MiSeq High-throughput Sequencing Technology Research Articles

Comparison of Bacterial Community Composition in Gut of Chinese Mitten Crabs from Three Distinct Rivers in Korea

The Chinese mitten crab (CMC) also known as Eriocheir sinensis has great significance in the aquaculture industry. The bacterial communities inhabiting the CMC’s gut may differ depending on the host habitat and can aid in their normal biological functioning. These microbes are also known to have certain effects on their flavor. In this study, we utilized MiSeq high-throughput sequencing technology to explore the diversity of bacterial communities in the gut of CMCs from three different geographical locations in Korea: the Geum (GD), Han (HD), and Tamjin (TD) rivers. Although most of the environmental parameters were similar at the three sites, significant differences in conductivity (CDS), dissolved oxygen (DO), and salinity were observed. The results show that CMCs sampled from these locations exhibited distinct microbial composition and abundance. For example, the genus Candidatus Hepatoplasma displayed significantly higher abundance in CMCs from HD than those in the other locations, suggesting nutritional stress. Similarly, the crabs collected from TD showed a higher abundance of pathogenic Helicobacter than those from HD and GD sites. We also observed differences in the amino acid, nucleotide, and lactic acid concentrations between different tissues such as the muscle, hepatopancreas, and testis of CMCs. However, only small differences were observed when these characteristics were compared in CMCs from different locations. Our results offer important insights into the intestinal bacterial composition in CMCs which in turn may help in designing better culturing strategies for these important species of crabs.

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 < 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 < 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.

Response of Carbon-Fixing Bacteria to Patchy Degradation of the Alpine Meadow in the Source Zone of the Yellow River, West China.

This study aims to enlighten our understanding of the distribution of soil carbon-fixing bacteria (cbbL-harboring bacteria) and their community diversity in differently degraded patches at three altitudes. MiSeq high-throughput sequencing technology was used to analyze the soil carbon-fixing bacteria community diversity of degraded patches and healthy meadow at three altitudes. Redundancy analysis (RDA) and structural equation model (SEM) were used to analyze the correlation and influence path between environmental factors and carbon-fixing bacteria. The results showed that degradation reduced the relative abundance of Proteobacteria from 99.67% to 95.57%. Sulfurifustis, Cupriavidus, and Alkalispirillum were the dominant genera at the three altitudes. Hydrogenophaga and Ectothiorhodospira changed significantly with altitude. RDA results confirmed that available phosphorus (AP) was strongly and positively correlated with Proteobacteria. AP and total nitrogen (TN) were strongly and positively correlated with Hydrogenophaga. Grass coverage and sedge aboveground biomass were strongly and positively correlated with Sulfurifustis and Ectothiorhodospira, respectively. Elevation adversely affected the relative abundance of dominant carbon-fixing bacteria and diversity index by reducing the coverage of grass and soil volumetric moisture content (SVMC) indirectly, and also had a direct positive impact on the Chao1 index (path coefficient = 0.800). Therefore, increasing the content of nitrogen, phosphorus and SVMC and vegetation coverage, especially sedge and grass, will be conducive to the recovery of the diversity of soil carbon-fixing bacteria and improve the soil autotrophic microbial carbon sequestration potential in degraded meadows, especially in high-altitude areas.

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.

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.

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.

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.

Soil Bacterial Community Structure and Function Prediction of Millet/Peanut Intercropping Farmland in the Lower Yellow River

