Illumina MiSeq High-throughput Sequencing Research Articles

Effect of Thermal Hydrolysis Pretreatment Time on Microbial Community Structure in Sludge Anaerobic Digestion System

To evaluate the effect of thermal hydrolysis pretreatment time on the sludge anaerobic digestion system of wastewater treatment plants (WWTPs) in Daxing district, Beijing, the structure and diversity of microbial communities in primary sludge and an activated sludge anaerobic digestion system with different thermal hydrolysis pretreatment times (15 min, 30 min, and 45 min) were analyzed using Illumina MiSeq high-throughput sequencing. The results showed that the dominant groups of digested sludge were mainly distributed in Firmicutes, Cloacimonadota, Chloroflexi, and Synergistota, with W5 being the most common genus. The sum of relative abundance of the dominant phylum was greater than 60%, and W5 accounted for 20.8%-54.5%, showing a high abundance of a few dominant species. During the anaerobic digestion of thermo-hydrolyzed sludge, the relative abundance of acetogenic methanogens decreased due to high levels of volatile fatty acids (VFAs) and ammonia nitrogen (NH4+-N) concentrations, which suggested that the hydrogenophilic methanogenic pathway was more than that of the acetogenic methanogenic pathway. Correlation analysis showed that the soluble protein and pH of thermo-hydrolyzed sludge, NH4+-N of digested sludge, and thermal hydrolysis pretreatment time were the four main environmental factors affecting microbial community structure, and NH4+-N of digested sludge had the largest negative correlation with methanogens. The thermal hydrolysis pretreatment time was negatively correlated with both the Chao index and Shannon index, so longer thermal hydrolysis pretreatment time was not conducive to microbial flora during anaerobic digestion.

Fast Bacterial Succession Associated with the Decomposition of Larix gmelinii Litter in Wudalianchi Volcano.

In order to understand the role of microorganisms in litter decomposition and the nutrient cycle in volcanic forest ecosystems, the dominant forest species Larix gmelinii in the volcanic lava plateau of the Wudalianchi volcano was considered as the research object. We analyzed the response of bacterial community structure and diversity to litter decomposition for 1 year, with an in situ decomposition experimental design using litter bags and Illumina MiSeq high-throughput sequencing. The results showed that after 365 days, the litter quality residual rate of Larix gmelinii was 77.57%, and the litter N, P, C:N, C:P, and N:P showed significant differences during the decomposition period (p < 0.05). The phyla Cyanobacteria and the genus unclassified_o_Chloroplast were the most dominant groups in early decomposition (January and April). The phyla Proteobacteria, Actinobacteriota, and Acidobacteriota and the genera Massilia, Pseudomonas, and Sphingomona were higher in July and October. The microbial communities showed extremely significant differences during the decomposition period (p < 0.05), with PCoa, RDA, and litter QRR, C:P, and N as the main factors driving litter bacteria succession. Microbial functional prediction analysis showed that Chloroplasts were the major functional group in January and April. Achemoheterotrophy and aerobic chemoheterotrophy showed a significant decrease as litter decomposition progressed.

High-throughput sequencing-based analysis of the composition and diversity of the endophyte community in roots of Stellera chamaejasme

Stellera chamaejasme (S. chamaejasme) is an important medicinal plant with heat-clearing, detoxifying, swelling and anti-inflammatory effects. At the same time, it is also one of the iconic plants of natural grassland degradation in northwest China, playing a key role in the invasion process. Plant endophytes live in healthy plant tissues and can synthesize substances needed for plant growth, induce disease resistance in host plants, and enhance plant resistance to environmental stress. Therefore, studying the root endophytes of S. chamaejasme is of great significance for mining beneficial microbial resources and biological prevention and control of S. chamaejasme. This study used Illumina MiSeq high-throughput sequencing technology to analyze the composition and diversity of endophytes in the roots of S. chamaejasme in different alpine grasslands (BGC, NMC and XGYZ) in Tibet. Research results show that the main phylum of endophytic fungi in the roots of S. chamaejasme in different regions is Ascomycota, and the main phyla of endophytic bacteria are Actinobacteria, Proteobacteria and Firmicutes (Bacteroidota). Overall, the endophyte diversity of the NMC samples was significantly higher than that of the other two sample sites. Principal coordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA) results showed significant differences in the composition of endophytic bacterial and fungal communities among BGC, NMC and XGYZ samples. Co-occurrence network analysis of endophytes showed that there were positive correlations between fungi and some negative correlations between bacteria, and the co-occurrence network of bacteria was more complex than that of fungi. In short, this study provides a vital reference for further exploring and utilizing the endophyte resources of S. chamaejasme and an in-depth understanding of the ecological functions of S. chamaejasme endophytes.

