Comprehensive analysis of environmental factors mediated microbial community succession in nitrogen conversion and utilization of ex situ fermentation system

Effects of straws on greenhouse gas emissions in the ectopic fermentation system

Straws are commonly used padding materials in the ectopic fermentation system, but their effects on greenhouse gas emissions are not well understood. This study compared the effects of rape, rice and corn straws on the fermentation performance of the ectopic fermentation system. Compared with corn straw, the treatment groups with rape straw and rice straw significantly increased the alpha diversity of the fermentation system, and simultaneously mitigated the cumulative emissions of CO2 and N2O by up to 32.4% and 93.9%, respectively. The CO2 and N2O peak emission in the treatment group with corn straw reached 1.4 × 106 and 36.2 mg/m2/d, respectively. CH4 peak emission was one order of magnitude lower than that of N2O in the ectopic fermentation system. Redundancy analysis showed that Pseudoxanthomonas sp000510725 was the key specie that positively affect the fermentation temperature, CO2 and N2O emissions in the fermentation system. Nitrogen metabolism genes, such as nosZ, nirK, and nirS were more abundant in the surface layer of the fermentation system, indicating more active nitrogen metabolism in this region, and the core zone could be the primary source of N2O emissions. Those findings indicated that rape and rice straw can be potential padding materials for mitigating greenhouse gas emissions in large-scale ectopic fermentation system.

Transformation and drive mechanism of nitrogen functional genes at estuaries in dry and wet seasons

The nitrogen cycle plays a vital role in maintaining ecological health and biodiversity. In aquatic systems, nitrogen transformation genes significantly contribute to biological nitrogen cycling. Although the function of these genes is known to be influenced by environmental factors, there is limited research exploring the relationship between nitrogen transformation genes and environmental factors. Therefore, the correlations, between nitrogen transformation genes and environmental factors, were investigated at the estuaries of Chaohu lake (China) in different seasons. The results showed that the values of temperature, pH, organic compounds, nitrogen, and dissolved oxygen were higher in dry season, whereas the abundance of the genes was lower in dry season. In addition, the abundance of the anaerobic ammoxidation gene was much lower than the nitrification gene and denitrification gene. The results indicated that biological nitrification and denitrification were the primary mechanisms for nitrogen removal at estuaries in different seasons, and the reduction of nitric oxide may be a limiting step in the denitrification process. The Co-occurrence Network and Mantel test indicated that, during the dry season, the temperature was the primary driver of ammonification and nitrification functions, the NO3- and NO2- were the primary drivers of denitrification, and the total nitrogen (TN) and NH4+ were the main drivers of anaerobic ammonia oxidation. During the wet season, the dissolved oxygen was the primary driver of ammonification and nitrification functions, the chemical oxygen demand was the primary driver of denitrification, and the TN was the main driver of anaerobic ammonia oxidation. This study provides valuable insights into nitrogen cycling in surface water, contributing to a better understanding of this important process.

Seasonal environmental factors drive microbial community succession and flavor quality during acetic acid fermentation of Zhenjiang aromatic vinegar

This study investigated the impact of seasonal environmental factors on microorganisms and flavor compounds during acetic acid fermentation (AAF) of Zhenjiang aromatic vinegar (ZAV). Environmental factors were monitored throughout the fermentation process, which spanned multiple seasons. Methods such as headspace solid phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS), high performance liquid chromatography (HPLC), and high-throughput sequencing were employed to examine how these environmental factors influenced the flavor profile and microbial community of ZAV. The findings suggested that ZAV brewed in autumn had the strongest flavor and sweetness. The key microorganisms responsible for the flavor of ZAV included Lactobacillus acetotolerans, Lactobacillus plantarum, Lactobacillus reuteri, Lactobacillus fermentum, Acetobacter pasteurianus. Moreover, correlation analysis showed that room temperature had a significant impact on the composition of the microbial community, along with other key seasonal environmental factors like total acid, pH, reducing sugar, and humidity. These results provide a theoretical foundation for regulating core microorganisms and environmental factors during fermentation, enhancing ZAV quality.