The objective of this study was to explore the microecological variability in farmland soil fertility in response to millet-peanut intercropping patterns by clarifying the effects of millet-peanut 4:4 intercropping on soil bacterial community structure and its diversity, as well as to provide a reference basis for promoting ecological restoration and arable land quality improvement in the lower Yellow River farmland. The Illumina MiSeq high-throughput sequencing technology and QIIME 2 platform were used to analyze the differences in bacterial community composition and their influencing factors in five soils[sole millet (SM), sole peanut (SP), intercropping millet (IM), intercropping peanut (IP), and millet-peanut intercropping (MP)] and to predict their ecological functions. The results showed that the α-diversity of intercropping soil bacterial communities differed from that of monocropping, though not significantly, whereas the β-diversity was significantly different (P<0.05). A total of 7081 ASVs were obtained from all soil samples, classified into 34 phyla, 109 orders, 256 class, 396 families, 710 genera, and 1409 species, of which 727 ASVs were shared, accounting for 24.5% to 27.8% in five soil species. The bacterial communities of millet-peanut intercropping and its monocropping soils were similar in phylum composition but varied in relative abundance. All five soils were dominated by the Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi, with a relative abundance of 79.40%-81.33%. Soil organic carbon and alkaline nitrogen were the most important factors causing differences in the structures of the five soil bacterial communities at the phylum and genus levels, respectively. The PICRUSt functional prediction revealed that the relative abundance of primary functional metabolism was the largest (78.9%-79.3%), and the relative abundance of secondary functional exogenous biodegradation and metabolism fluctuated the most (CV=3.782%). In terms of the BugBase phenotype, the relative abundance of oxidative stress-tolerant bacteria increased in intercropping millet or peanut soils compared to that in the corresponding monocultures and significantly increased in intercropping millet soils compared to that in sole millet (P<0.05). Oxidative stress-tolerant, Gram-positive, and aerobic phenotypes were highly significantly positively correlated with each other (P<0.01), and all three showed highly significant negative correlations with potential pathogenicity and Gram-negative and anaerobic phenotypes (P<0.01). This showed that millet-peanut intercropping resulted in differences in soil bacterial community diversity, abundance, and metabolic functions and the possibility of reducing the occurrence of potential soil diseases. It can be used to regulate the soil microbiological environment to promote ecological restoration and sustainable development of farmland in the lower Yellow River.

Effects of grazing prohibition on nirK- and nirS-type denitrifier communities in salt marshes.

Grazing prohibition is an effective management practice to restore salt marsh functioning. However, the effects of grazing exclusion on denitrifying microbial communities and their controlling factors in salt marshes remain unclear. In this study, we surveyed soil physicochemical properties and above- and below-ground biomass and using quantitative polymerase chain reaction and Illumina MiSeq high-throughput sequencing technology to determine the relative abundance, composition, and diversity of nitrite reductase nirS- and nirK-type denitrifying bacterial communities associated with grazing prohibition treatments and elevations. The abundance of nirS-type denitrifiers increased with grazing prohibition time, whereas the abundance of nirK-type denitrifiers remained unaltered. Moreover, nirS-type denitrifiers were more abundant and diverse than nirK-type denitrifiers in all treatments. Grazing prohibition significantly altered the operational taxonomic unit richness, abundance-based coverage estimator, and Chao1 indices of the nirS-type denitrifying bacterial communities, whereas it only minimally affected the structure of the nirK-type denitrifying bacterial community. The results imply that the nirS community, rather than nirK, should be the first candidate for use as an indicator in the process of salt marsh restoration after grazing prohibition. Substances of concern, total nitrogen, and salinity were the key environmental factors affecting the abundance and community composition of nirS and nirK denitrifiers. The findings of this study provide novel insights into the influence of the length of grazing prohibition and elevation on nirS- and nirK-type denitrifying bacterial community composition in salt marshes.

Evaluation and comparison of physicochemical properties, volatile substances, and microbial communities of leaf mustard (Brassica juncea var. multiceps) under natural and inoculated fermentation.

