategies. Furthermore, compost quality, maturity specifically, remained substantially unaffected at a GI of 80 %, with the composting process maintaining adequate thermophilic conditions to ensure hygienic quality and maturity. This study also highlighted the need for further studies, including the establishment of uniform GI testing standards and comprehensive life cycle analyses for integrated composting and land application practices. The insights gained from this study would offer new avenues for enhancing C and N retention during composting, contributing to the advancement of high-quality compost production within the framework of sustainable agriculture.

Paddy cultivation in degraded karst wetland soil can significantly improve the physiological and ecological functions of carbon-fixing resident microorganisms

Microorganisms play an important role in carbon fixation in karst wetland soils. However, the carbon fixation capacity of karst wetland soils and active microorganisms involved in the carbon fixation process are poorly understood. In this study, carbon fixation capacity and active microorganisms involved in the fixation of inorganic carbon into organic carbon were studied in native, naturally degraded, and reclaimed karst wetland soils by the combination of stable isotope probing (SIP) and high-throughput sequencing. Under light conditions, the soil carbon fixation capacity ranked: the reclaimed wetland soil (1.58 mg C kg-1 day-1) > native wetland soil (1.43 mg C kg-1 day-1) > degraded wetland soil (0.62 mg C kg-1 day-1). In the dark, the soils ranked: the native wetland soil (0.24 mg C kg-1 day-1) > reclaimed wetland soil (0.18 mg C kg-1 day-1) > degraded wetland soil (0.06 mg C kg-1 day-1). Active microorganisms fixing inorganic carbon in the karst wetland soils were mainly Sulfurovum, Thermovirga, Dethiosulfatibacter, Allochromatium, Methylorubrum, and Bradyrhizobium. Thus, paddy cultivation can restore the carbon fixation capacity of microorganisms in the degraded karst wetland soil. This study provides an experimental basis for improving soil carbon fixation capacity and repairing degraded soil in karst wetlands.

Mammalian carcass decay increases carbon storage and temporal turnover of carbon-fixing microbes in alpine meadow soil

Corpse decomposition is of great significance to the carbon cycle of natural ecosystem. Carbon fixation is a carbon conversion process that converts carbon dioxide into organic carbon, which greatly contributes to carbon emission reduction. However, the effects of wild animal carcass decay on carbon-fixing microbes in grassland soil environment are still unknown. In this research, thirty wild mammal (Ochotona curzoniae) corpses were placed on alpine meadow soil to study the carbon storage and carbon-fixing microbiota succession for a 94-day decomposition using next-generation sequencing. Our results revealed that 1) the concentration of total carbon increased approximately 2.24-11.22% in the corpse group. 2) Several carbon-fixing bacterial species (Calothrix parietina, Ancylobacter rudongensis, Rhodopseudomonas palustris) may predict the concentration of total carbon. 3) Animal cadaver degradation caused the differentiation of carbon-fixing microbiota structures during succession and made the medium-stage networks of carbon-fixing microbes more complicated. 4) The temporal turnover rate in the experimental groups was higher than that in the control groups, indicating a quick change of gravesoil carbon-fixing microbiota. 5) The deterministic process dominates the assembly mechanism of experimental groups (ranging from 53.42% to 94.94%), which reflects that the carbon-fixing microbial community in gravesoil can be regulated. Under global climate change, this study provides a new perspective for understanding the effects of wild animal carcass decay on soil carbon storage and carbon-fixing microbes.

Competition and interaction between DNRA and denitrification in composting ecosystems: insights from metagenomic analysis

This study investigated denitrification and dissimilatory nitrate reduction to ammonium (DNRA) competition for nitrite in composting of sugarcane pith and cow manure. Metagenomic analysis showed that Actinobacteria was the main DNRA microorganism. During heating phase and thermophilic phase, the abundances of denitrification functional genes (nirK and nirS decreased by 40.22% and 98.60%, respectively) and DNRA functional genes (nirB, nirD increased by 195.24% and 176.61%, and nrfA decreased by 45%, respectively) showed different trends. Interestingly, the abundance of nrfA increased by 250% during cooling and maturity phases. Mantel test revealed that competition between denitrification and DNRA microorganisms for NO₂^--N limited the succession of their respective communities (P < 0.01). Network analysis showed that unclassified Solirubrobacterales, Altererythrobacter and Microbacterium were the key microorganisms in DNRA microbial communities. The results provided new insights into the key microorganisms and their driving factors affecting DNRA and nitrogen management in the composting ecosystems.