Effects of Water and Nitrogen on Growth, Rhizosphere Environment, and Microbial Community of Sophora alopecuroides: Their Interrelationship

The effective management of water and nitrogen is crucial in the artificial cultivation of medicinal plants. Sophora alopecuroides, a perennial herbaceous plant in the Fabaceae family, is extensively used in medicine, with alkaloids as its primary bioactive constituents. Nevertheless, there remains a significant knowledge gap regarding how rhizospheric microbial communities respond to varying water and nitrogen conditions and their intricate relationships with soil environments and the growth of S. alopecuroides. In this study, two-year-old S. alopecuroides were used in a two-factor, three-level water-nitrogen interaction experiment. The irrigation levels included W1 (30-35% of maximum water holding capacity), W2 (50-55%), and W3 (70-75%), while nitrogen levels comprised N1 (32 mg/kg), N2 (64 mg/kg), and N3 (128 mg/kg). The study assessed plant growth indicators, total alkaloid content, and rhizospheric soil physicochemical parameters of S. alopecuroides. High-throughput sequencing (16S rRNA and ITS) was employed to analyze variations in rhizospheric microbial community composition and structure. The results showed that Proteobacteria and Ascomycota are the predominant bacterial and fungal phyla in the rhizosphere microbial community of S. alopecuroides. The highest biomass and alkaloid accumulation of S. alopecuroides were observed under the N1W3 treatment (50% nitrogen application and 70-75% of maximum water holding capacity). Specifically, six bacterial genus-level biomarkers (TRA3_20, MND1, env_OPS_17, SBR1031, Haliangium, S0134_terrestrial_group) and six fungal genus-level biomarkers (Pseudeurotium, Rhizophagus, Patinella, Pseudeurotium, Patinella, Rhizophagus) were identified under the N1W3 treatment condition. In the partial least squares path modeling (PLS-PM), water and nitrogen treatments demonstrated markedly positive direct effects on soil physicochemical parameters (p < 0.01), while showing significant negative direct impacts on alkaloid accumulation and plant growth indicators (p < 0.05). Soil physicochemical parameters, in turn, significantly negatively affected the rhizosphere fungal community (p < 0.05). Additionally, the rhizosphere fungal community exhibited highly significant negative direct effects on both the plant growth indicators and total alkaloid content of S. alopecuroides (p < 0.01). This study provides new insights into the interactions among rhizosphere soil environment, rhizosphere microbiota, plant growth, and alkaloid accumulation under water and nitrogen regulation, offering a scientific basis for the water and nitrogen management in the cultivation of S. alopecuroides.

Mitigating Tetracycline antibiotic contamination in chicken manure using ex situ fermentation system

Excessive use of tetracycline antibiotics in poultry farming results in significant concentrations of these drugs and tetracycline resistance genes (TRGs) in chicken manure, impacting both environmental and human health. Our research represents the first investigation into the removal dynamics of chlortetracycline (CTC) and TRGs in different layers of an ex situ fermentation system (EFS) for chicken waste treatment. By pinpointing and analyzing dominant TRGs-harboring bacteria and their interactions with environmental variables, we've closed an existing knowledge gap. Findings revealed that CTC's degradation half-lives spanned 3.3-5.8 days across different EFS layers, and TRG removal efficiency ranged between 86.82% and 99.52%. Network analysis highlighted Proteobacteria and Actinobacteria's essential roles in TRGs elimination, whereas Chloroflexi broadened the potential TRG hosts in the lower layer. Physical and chemical conditions within the EFS influenced microbial community diversity, subsequently impacting TRGs and integrons. Importantly, our study reports that the middle EFS layer exhibited superior performance in eliminating CTC and key TRGs (tetW, tetG, and tetX) as well as intI2. Our work transcends immediate health and environmental remediation by offering insights that encourage sustainable agriculture practices.