Due to the uncontrolled fermentation process and unstable quality of naturally fermented leaf mustard, inoculated fermentation is receiving more attention. Here, the physicochemical properties, volatile compounds, and microbial community in leaf mustard under natural fermentation (NF) and inoculated fermentation (IF) were analyzed and compared. The contents of total acid, crude fiber, and nitrite of leaf mustard were measured. Headspace-solid phase microextraction-gas chromatography-mass spectrometry and orthogonal projection on latent structure-discriminant analysis were used to analyze the differences of volatile compounds in NF and IF leaf mustard. Moreover, Illumina MiSeq high-throughput sequencing technology was employed to reveal the composition of microbiota. The results showed that the nitrite content in leaf mustard after IF (3.69mg/kg) was significantly lower than that after NF (4.43mg/kg). A total of 31 and 25 kinds of volatile components were identified in IF and NF, respectively. Among the detected compounds, 11 compounds caused the differences between IF and NF leaf mustard. The results of inter-group difference analysis showed that there were significant differences in fungal flora between IF and NF samples. Saccharomycetes, Kazachstania, and Ascomycota were the landmark microorganisms in IF leaf mustard and the landmark microorganisms in NF were Mortierellomycota, Sordariomycetes, and Eurotiomycetes. The abundance of probiotics (such as Lactobacillus) in IF leaf mustard (51.22%) was higher than that in NF (35.20%) and the abundance of harmful molds (such as Mortierella and Aspergillus) was opposite. Therefore, IF leaf mustard showed the potential to reduce the content of nitrite and harmful molds and increase the beneficial volatile compounds and probiotics. PRACTICAL APPLICATION: Leaf mustard of inoculated fermentation (IF) showed better fermented characteristics than natural fermentation in terms of lower nitrite content, greater beneficial volatile substances, and better potential for increasing probiotics and reducing harmful molds. These results provided a theoretical basis for IF leaf mustard and contributed to the industrial production of fermented leaf mustard.

Effects of long-term fertilization patterns on bacterial community structure and soil nutrients in dryland of yellow soil.

Understanding the responses of soil bacterial community to long-term fertilization in dryland of yellow soil could provide theoretical basis for establishing scientific fertilization system and cultivating healthy soil. Based on a 25-year long-term fertilization experiment on yellow soil, we collected soil samples from 0-20 cm layer under different fertilization treatments: no fertilization (CK), balanced application of N, P and K fertilizers (NPK), single application of organic fertilizer (M), combined application of constant organic and inorganic fertilizer (MNPK), and 1/2 organic fertilizer instead of 1/2 chemical fertilizer (MNP). Illumina MiSeq high-throughput sequencing technology was used to examine the effects of different fertilization patterns on soil bacterial community structure and soil nutrient content. The main driving factors of soil bacterial community were explored. The results showed that soil pH and organic matter content under treatments with organic fertilizer increased by 11.4%-13.5% and 28.8%-52.0%, respectively, compared to that under NPK treatment. Long-term fertilization did not affect soil bacterial α diversity, but significantly affected soil bacterial β diversity. Compared with CK and NPK treatment, treatments of M, MNP, and MNPK significantly changed soil bacterial community structure, and increased the relative abundance of Fusobacteria and Anaerobes. Four fertilization treatments increased the relative abundance of Bacteroidetes, and decreased the relative abundance of Actinomyces and Campylobacter, compared to CK. Soil pH was the most important factor affecting soil bacterial community structure. Fertilization-stimulated rare microbial taxa (Pumilomyces and Anaerobes) were more sensitive to changes in different environmental factors and were the main drivers of the formation of community versatility. In conclusion, organic fertilizer improved soil properties and fertility and changed soil bacterial community structure, which are conducive to cultivating healthy soil.

Analysis of yeast diversity during spontaneous fermentation of red and white pitaya