Heterotrophic Bioleaching of Vanadium from Low-Grade Stone Coal by Aerobic Microbial Consortium

Bioleaching is a viable method that assists in increasing the vanadium output in an economical and environmentally friendly manner. Most bioleaching is conducted by pure cultures under autotrophic conditions, which frequently require strong acidity and produce acid wastewater. However, little is known about heterotrophic bioleaching of vanadium by mixed culture. This study investigated the bioleaching of vanadium from low-grade stone coal by heterotrophic microbial consortium. According to the results, vanadium was efficiently extracted by the employed culture, with the vanadium recovery percentage in the biosystem being 7.24 times greater than that in the control group without inoculum. The average vanadium leaching concentration reached 680.7 μg/L in the first three cycles. The kinetic equation indicated that the main leaching process of vanadium was modulated by a diffusion process. Scanning electron microscopy revealed traces of bacterial erosion with fluffy structures on the surface of the treated stone coal. X-ray photoelectron spectroscopy confirmed the reduction of the vanadium content in the stone coal after leaching. Analysis of high-throughput 16S rRNA gene sequencing revealed that the metal-oxidizing bacteria, Acidovorax and Delftia, and the heterotrophic-metal-resistant Pseudomonas, were significantly enriched in the bioleaching system. Our findings advance the understanding of bioleaching by aerobic heterotrophic microbial consortium and offer a promising technique for vanadium extraction from low-grade stone coals.

Response of cbbL-harboring microorganisms to precipitation changes in a naturally-restored grassland

The impact of the long-term uneven precipitation distribution model on the diversity and community composition of soil C-fixing microorganisms in arid and semiarid grasslands remains unclear. In 2015, we randomly set up five experimental plots with precipitation gradients on the natural restoration grassland of the Loess Plateau (natural precipitation, NP; ± 40% natural precipitation: decreased precipitation (DP), DP40; increased precipitation (IP), IP40; ± 80% natural precipitation: DP80; IP80). In the third and fifth years after the experimental layout (spanned two years), we explored the cbbL-genes, which are functional genes in the Calvin cycle, harboring microbial diversity and community composition under different precipitation treatments. The results showed that the increase in mean annual precipitation significantly changed the cbbL-harboring microbial alpha diversity, especially when controlling for 40% natural precipitation. The response of the dominant microbial communities to interannual increased precipitation variation shifted from Gammaproteobacteria (Bradyrhizobium) to Betaproteobacteria (Variovorax). The structural equation model showed that precipitation directly affected the cbbL-harboring microbial diversity and community composition and indirectly by affecting soil NO₃^- (mg N kg ^-1), soil organic matter, dissolved organic N content, and above- and underground biomass. In conclusion, studying how cbbL-harboring microbial diversity and community composition respond to uneven precipitation variability provides new insights into the ecological processes of C-fixing microbes in semi-arid naturally-restored grasslands dominated by the Calvin cycle.

Effects of Temperature and Nitrogen Application on Carbon and Nitrogen Accumulation and Bacterial Community Composition in Apple Rhizosphere Soil

Malus sieversii grows on the slopes of the Tianshan Mountains in Xinjiang where the difference in daily temperature is significant. In recent years, the rhizosphere soil health of Malus sieversii has been severely impacted by anthropogenic disturbance and pathogenic infestation. The soil nutrient content and soil microorganism diversity are the main components of soil health. Low temperature has negative effects on soil bacterial community structure by inhibiting the accumulation of carbon and nitrogen. However, the effects of temperature and nitrogen application on soil carbon and nitrogen accumulation and the bacterial community composition in the rhizosphere soil of Malus sieversii are unclear. We set two temperature levels, i.e., low temperature (L) and room temperature (R), combined with no nitrogen (N0) and nitrogen application (N1) to explore the response of plant carbon and nitrogen uptake, rhizosphere soil carbon and nitrogen accumulation and bacterial community composition to temperature and nitrogen fertilization. At the same temperature level, plant 13C abundance (P-Atom13C), plant 15N absolute abundance (P-Con15N), soil 15N abundance (S-Atom15N) and soil urease, protease and glutaminase activities were significantly higher under nitrogen application compared with the no-nitrogen application treatment. The bacterial community diversity and richness indices of the apple rhizosphere soil in the N1 treatment were higher than those in the N0 treatment. The relative abundances of Actinobacteria, Rhodopseudomonas, and Bradyrhizobium were higher in the LN1 treatment than in the LN0 treatment. Redundancy analysis (RDA) showed that plant 13C absolute abundance (P-Con13C) and plant 15N absolute abundance (P-Con15N) were the main factors affecting the soil bacterial community composition. In summary, Nitrogen application can alleviate the effects of low temperature stress on the soil bacterial community and is of benefit for the uptakes of carbon and nitrogen in Malus sieversii plants.