The application of entomopathogenic nematode modified microbial communities within nesting mounds of the red imported fire ants, Solenopsis invicta

Entomopathogenic microorganisms (e.g., fungi, bacteria, nematodes) have been widely used in biological control of soil-dwelling pests, including the red imported fire ant (RIFA), Solenopsis invicta, a notorious invasive pest worldwide. The application of large amounts of entomopathogenic microorganisms to soil may affect the indigenous soil microbial communities. However, reports about the effect of entomopathogenic nematodes (EPN) on soil microbial communities are very few. In this study, the effects of EPN on RIFA populations and microbial communities in mounds were investigated. Our results showed that the application of the EPN Steinernema carpocapsae. All strain on mounds efficaciously suppressed RIFA worker populations, without forming significantly more satellite mounds compared with the control treatment. The application of EPN did not impact the bacterial and fungal diversity in soils derived from the RIFA mounds. However, it slightly altered the taxonomic make-up of the bacterial communities, but significantly altered the taxonomic composition of fungal communities at the phylum, family, and genus levels. The abundances of some beneficial bacteria and fungi, such as Streptomyces, decreased, while those of plant and animal pathogenic bacteria and fungi, dramatically increased, after EPN treatment. On the other hand, the abundances of some entomopathogenic fungi, such as Fusicolla, Clonostachys, and Mortierella, increased. Redundancy analysis or canonical correspondence analysis revealed a positive correlation between the efficacious EPN control and the presence of the insect-resistant bacteria, Sinomonas, as well as entomopathogenic fungi Fusicolla and Mortierella. This suggests that the interactions between EPN and entomopathogenic fungi may play a role in the biological control of RIFA. Our discoveries shed light on the interactions among EPN, RIFA, and soil microbial communities, and emphasize a possible mutualistic relationship between EPN and entomopathogenic fungi in the biological control of RIFA.

Core microbiota for nutrient digestion remained and ammonia utilization increased after continuous batch culture of rumen microbiota in vitro

Introduction

This study aimed to investigate the digestive function, urea utilization ability, and bacterial composition changes in rumen microbiota under high urea (5% urea in diet) over 23 days of continuous batch culture in vitro.

Methods

The gas production, dry matter digestibility, and bacterial counts were determined for the continuously batch-cultured rumen fluid (CRF). The changes in fermentation parameters, NH3-N utilization efficiency, and microbial taxa were analyzed in CRF and were compared with that of fresh rumen fluid (RF), frozen rumen fluid (FRF, frozen rumen fluid at -80°C for 1 month), and the mixed rumen fluid (MRF, 3/4 RF mixed with 1/4 CRF) with in vitro rumen fermentation.

Results

The results showed that the dry matter digestibility remained stable while both the microbial counts and diversity significantly decreased over the 23 days of continuous batch culture. However, the NH3-N utilization efficiency of the CRF group was significantly higher than that of RF, FRF, and MRF groups (p < 0.05), while five core genera including Succinivibrio, Prevotella, Streptococcus, F082, and Megasphaera were retained after 23 days of continuous batch culture. The NH3-N utilization efficiency was effectively improved after continuous batch culture in vitro, and Streptococcus, Succinivibrio, Clostridium_sensu_stricto_1, p.251.o5, Oxalobacter, Bacteroidales_UCG.001, and p.1088.a5_gut_group were identified to explain 75.72% of the variation in NH3-N utilization efficiency with the RandomForest model.

Conclusion

Thus, core bacterial composition and function retained under high urea (5% urea in diet) over 23 days of continuous batch culture in vitro, and bacterial biomarkers for ammonia utilization were illustrated in this study. These findings might provide potential applications in improving the efficiency and safety of non-protein nitrogen utilization in ruminants.