Characteristics of the Rhizospheric AMF Community and Nutrient Contents of the Dominant Grasses in Four Microhabitats of the Subalpine Zone in Northwestern Yunnan, China

At the southeastern periphery of the Tibetan Plateau, the subalpine ecosystem hosts grasses as some of the most substantial species. However, the community and function of arbuscular mycorrhizal fungi (AMF) around the rhizospheres of grasses in the subalpine zone are still poorly understood. In the present study, 28 soils and 11 species of dominant grasses collected from four microhabitats (shrubland, grassland, woodland, and forest) in the subalpine zone of northwestern Yunnan, China, were used to investigate the AMF community by Illumina MiSeq high-throughput sequencing technology as well as nutrient contents. Among the four microhabitats, the maximum soil nutrient levels around the rhizospheres of grasses were observed in woodland. The nitrogen, phosphorus, and potassium concentrations in Dactylis glomerata shoots were significantly higher than those in the other 10 grass species. The AMF diversity of grassland in summer was substantially greater than that of the other three microhabitats (p &lt; 0.05). Discrepancies were observed within a given plant species across microhabitats; for example, in summer, the nitrogen concentration in the shoot of Iris tectorum in woodland was significantly higher than that in both forest and shrubland (p &lt; 0.05). A total of eight genera were detected in the AMF communities, which were dominated by Glomus, with a relative abundance of 45.4–94.4% in summer and 60.5–84.3% in winter. Moreover, the abundance of Glomus was significantly positively correlated with the content of alkali-hydrolyzable nitrogen in soil and nitrogen in grasses according to the Mantel test. As a critical nutrient element in soil, nitrogen is beneficial for plant growth. Thus, these results provide a better understanding of the resilience of soil AMF community and the ecological adaptability of grasses in the subalpine ecosystems of northwestern Yunnan.

Soil bacterial community characteristics and its effect on organic carbon under different fertilization treatments.

By implementing small-scale and efficient fertilization techniques, it is possible to enhance the activity of microorganisms, thereby improving soil carbon sequestration and ecological value in agriculture. In this study, field experiments were conducted using various types of fertilizers: organic fertilizer, microbial fungal fertilizer, composite fertilizer, and an unfertilized control (CK). Additionally, different dosages of compound fertilizers were applied, including 0.5 times compound fertilizers, constant compound fertilizers, 1.5 times compound fertilizers and CK. Using advanced technologies such as Illumina MiSeq high-throughput sequencing, PICRUSt2 prediction, Anosim analysis, redundancy analysis, canonical correlation analysis, and correlation matrix, soil organic carbon (SOC) content and components, bacterial diversity, metabolic functions, and interaction mechanisms were examined in different fields. The results showed pronounced effects of various fertilization modes on SOC and the bacterial community, particularly in the topsoil layer (0-20 cm). Organic fertilizer treatments increased the richness and diversity of bacterial communities in the soil. However, conventional doses and excessive application of compound fertilizers reduced the diversity of soil bacterial communities and SOC content. Additionally, different fertilization treatments led to an increase in easily oxidizable organic carbon (EOC) contents. Interestingly, the relationship between SOC components and soil bacteria exhibited inconsistency. EOC was positively correlated with the bacterial diversity index. Additionally, Chloroflexi exhibited a negative correlation with both SOC and its components. The influence of metabolismon primary metabolic functions on the content of SOC components in the soil was more notable. It included seven types of tertiary functional metabolic pathways significantly correlated with SOC components (p < 0.05). These findings enhance the understanding of the relative abundance of bacterial communities, particularly those related to the carbon cycle, by adjusting agricultural fertilization patterns. This adjustment serves as a reference for enhancing carbon sinks and reducing emissions in agricultural soils.