Biochar reinforced the populations of cbbL-containing autotrophic microbes and humic substance formation via sequestrating CO2 in composting process

The quality of compost is drastically reduced due to the loss of carbon, which negatively impacts the environment. Carbon emission reduction and carbon dioxide (CO₂) fixation have attracted much attention in composting research. In this study, the relationship between CO₂ emission, humic substances (HS) formation and cbbL-containing autotrophic microbes (CCAM) was analyzed by adding biochar during cow manure composting. The results showed that biochar can facilitate the degradation of organic matter (OM) and formation of HS, as well as reinforce the diversity and abundance of CCAM community, thereby promoting CO₂ fixation and reducing carbon loss during composting. High-throughput sequencing analysis revealed significant increase in Actinobacteriota and Proteobacteria abundance by 30.97 % and 10.48 %, respectively, thus increasing carbon fixation by 32.07 %. Additionally, Alpha diversity index increased significantly during thermophilic phase, while Shannon index increased by 143.12 % and Sobs index increased by 51.62 %. Redundancy analysis (RDA) indicated that CO₂ was positively correlated with C/N, temperature, HS and dissolved organic matter (DOM), while the abundance of Paeniclostridium, Corynebacterium, Bifidobacterium, Clostridium, Turicibacter and Romboutsia were positively correlated with temperature, CO₂, C/N and E₂/E₄ (p <  0.01).

Nitrogen Deposition Reduces the Diversity and Abundance of cbbL Gene-Containing CO2-Fixing Microorganisms in the Soil of the Stipa baicalensis Steppe

CO₂ fixation by autotrophic microbes has a significant effect on the carbon cycle in temperate grasslands. Nitrogen (N) deposition in soil has been steadily increasing for decades, which has consequences for soil microorganisms. However, the impact of this deposition on the diversity and abundance of CO₂-fixing soil microorganisms remains unclear in temperate grasslands. In the present study, the cbbL gene, a key gene in the Calvin–Benson–Bassham cycle that encodes the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase, was used to study CO₂-fixing microbes under different rates of N addition (0, 15, 30, 50, 100, and 150 kg N ha^–1 yr^–1) in a 9-year field experiment in a temperate grassland. The results showed that N addition led to significant reductions in cbbL gene abundance and genetic diversity and altered cbbL gene community composition. High N addition enhanced the relative abundances of Acidiferrobacterales and Rhizobiales but reduced those of Burkholderiales and Rhodobacterales. Structural equation modeling further revealed that N addition primarily reduced cbbL genetic diversity by increasing the soil NO₃-N content and decreasing the soil pH. N addition indirectly reduced cbbL gene abundance, possibly by increasing the soil N/phosphorus (P) ratio and decreasing the soil pH. These findings suggest that N addition increases the soil available N and causes soil acidification, which may inhibit growth of CO₂-fixing microbes to some extent.

The degradation of organic matter coupled with the functional characteristics of microbial community during composting with different surfactants

The purpose of this study was to investigate the effects of anionic and cationic surfactants on the physico-chemical properties, organic matter (OM) degradation, bacterial community structure and metabolic function during composting of dairy manure and sugarcane bagasse. The results showed that the surfactant could optimize the composting conditions to promote the degradation of OM. The most OM degradation and humic substances (HS) synthesis were observed in SAS. Firmicutes and Proteobacteria were more abundant in SAS and CTAC, and Actinobacteria in CK. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed that SAS and CTAC are more abundant than CK in genes related to metabolism, environmental and genetic information processing. The correlation analysis showed that the dominant bacteria had more significant correlation with environmental factors. In general, the anionic surfactant could better promote the degradation of OM, change the structure of microbial community, and improve the quality of compost.

Understanding the key regulatory functions of red mud in cellulose breakdown and succession of β-glucosidase microbial community during composting

The purpose of this research was to explore the effects of red mud on cellulose degradation and the succession of β-glucosidase microbial community in composting to better enhance the quality of compost. The activity of β-glucosidase in the treatment group with red mud (T) was 0.42-1.07 times higher than that in the control group without red mud (CK) from day 7 to 21 of composting. The final cellulose degradation ratios of the T (84.73%) were 10.02% higher than that of the CK (74.71%). In addition, Proteobacteria, Actinobacteria, Firmicutes, and Ascomycota were the most dominant β-glucosidase-producing microbes, and these microbes were also the phyla causing composting performances differences in the high temperature, cooling, and maturity periods of CK and T. These results indicated that adding red mud can improve β-glucosidase activity and boost the breakdown of cellulose in composting process.