The impact of main Areca Catechu root exudates on soil microbial community structure and function in coffee plantation soils

Coffee is an important cash crop worldwide, but it has been plagued by serious continuous planting obstacles. Intercropping with Areca catechu could alleviate the continuous planting obstacle of coffee due to the diverse root secretions of Areca catechu. However, the mechanism of Areca catechu root secretion in alleviating coffee continuous planting obstacle is still unclear. The changes of coffee rhizosphere soil microbial compositions and functions were explored by adding simulated root secretions of Areca catechu, the primary intercropping plant species (i.e., amino acids, plant hormone, organic acids, phenolic acids, flavonoids and sugars) in current study. The results showed that the addition of coffee root exudates altered soil physicochemical properties, with significantly increasing the availability of potassium and organic matter contents as well as promoting soil enzyme activity. However, the addition of plant hormone, organic acids, or phenolic acids led to a decrease in the Shannon index of bacterial communities in continuously planted coffee rhizosphere soil (RS-CP). The inclusion of phenolic acids specifically caused the decrease of fungal Shannon index. Plant hormone, flavonoids, phenolic acids, and sugars increased the relative abundance of beneficial bacteria with reduced bacterial pathogens. Flavonoids and organic acids increased the relative abundance of potential fungal pathogen Fusarium. The polyphenol oxidase, dehydrogenase, urease, catalase, and pH were highly linked with bacterial community structure. Moreover, catalase, pH, and soil-available potassium were the main determinants of fungal communities. In conclusion, this study highlight that the addition of plant hormone, phenolic acids, and sugars could enhance enzyme activity, and promote synergistic interactions among microorganisms by enhancing the physicochemical properties of RS-CP, maintaining the soil functions in coffee continuous planting soil, which contribute to alleviate the obstacles associated with continuous coffee cultivation.

Bacterial dynamics and functions driven by biomass wastes to promote rural toilet blackwater absorption and recycling in an ectopic fermentation system

Due to high concentration of organic matter and the ease of disease transmission, blackwater pose a serious threat to both the environment and human health, especially in rural areas where wastewater treatment is dispersed. The reuse of biomass waste is also a difficult issue to be addressed urgently. In this study, an ectopic fermentation system (EFS) was used to treat toilet blackwater, and the effects of different biomass waste combinations on bacterial communities and functions during aerobic fermentation of blackwater were compared. The results showed that adding bran powder prolonged the high temperature period of 11 d, improved blackwater absorption capacity by 7.5% and was beneficial to microbial metabolic activities to enhance organic degradation. By contrast, the combination of corn straw and rice husk obtained abundant bacterial OTUs and diversity. Bacillus, Thermobifida and Thermopolyspora were the main microorganisms involved in the degradation of organic matter in EFS, and their abundance varied in different filler combinations. Bacterial communities were directly affected by environmental factors such as temperature, NH₄⁺-N and organic carbon as well as biomass materials during fermentation. This study revealed the role of corn straw, rice husk and bran powder in EFSs, provided new technical support for blackwater treatment and a new direction for the resource utilization of agricultural biomass waste.

Populus root exudates are associated with rhizosphere microbial communities and symbiotic patterns

Introduction

Microbial communities in the plant rhizosphere are critical for nutrient cycling and ecosystem stability. However, how root exudates and soil physicochemical characteristics affect microbial community composition in Populus rhizosphere is not well understood.

Methods

This study measured soil physiochemistry properties and root exudates in a representative forest consists of four Populus species. The composition of rhizosphere bacterial and fungal communities was determined by metabolomics and high-throughput sequencing.

Results

Luvangetin, salicylic acid, gentisic acid, oleuropein, strigol, chrysin, and linoleic acid were the differential root exudates extracted in the rhizosphere of four Populus species, which explained 48.40, 82.80, 48.73, and 59.64% of the variance for the dominant and key bacterial or fungal communities, respectively. Data showed that differential root exudates were the main drivers of the changes in the rhizosphere microbial communities. Nitrosospira, Microvirga, Trichoderma, Cortinarius, and Beauveria were the keystone taxa in the rhizosphere microbial communities, and are thus important for maintaining a stable Populus microbial rhizosphere. The differential root exudates had strong impact on key bacteria than dominant bacteria, key fungi, and dominant fungi. Moreover, strigol had positively effects with bacteria, whereas phenolic compounds and chrysin were negatively correlated with rhizosphere microorganisms. The assembly process of the community structure (keystone taxa and bacterial dominant taxa) was mostly determined by stochastic processes.