Effect of Bacillus amyloliquefaciens QST713 on Inter-Root Substrate Environment of Cucumber under Low-Calcium Stress

(1) Background: Low-calcium stress can have adverse effects on the rhizosphere environment of cucumber, subsequently impacting cucumber growth. However, plant-growth-promoting rhizobacteria can directly or indirectly enhance plant growth and induce plant tolerance, thereby mitigating the detrimental effects of low-calcium stress on cucumber growth. This study aims to elucidate the role of Bacillus amyloliquefaciens QST713 in the rhizosphere environment of cucumber under low-calcium stress, providing a theoretical basis for the application and promotion of Bacillus amyloliquefaciens. (2) Methods: This study used the ‘JinYou NO.4′ cucumber variety as test material, setting four treatments of CK, CK+Q, LCa, LCa+Q. We conducted measurements of plant height and stem diameter for four groups of cucumber plants: before treatment (0 d), and at 10 d, 20 d, 30 d, and 60 d after treatment. Additionally, we determined the biomass of cucumber plants under different treatments during the peak fruiting period. Inter-root matrix samples of cucumber were collected during the fruiting late period, and the physical and chemical properties and nutrient contents of the inter-root matrix of cucumber were determined, and bacterial microbial diversity and bacterial microbial communities were analysed using Illumina-MiSeq high-throughput sequencing technology. (3) Results: Low-calcium stress significantly inhibits the growth of cucumber plants. However, the application of Bacillus amyloliquefaciens QST713 effectively mitigates the inhibitory effects of low-calcium stress on cucumber growth. The application of Bacillus amyloliquefaciens QST713 was able to improve the physicochemical environment of the matrix and enhanced the absorption and utilisation of matrix nutrients in cucumber. The high-throughput sequencing analysis showed that the richness and diversity of bacterial communities and the number of bacteria decreased significantly under low-calcium stress, and increased significantly after the application of Bacillus amyloliquefaciens QST713. The composition of the dominant bacterial groups of the inter-root matrix of cucumber was basically the same among the four treatments, and the main difference was in the abundance of bacteria. The application of Bacillus amyloliquefaciens QST713 increased the relative abundance of bacteria that decreased under low-calcium stress, and decreased the relative abundance of bacteria that increased under low-calcium stress. (4) Conclusions: The results of this study elucidated the positive effects of Bacillus amyloliquefaciens QST713 on the growth and inter-root environment of cucumber under low-calcium stress, and provided a theoretical basis for in-depth research on the resistance of Bacillus amyloliquefaciens and its popularised application.

Decrease in beneficial bacteria and increase in harmful bacteria in Gastrodia seedlings and their surrounding soil are mainly responsible for degradation of Gastrodia asexual propagation.

Asexual reproduction of Gastrodia elata Bl. f. glauca S. chow (GeB) produces degeneration with increasing number of GeB. Therefore, we analyzed the microorganisms of GeB seedlings and surrounding soil by Illumina Miseq high-throughput sequencing technology. In this study, Illumina Miseq high-throughput sequencing technology was applied to analyze the types and quantities of GeB seedlings and surrounding soil microorganisms in the first to third generations of asexual reproduction, isolated and identified the dominant strains of GeB in the first to third generations and screened the antagonistic bacteria of its pathogenic fungi, and evaluated the effects of beneficial bacteria on the production performance of seedlings planted with GeB. With an increase in the number of asexual reproductive generations, the number of pathogenic fungi and bacteria in GeB seedlings and the surrounding soil increased, and the number of beneficial fungi and bacteria decreased. Pseudomonas sp., Agrobacterium rhizomes, and Herbaspirillum hiltneri were isolated and identified in the first generation, and Trichoderma harzianum, Penicillium viridiatum, Fusarium oxysporum, and Novosphingobium sp. Were isolated and identified in the third generation. Antagonistic strains of the three pathogenic bacterial strains were screened. In conclusion, beneficial bacteria significantly improved the production performance of asexual reproductive seedlings planted with GeB. In conclusion, our findings suggested that the microorganisms of GeB seedlings and the surrounding soil change as the number of generations of GeB reproduction increases, disrupts the microecological balance of surrounding soil and endophytic microbiomes.This study provides a theoretical basis for the degradation of asexual reproduction in GeB.