Yeast communities during spontaneous fermentation of red and white pitaya were characterised and compared to provide a reference for the isolation of pitaya yeast strains. Using Illumina MiSeq high-throughput sequencing technology, we investigated the composition and diversities of yeast communities during five stages of spontaneous fermentation (1, 3, 5, 7, and 15 d), and the results showed 584,055 and 699,120 valid sequences from red and white pitaya, respectively. The sequences were classified into 86 and 42 operational taxonomic units, then assigned to 69 species in 49 genera (red pitaya) and 37 species in 32 genera (white pitaya). Taxonomic composition and diversity analysis results showed high yeast diversity during the early stage of spontaneous fermentation (RF1) for red pitaya, and during the middle stage (WF5) for white pitaya fermentation. The dominant yeast species was unclassified_o_Saccharomycetales in red pitaya, and Clavispora opuntiae in white pitaya, and these species showed opposite trends during red and white pitaya fermentation. One-way ANOVA showed highly significant differences in unclassified_o_Saccharomycetales (p ≤ 0.01) in red pitaya, and in Clavispora opuntiae (p ≤ 0.001) in white pitaya across the five spontaneous fermentation stages. In addition, phylogenetic analysis revealed that unclassified_o_Saccharomycetales and Clavispora opuntiae were positioned farthest from other yeast species. Overall, yeast community diversity during spontaneous fermentation was higher in red rather than white pitaya.

Effects of Biochar Application on Soil Bacterial Community Diversity and Winter Wheat Growth in Wheat Fields

A long-term field experiment was conducted to study the diversity of soil bacterial communities and the response of crop growth to biochar application, in order to provide a scientific basis for the rational application of biochar in agricultural fields. Four treatments were applied at 0 (B0 blank), 5 (B1), 10 (B2), and 20 t·hm-2(B3) to investigate the effects of biochar on soil physical and chemical properties, soil bacterial community diversity, and growth of winter wheat using Illumina MiSeq high-throughput sequencing technology. The results showed that soil water content, pH value, soil organic carbon, total nitrogen, nitrate nitrogen content, winter wheat biomass, nitrogen uptake, and yield showed an increasing trend with the increase in biochar amount. The high-throughput sequencing results showed that the B2 treatment significantly reduced the alpha diversity of the bacterial community at the flowering stage. The overall response of soil bacterial community composition to different application rates of biochar and phenological phases was taxonomically consistent. In this study, Proteobacteria, Acidobacteria, Planctomycetes, Gemmatimonadetes, and Actinobacteria were the dominant bacterial phyla. The relative abundance of Acidobacteria decreased, but the relative abundance of Proteobacteria and Planctomycetes increased with biochar application. The results of redundancy analysis, co-occurrence network analysis, and PLS-PM analysis indicated that bacterial community compositions were closely associated with soil parameters such as soil nitrate and total nitrogen. The average connectivity between 16S OTUs was higher under the B2 and B3 treatments (16.966 and 14.600) than under the B0 treatment. The variation in soil bacterial community (89.1%) was regulated by biochar and sampling period and partly explained the changes in the growth dynamics of winter wheat (0.077). In conclusion, biochar application could regulate the changes in the soil bacterial community and promote crop growth after seven years of application. It is suggested that 10-20 t·hm-2 biochar should be applied in semi-arid agricultural areas to achieve sustainable agricultural development.

Distribution Pattern of Bacterial Community in Soil Profile of Larix principis-rupprechtii Forest in Luya Mountain

Microbial communities are the key component to maintaining the structure and function of forest soil ecosystems. The vertical distribution of bacterial communities on the soil profile has an important impact on forest soil carbon pools and soil nutrient cycling. Using Illumina MiSeq high-throughput sequencing technology, we analyzed the characteristics of bacterial communities in the humus layer and 0-80 cm soil layer of Larix principis-rupprechtii in Luya Mountain, China, to explore the driving mechanisms affecting the structure of bacterial communities in soil profiles. The results showed that the α diversity of bacterial communities decreased significantly with increasing soil depth, and community structure differed significantly across soil profiles. The relative abundance of Actinobacteria and Proteobacteria decreased with increased soil depth, whereas the relative abundance of Acidobacteria and Chloroflexi increased with the increase in soil depth. The results of RDA analysis showed that soil NH+4, TC, TS, WCS, pH, NO-3, and TP were important factors determining the bacterial community structure of the soil profile, among which soil pH had the most significant effect. Molecular ecological network analysis showed that the complexity of bacterial communities in the litter layer and subsurface soil (10-20 cm) was relatively high, whereas the complexity of bacterial communities in deep soil (40-80 cm) was relatively low. Proteobacteria, Acidobacteria, Chloroflexi, and Actinobacteria played important roles in the structure and stability of soil bacterial communities in Larch. The species function prediction of Tax4Fun showed a gradual decline in microbial metabolic capacity along the soil profile. In conclusion, soil bacterial community structure showed a certain distribution pattern along the vertical profile of soil, the community complexity gradually decreased, and the unique bacterial groups of deep soil and surface soil were significantly different.