Discussion

This study showed the association of rhizosphere microorganisms (dominant and keystone taxa) with differential root exudates in the rhizosphere of Populus plants, and revealed the assembly process of the dominant and keystone taxa. It provides a theoretical basis for the identification and utilization of beneficial microorganisms in Populus rhizosphere.

Performance exploration and microbial dynamics of urine diverting composting toilets in rural China

The ongoing "toilet revolution" in China provides new opportunities to improve the rural living environment and sanitation, and the introduction of new sanitation facilities such as urine diverting composting toilets (UDCTs) is conducive to the effective treatment and resource utilization of feces. This study revealed the degradation performance and microbial community dynamics of UDCTs and clarified the influence mechanism of fecal volume in aerobic composting treatment. The results showed that UDCTs could effectively decompose human feces, with an organic matter degradation rate of 25%⁓30%. The temperature, water content, NH₄⁺-N and nutrient accumulation were higher in the high fecal volume treatment than in the low fecal volume treatment. Bacterial community composition and structure in UDCTs varied with composting stage and fecal volume. The diversity and richness of bacterial community in compost were changed with different fecal volumes, but the dominant groups were similar. Redundancy analysis (RDA) showed that nitrogen and organic carbon were the main drivers of bacterial community changes during composting. Highly nutritious and non-phytotoxic compost products were suitable for agronomic uses. Based on these results, UDCTs can be an effective way to solve the problem of fecal pollution in rural areas, and fecal dosage is a potential influencing factor in the operation and maintenance of composting systems.

COD/TN ratios shift the microbial community assembly of a pilot-scale shortcut nitrification-denitrification process for biogas slurry treatment

In this study, effects of carbon to nitrogen (COD/TN) ratios of biogas slurry on shortcut nitrification-denitrification in a pilot-scale integrated fixed film activated sludge (IFAS) system were investigated. Lowering the COD/TN ratio from 11.7 to 6.2 exerted a negative impact on shortcut nitrification-denitrification performance. Accordingly, the NH₃-N and TN removal rates decreased from 94.4 to 91.2% and 92.3 to 85.9%, respectively. The dynamics of microbial assembly was analyzed by MiSeq sequencing, and the denitrifying functional genes were quantified by qPCR. The results showed that ammonia oxidizing bacteria and amoA gene were more abundant on the biofilm of oxic tank, indicating they play a key role in NH₃-N removal. Autotrophic, endogenous, and fast heterotrophic kinetics denitrifiers were coexisted and enriched in the IFAS system with a decreasing of COD/TN ratio. TN removal was mainly affected by denitrifiers (including Arenimonas, Acidovorax, and Thaurea) harboring narG and nirS genes. Canonical correspondence analysis proved that COD/TN ratio was the most critical factor driving the succession of microbial community. Dissolved oxygen (DO) and pH were found positively correlated with denitrifiers at low COD/TN ratio conditions. As a result, NH₃-N and TN removal were effectively enhanced when the DO level in the oxic tank of IFAS system was increased to 1.0-3.0 mg/L.

Can a compact biological system be used for real hydraulic fracturing wastewater treatment?

Hydraulic fracturing wastewater (HFW), a byproduct of hydraulic fracturing oil extraction, contains a complex mixture of oil, aldehydes, and benzene compounds. Efficient and eco-friendly HFW treatment means are critical for the oil extraction industry, particularly in developing countries. In this study, two biological processes namely an anaerobic/anoxic/moving bed biofilm reactor (A²-MBBR) and an A²-MBBR with a microfiltration membrane (A²-MFMBBR) were established, and assessed for the real HFW treatment. Removal efficiencies of chemical oxygen demand (COD) and NH₄⁺-N were over 92% and 95%, respectively, in both processes with a hydraulic retention time of 72 h. The majority of organic compounds in both systems identified by GC-MS were degraded in the anaerobic units. In comparison, A²-MFMBBR demonstrated higher removal efficiencies for oil, total suspended solids, and complex compounds. The average relative abundances of refractory compound degrading bacteria were 43.4% and 51.6% in the A²-MBBR and A²-MFMBBR, respectively, which was consistent with the COD and oil removal, and suggested that the MBR could maintain a high diversity of microorganisms and contribute to deep recalcitrant organics degradation. This study sheds light on the potential of using a compact biological process for the real HFW treatment.