Effect of plasma-activated lactic acid on microbiota composition and quality of puffer fish (Takifugu obscurus) fillets during chilled storage

Fresh puffer fish (Takifugu obscurus) are susceptible to microbial contamination and have a very short shelf-life of chilled storage. Hence, this study aimed to evaluate the effects of plasma-activated lactic acid (PALA) on microbiota composition and quality attributes of puffer fish fillets during chilled storage. The results showed that PALA treatment effectively reduced the growth of bacteria and attenuated changes in physicochemical indicators (total volatile basic nitrogen, pH value, K value, and biogenic amines) of puffer fish fillets. Additionally, insignificant changes were observed in lipid oxidation during the first 8 days (p > 0.05). Illumina-MiSeq high-throughput sequencing revealed that PALA effectively inhibited the growth of Pseudomonas in puffer fish fillets and maintained the diverse characteristics of the microbial community. In combination with sensory analysis, PALA extended the shelf life of puffer fish fillets for 4 days, suggesting that PALA could be considered a potential fish fillet preservation method.

Response Characteristics of Soil Fungal Community Structure to Long-term Continuous Cropping of Pepper

This study aimed to clarify the effect of long-term continuous cropping of pepper on soil fungal community structure, reveal the mechanism of continuous cropping obstacles, and provide a theoretical basis for the ecological safety and sustainable development of pepper industry. We took the pepper continuous cropping soil in the vegetable greenhouse planting base of Tongren City as the research object. The diversity and community structure of fungi in farmland soil were analyzed using Illumina MiSeq high-throughput sequencing, the responses of soil physio-chemical properties and fungal community characteristics to long-term continuous pepper cropping were discussed, and the relationships between the characteristics of fungal community structure and environmental factors were determined using CCA and correlation network analysis. The results showed that with the extension of pepper continuous cropping years, the soil pH value and organic matter (OM) content decreased, total phosphorus (TP) and available phosphorus (AP) contents increased, hydrolyzed nitrogen (AN) and available potassium (AK) contents decreased first and then increased, and total nitrogen (TN) and total potassium (TK) contents did not change significantly. Long-term continuous cropping decreased the Chao1 index and observed species index and decreased the Shannon index and Simpson index. The change in continuous cropping years had a significant effect on the relative abundance of soil fungal dominant flora. At the phylum level, the relative abundance of Mortierellomycota decreased with the extension of pepper continuous cropping years, the relative abundance of Ascomycota increased first and then decreased, and the relative abundance of Basidiomycota decreased first and then increased. At the genus level, with the increasing of pepper continuous cropping years, the relative abundance of Fusarium increased, and the relative abundance of Mortierella and Penicillium decreased. In addition, long-term continuous cropping simplified the soil fungal symbiosis network. CCA analysis indicated that pH, OM, TN, AN, AP, and AK were the driving factors of soil fungal community structure, and correlation network analysis showed that pH, OM, TN, TP, TK, AN, AP, and AK were the driving factors of soil fungal community structure, including Fusarium, Lophotrichus, Penicillium, Mortierella, Botryotrichum, Staphylotrichum, Plectosphaerella, and Acremonium. In conclusion, continuous cropping changed the soil physical and chemical properties, affected the diversity and community structure of the soil fungal community, changed the interaction between microorganisms, and destroyed the microecological balance of the soil, which might explain obstacles associated with continuous cropped pepper.

Effects of Different Proportions of Organic Fertilizer in Place of Chemical Fertilizer on Microbial Diversity and Community Structure of Pineapple Rhizosphere Soil

With the development of sustainable agriculture, the application of organic fertilizers to crops instead of chemical fertilizers has become an inevitable trend. However, little is known about the proportion of organic fertilizers replacing chemical fertilizers and how it affects the underlying microbial mechanisms of continuous pineapple soil. In this study, we used the Illumina Miseq high-throughput sequencing platform to study the rhizosphere soil of continuously cropped pineapples to study the diversity and community structure of pineapple rhizosphere microorganisms. The results showed that, with 97% similarity, the number of OTUs of all samples obtained using hierarchical clustering analysis is 3645. Both conventional fertilization (CF) and optimal fertilization (YF) increased the relative abundance of Proteobacteria, Actinomycetes, and Sclericutes, and decreased the relative abundance of Acidobacteria, Bacteroidetes, Blastomonas, and Verrucobacteria. The replacement of organic fertilizers increased the relative abundance of Bacteroidetes, among which the relative abundance of chlorocurvus treated with the replacement of organic fertilizers of 80% was the highest. Different fertilization methods also changed the diversity and abundance of bacteria in the soil of the pineapple rhizosphere; the diversity of the species was E &gt; D &gt; C &gt; CK &gt; B &gt; YF &gt; CF. Based on the analysis of the PCoA and NMDS of soil bacterial communities, treatment E was similar to treatment D, treatment CK was similar to treatment YF, and treatment C and treatment D had little structural difference. On the basis of an analysis of the composition and function of the flora, it can be found that different fertilization methods have significant differences in the bacterial groups of the rhizosphere bacterial community of pineapple soil. The relative abundance of beneficial bacteria was increased. When organic fertilizer replaces chemical fertilizer, it promotes the role of bacteria related to the carbon cycle in the rhizosphere.

Effect of chlorogenic acid grafted chitosan on microbiological compositions of sea bass (Lateolabrax japonicus) fillets: Dominant spoilage bacteria, inhibition activity and membrane damage mechanisms

This study investigated the effect of chlorogenic acid grafted chitosan (CS-g-CA) on the microbiota composition of sea bass (Lateolabrax japonicus), isolated and identified the specific spoilage organisms (SSOs) in the late stage of refrigerated fillets and evaluation of their spoilage potential. Moreover, antibacterial activity and membrane damage mechanism of CS-g-CA against spoilage bacteria was also investigated. Illumina-MiSeq high throughput sequencing results showed that CS-g-CA retarded the growth of Pseudomonas spp., which largely contributed to delaying the quality degradation of sea bass during storage. Then nine spoilage bacteria were isolated and identified from the fillets at the end of storage and inoculated into sterile fish fillets to determine their spoilage capacity. Results showed that fish fillets inoculated with spoilage bacteria exhibited a significant increase in TVB-N, TBA and putrescine content and decreased sensory quality during storage. Subsequently, the inhibitory activity of CS-g-CA against spoilage bacteria was investigated and strains that were more sensitive to the CS-g-CA with a strong spoilage capacity were selected for the study of the inhibition mechanism. Results suggested that CS-g-CA had strong inhibitory activity and led to bacterial death through the mechanism of membrane damage. Overall, this study analyzed the effect of CS-g-CA on the preservation of fish fillets from a microbiological point of view to provide a reference for the anti-bacterial preservation of aquatic products.

Fungal communities and their correlation with the sensory quality of rice wine from the Xiaogan and Dazhou regions in China

In this study, we performed a comparative analysis of fungal communities and cultivable yeast isolates in rice wine from the Xiaogan and Dazhou regions using Illumina MiSeq high-throughput sequencing technology and traditional culture-dependent methods. And we further explored the correlation between the sensory quality and fungal communities in rice wine. The results demonstrated no significant difference (P > 0.05) in the abundance and diversity of fungal communities and cultivable yeast isolates between Xiaogan and Dazhou rice wine. The dominant fungal genera were Rhizopus and Saccharomyces, with Saccharomyces cerevisiae accounting for the greatest proportion of yeast isolates. The rice wine samples could be divided into two types based on the composition of fungal communities. Type 1 mainly contained Rhizopus and Saccharomyces, while type 2 mainly contained Rhizopus. Properties such as lightness, blueness-yellowness, methane levels, ethanol levels, organic sulfide content, and soluble solids content accounted for the main differences between the two types of rice wine. In addition, Candida and Clavispora showed a significant positive correlation (P < 0.05) with the aromatic substances in rice wine. The findings of the study enrich our understanding of traditional rice wine, providing meaningful information for the improvement and development of the traditional rice wine industry.

The Dynamic Changes in the Composition and Diversity of Vaginal Microbiota in Women of Different Pregnancy Periods.

The vaginal microbiota undergoes subtle changes during pregnancy, which may affect different pregnancy responses. This study used the Illumina MiSeq high-throughput sequencing method to analyze the 16S rRNA gene amplicons of pregnant women and the vaginal microbiota structure of pregnant women at different pregnancy periods. There were a total of 15 pregnant women, with 45 samples were taken from these women, within half a year before becoming pregnant, in the last trimester, and 42 days postpartum. Before and after pregnancy, the female vaginal microbiota was mainly composed of Firmicutes, followed by Actinobacteriota and Proteobacteria. The abundance of Lactobacillus was relatively high. The α-diversity and microbial abundance were relatively low, and there was no significant difference in microbial composition between the two. After childbirth, the diversity and abundance of women's vaginal bacterial communities were higher, with a decrease in the number of Firmicutes and a higher abundance of Actinobacteria, Proteobacteria, and Bacteroidota. There was a significant difference in the microbial community structure before and after pregnancy. This study showed that the microbiota structure of the vagina of pregnant women was similar to before pregnancy, but after childbirth, there were significant changes in the microbiota of the vagina, with a decrease in the number of probiotics and an increase in the number of harmful bacteria, increasing the risk of illness.