Mechanisms of nitrogen transformation driven by functional microbes during thermophilic fermentation in an ex situ fermentation system

In this study, we explored the pathways and mechanisms of nitrogen (N) transformation driven by functional microbes carrying key genes in an ex situ fermentation system (EFS). Temperature and N content were found to be the most important factors driving variation in bacterial and fungal communities, respectively; Bacillus became the most abundant bacteria and Batrachochytrium became the most abundant fungi. Co-occurrence network analysis showed that some bacteria including Halomonas, Truepera, and Gemmatimonas species carry genes that promote mineralization, nitrification, dissimilatory/assimilatory nitrate reduction, denitrification, anammox reactions, and N fixation. The maximum rate of total mineralization reached 136.60 μg N g^-1 d^-1. Functional microbes promoted various N conversion processes at different rates in the EFS, with levels increasing by at least 0.23 μg N g^-1 d^-1. These results provide a theoretical basis for feasible optimization measures to address N loss during fermentation.

Microbiology combined with metabonomics revealing the response of soil microorganisms and their metabolic functions exposed to phthalic acid esters

As microplastics became the focus of global attention, the hazards of plastic plasticizers (PAEs) have gradually attracted people's attention. Agricultural soil is one of its hardest hit areas. However, current research of its impact on soil ecology only stops at the microorganism itself, and there is still lack of conclusion on the impact of soil metabolism. To this end, three most common PAEs (Dimethyl phthalate: DMP, Dibutyl phthalate: DBP and Bis (2-ethylhexyl) phthalate: DEHP) were selected and based on high-throughput sequencing and metabolomics platforms, the influence of PAEs residues on soil metabolic functions were revealed for the first time. PAEs did not significantly changed the alpha diversity of soil bacteria in the short term, but changed their community structure and interfered with the complexity of community symbiosis network. Metabolomics indicated that exposure to DBP can significantly change the soil metabolite profile. A total of 172 differential metabolites were found, of which 100 were up-regulated and 72 were down-regulated. DBP treatment interfered with 43 metabolic pathways including basic metabolic processes. In particular, it interfered with the metabolism of residual steroids and promoted the metabolism of various plasticizers. In addition, through differential labeling and collinear analysis, some bacteria with the degradation potential of PAEs, such as Gordonia, were excavated.

Integrated microbiology and metabolomics analysis reveal plastic mulch film residue affects soil microorganisms and their metabolic functions

Research on microplastic pollution of terrestrial soils is catching up with the aquatic environment, especially agricultural soil systems. Plastic residues have caused various environmental problems in mulch film extensively used agricultural areas. However, studies focusing specifically on the potential influence of mulch film residues on the metabolic cycle of soil systems have yet to be conducted. Here, high-throughput sequencing combined with metabolomics were first used to study the effects of residual mulch on soil microbial communities and related metabolic functions. Plastic film treatment did not significantly affect soil physicochemical properties including pH, organic matter and nitrogen, etc in short term. However, it did significantly changed overall community structure of soil bacteria, and interfered with complexity of soil bacterial symbiosis networks; exposure time and concentration of residues were particularly important factors affecting community structure. Furthermore, metabolomics analysis showed that film residue significantly changed soil metabolite spectrum, and interfered with basic carbon and lipid metabolism, and also affected basic cellular processes such as membrane transport and, in particular, interfered with the biosynthesis of secondary metabolites, as well as, biodegradation and metabolism of xenobiotics. Additionally, through linear discriminant and collinear analysis, some new potential microplastic degrading bacteria including Nitrospira, Nocardioidaceae and Pseudonocardiaceae have been excavated.