Effects of microbial agent and microbial fertilizer input on soil microbial community structure and diversity in a peanut continuous cropping system

IntroductionThe soil harbors a diverse array of microorganisms, and these are essential components of terrestrial ecosystems. The presence of microorganisms in the soil, particularly in the rhizosphere, is closely linked to plant growth and soil fertility. ObjectiveThe primary objective of this study is to assess the potential advantages of integrating microbial inoculants with compound fertilizer in enhancing peanut yield. MethodsWe utilized Illumina MiSeq high-throughput sequencing technology to conduct our investigation. The experimental design consists of four treatment groups: compound fertilizers (CF), compound fertilizers supplemented with microbial agents (CF+MA), compound fertilizers supplemented with microbial fertilizers (CF+MF), and compound fertilizers supplemented with both microbial agents and microbial fertilizers (CF+MM). ResultsThe experimental results demonstrated a significant increase in peanut yield upon application of CF+MA, CF+MF, and CF+MM treatments. During the blossom stage and pod-setting stage, the soil's catalase, urease, and acid phosphatase activities were significantly increased in the CF+MA, and CF+MM treatments compared to the CF treatment. The application of CF+MA resulted in an increase in bacterial richness in the rhizosphere soil of peanuts, as indicated by the sequencing results. The application of CF+MA, CF+MF, and CF+MM resulted in a reduction of fungal diversity. Proteobacteria, Actinobacteria, and Acidobacteria were the dominant bacterial phyla, while Ascomycota and Basidiomycota were the dominant phyla in the fungal component of the rhizosphere soil microbiome across all experimental treatments. ConclusionMicrobial agents and fertilizers modify the peanut rhizosphere soil's microbial community structure, as per our findings. The abundance of potentially beneficial bacteria (Bradyrhizobium, Rhizobium, and Burkholderia) and fungi (Trichoderma and Cladophialophora) could increase, while pathogenic fungi (Penicillium and Fusarium) decreased, thereby significantly promoting plant growth and yield of peanut.

Correlation between rhizosphere environment and content of medicinal components of Arnebia euchroma

This study aimed to explore the correlation between rhizosphere soil microorganisms of wild Arnebia euchroma and the content of medicinal components to provide guidance for the selection of the ecological planting base. The total DNA of rhizosphere soil microorganisms of wild A. euchroma was extracted, and the microbial community structure of rhizosphere soil microorganisms was analyzed by IlluminaMiseq high-throughput sequencing technology. The content of total hydroxynaphthoquinone pigment and β,β'-dimethylacrylalkannin in medicinal materials was determined by high-performance liquid chromatography(HPLC). The physicochemical pro-perties of rhizosphere soil of wild A. euchroma in main producing areas were determined, and the correlation of soil microbial abundance with index component content and soil physicochemical properties was analyzed by SPSS software. The results showed that the species composition of rhizosphere fungi and bacteria in A. euchroma from different habitats was similar at the phylum and genus levels, but their relative abundance, richness index(Chao1), and community diversity(Simpson) index were different. Correlation analysis showed that the content of available phosphorus in soil was positively correlated with the content of total hydroxynaphthoquinone pigment and β,β'-dimethylacrylalkannin, and the abundance of five fungal genera such as Solicoccozyma and six bacterial genera such as Pseudo-nocardia and Bradyrhizobium was positively correlated with the content of medicinal components in medicinal materials. The abundance of Bradyrhizobium was significantly positively correlated with the content of β,β'-dimethylacrylalkanin. The abundance of fungi such as Archaeorhizomyces was significantly positively correlated with the content of available phosphorus in rhizosphere soil, and Bradyrhizobium was significantly negatively correlated with soil pH. Therefore, the abundance of fungi and bacteria in the rhizosphere of A. euchroma has a certain correlation with the medicinal components and the physicochemical properties of the rhizosphere soil, which can provide a scientific basis for the selection of ecological planting bases in the later stage.

Community diversity and co-occurrence patterns of keratinophilic microorganisms in hospital garden soils

The hospital area is an important component of the urban ecosystem and a densely populated place. Hospital garden soil may act as a potential pool of keratinophilic taxa, which are the common skin disease-causing microorganisms in humans. However, the community diversity, co-occurrence properties and keratinophilic groups of soil microorganisms in hospital gardens remain poorly understood. Here, Illumina MiSeq high-throughput sequencing after the addition of a keratin-rich substrate (i.e., chicken feathers) to hospital garden soils was used to assess keratinophilic taxa in hospital (i.e., people’s hospital, traditional Chinese medicine hospital, and orthopedic hospital) garden soils from southern China (i.e., Jiangsu Province, Guizhou Province, and Hainan Province). Feather addition significantly decreased the soil microbial diversity, but increased the relative abundance of the dominant phyla. Keratinophilic microorganism such as Paenibacillus, Paenisporosarcina, Sporosarcina, Lysobacter, and Cellulosimicrobium, increased through feather enrichment. The relative abundances of Bacillus and Streptomyces (keratinophilic bacteria) and Chrysosporium (keratinophilic fungi) increased by 51–98 % in feather enrichment compared to control soils. However, Arthrobacter (keratinophilic bacteria) and Trichoderma (keratinophilic fungi) decreased by 76 % and 90 %, respectively. Co-occurrence network analysis revealed that the number of nodes, edges, average degree, and clustering coefficients of bacterial and fungal were decreased after feather enrichment treatment. The feather enrichment significant decreased the pH and C:N rates, but increased the carbon, nitrogen, and phosphorus contents of the hospital garden soil. Linear mixed model and correspondence analyses showed that pH, total nitrogen and soil organic carbon were the main factors responsible for changes in community diversity and structure. We then speculate that the keratinophilic microbial taxa are enriched by exposure to higher concentrations of keratin substrates such as human hair and skin surfaces. We suggest that future research should focus on keratinophilic taxa in some specialized habitats, particularly in hospitals.

Differences in Fungal Communities in Different Material Cellar Sediments and Their Correlation with Environmental Factors

There are rich and diverse fungal communities in rainfall-cellar sediments. Fungi play a key role in the rainfall-cellar ecosystem as a bridge and link for material exchange between the rainfall-cellar ecosystem and the sediments. The changes in fungal community structure are usually closely related to the changes in environmental factors. The 16S rRNA gene Illumina MiSeq high-throughput sequencing technology was used to study the diversity and difference of fungal communities in the cellar sediments under two different catchment environments. The results revealed that the cellar sediments under the concrete catchment environment had higher diversity and richness of fungal communities than those under the loess land catchment environment. The dominant bacteria of the fungal communities under the two catchment environments were the same, namely Ascomycota, Basidiomycota, and Zygomycota, which constituted more than 90% of the abundance of the bacteria; however, the former had better homogeneity and stability. The indicator species based on LEfSe analysis demonstrated that Basidiobolales had the largest contribution to the diversity in the catchment environment of the loess land, and Mycosphaerella had the smallest contribution; Saccharomycetales contributed the most to the diversity in the concrete concentration environment, whereas Periconia contributed the least. The results of the co-occurrence network of the microbial community and environmental factors demonstrated that the positive relationship between fungi and environmental factors was stronger than the negative relationship. The research results have enhanced the understanding of the diversity of fungal communities in the cellar sediments and provided a reference for ensuring the drinking safety of rainwater harvesting cellar water for humans and livestock and improving the quality of cellar water.

The Addition of a High Concentration of Phosphorus Reduces the Diversity of Arbuscular Mycorrhizal Fungi in Temperate Agroecosystems

Phosphorus (P) is an essential macronutrient crucial for both plant growth and crop production, playing a pivotal role in agriculture since the early 20th century. The symbiotic relationship between AMF and plants serves as a classic illustration. These fungi play a regulatory role in the growth and development of plants, especially in facilitating the absorption of P and carbon molecules by plants. While there has been a growing body of research on the community assembly of arbuscular mycorrhizal fungi (AMF) in recent decades, our knowledge of the processes governing the coexistence of these AMF communities influenced by P in agroecosystems remains limited. To investigate the impact of various P fertilizers on AMF communities in temperate agroecosystems, this study was conducted using soils sourced from wheat–maize rotation farmland at Henan Agricultural University Yuanyang Base. With the Illumina MiSeq high-throughput sequencing technique, we systematically examined the taxonomic composition of soil AMF at the Yuanyang Base of Henan Agricultural University in a wheat–maize rotation agricultural field. Our primary objective was to unravel the mechanisms behind AMF community assembly and stability under varying P gradient fertilization conditions. Nonmetric Multidimensional Scaling (NMDS) analysis revealed significant differences among AMF communities in field soil subjected to various treatments (p &lt; 0.05). A torus translations test demonstrated positive associations with the three treatments in 36 out of the 51 examined AMF operational taxonomic units (OTUs), making up 70.59% (p &lt; 0.05) of the results. Furthermore, 37.84% (14/37) of the OTUs displayed preferences for the low P concentration treatment, while 34.29% (12/35) and 32.26% (10/31) favored medium and high P concentrations, respectively. An analysis of the Normalized Stochasticity Ratio (NST) and Checkerboard Score (C-score) indicated that in temperate agroecosystems, deterministic processes predominantly governed AMF in all treatment groups, with high P conditions exerting a stronger influence than low or medium P conditions. This study underscores the profound impact of long-term P fertilizer application on AMF community structures within temperate agricultural systems employing wheat–maize rotation. Additionally, it highlights the dominant role played by deterministic processes in shaping the assembly of AMF communities in these temperate agricultural systems that use P fertilizers. These findings emphasize the need for balanced nutrient management, particularly concerning P, to ensure the stability of AMF communities.

Profiling bacterial communities of irrigation water and leafy green vegetables produced by small-scale farms and sold in informal settlements in South Africa

Morogo is an African indigenous term used for leafy green vegetables harvested in the wild or cultivated in small-scale farms and consumed by the local populations of the region. Small-scale farmers have gained recognition as important suppliers of morogo to informal settlements. In commercial production systems, leafy green vegetables have increasingly been reported as associated with foodborne pathogens and disease outbreaks. Little is known of the presence of these organisms on leafy green vegetables in the informal unregulated food systems. This study aimed to profile bacterial communities in irrigation water (flooding and overhead irrigation water) and leafy green vegetables (Brassica rapa L. chinensis and Brassica rapa varieties of morogo) to establish the natural bacterial flora at the water-fresh produce interface from five small-scale farms in two provinces in South Africa. Illumina MiSeq high-throughput sequencing showed that each farm exhibited a unique bacterial community composition, with an overall high relative abundance of Proteobacteria, Firmicutes and Actinobacteria, including prominent families such as Burkholderiaceae (48%), Enterobacteriaceae (34%), Bacillales Family XII (8%), Rhodobacteraceae (3%), Micrococcaceae (1.98%) and Pseudomonadaceae (1.79%). Specific Enterobacteriaceae Serratia, Enterobacter, Salmonella, Shigella, Escherichia coli, Buchnera, Citrobacter, Klebsiella and Proteus were identified, in addition to unique communities associated with plant or irrigation water source. These findings suggest that the edible plant microbiome can play an important role as transient contributor to the human gut and has the potential to affect overall health.

Phosphorus Coupled with High Nitrogen Addition Exerts a Great Influence on Soil Bacterial Community in a Semiarid Grassland.

Nitrogen (N) and phosphorus (P) addition, either individually or in combination, has been demonstrated to enhance plant productivity in grassland ecosystems. Soil bacterial community, which is the driver of litter decomposition and nutrient cycling, is assumed to control responses of terrestrial ecosystem structure and function to N and P addition. Using a high-throughput Illumina MiSeq sequencing platform, we conducted a 9-year field experiment of N (0, 5, 10, and 20 g N m-2 yr-1) and P (0 and 10 g P m-2 yr-1) additions in the Inner Mongolian steppes to elucidate long-term effects of N and P addition on soil bacterial richness, diversity and composition. We found that N addition reduced the relative abundance of Acidobacteria, Chloroflexi, and Nitrospirae, while increased that of Bacteroides. The results showed that the bacterial biomarker was enriched in P addition treatments, either individually or combined with N addition. Both N and P addition altered the bacterial community structure, while only N addition greatly decreased bacterial richness and diversity. More importantly, we showed that all of these effects were most significant in N3P treatment (20 g N m-2 yr-1 and 10 g P m-2 yr-1), implying that P coupled with a high-level N addition exerted a great influence on soil bacterial community. Structural equation models revealed that N and P addition had a great direct effect on soil bacterial community and an indirect effect on it mainly by changing the litter biomass. Our findings highlighted that severe niche differentiation was induced by P along with a high-level N, further emphasizing the importance of simultaneously evaluating response of soil bacterial community to N and P addition, especially in the context of increasing anthropogenic nutrient additions.