Coptischinensis Franch root rot infection disrupts microecological balance of rhizosphere soil and endophytic microbiomes.

The ecological balance of the plant microbiome, as a barrier against pathogens, is very important for host health. Coptis chinensis is one of the important medicinal plants in China. In recent years, Illumina Miseq high-throughput sequencing technology was frequently used to analyze root rot pathogens and the effects of root rot on rhizosphere microorganisms of C. chinensis. But the effects of root rot infection on rhizosphere microecological balance of C. chinensis have received little attention. In this study, Illumina Miseq high-throughput sequencing technology was applied to analyze the impact on microbial composition and diversity of C. chinensis by root rot. The results showed that root rot infection had significant impact on bacterial α-diversity in rhizome samples, but had no significant effect on that in leaf samples and rhizosphere soil samples, while root rot infection exhibited significant impact on the fungal α-diversity in leaf samples and rhizosphere soil samples, and no significant impact on that in rhizome samples. PCoA analysis showed that the root rot infection had a greater impact on the fungal community structure in the rhizosphere soil, rhizome, and leaf samples of C. chinensis than on the bacterial community structure. Root rot infection destroyed the microecological balance of the original microbiomes in the rhizosphere soil, rhizome, and leaf samples of C. chinensis, which may also be one of the reasons for the serious root rot of C. chinensis. In conclusion, our findings suggested that root rot infection with C. chinensis disrupts microecological balance of rhizosphere soil and endophytic microbiomes. The results of this study can provide theoretical basis for the prevention and control of C. chinensis root rot by microecological regulation.

Responses of soil microbial activities to soil overburden thickness in restoring a coal gangue mound in an alpine mining area

This study analyzes the changes in soil microbial community diversity after five years of restoration in an alpine mining area using different soil overburden thicknesses, in which MiSeq high-throughput sequencing technology was applied to analyze soil microbial community diversity and its influential environmental factors. The results showed that vegetation restoration obviously changed the species composition of soil microorganisms at the OTUs (Operational Taxonomic Units) level under different soil overburden thicknesses, and the OTUs species of soil fungi and bacteria changed significantly in the 15 cm soil overburden thickness. The bacterial diversity index was higher than that of fungal microorganisms in all three soil overburden thicknesses, and the microbial diversity index without soil overburden thickness was significantly higher than that in the soil overburden thickness (P < 0.05). The dominant phyla and genera of soil bacteria and fungi were almost the same. The bacteria were Proteobacteria, Pseudoarthrobacter and Sphinomonas, and the fungi were Ascomycota and Tricharina. The relative abundance of soil bacteria and fungi varied with the soil overburden thickness. Vegetation height, coverage, moss coverage, soil temperature, moisture, organic matter, nitrogen content, pH and soil overburden thickness were the key factors affecting the soil microbial community structure. A soil overburden thickness of 10 cm was recommended as an ideal soil reconstruction measure in apline mining areas. During the restoration period of the coal gangue mound in the alpine region, significant improvement was observed in the sensitivity of soil microorganisms to thickness over the course of five years. However, in order to facilitate continuous restoration of microorganisms, it is recommended to implement measures such as covering the area with non-woven fabrics and adjusting the pH of the soil to create more favorable conditions for microbial growth.

Effects of the Transformation from Natural Alpine Grassland to Mixed Artificial Grassland on the Characteristics of Soil Microbial Community

This study aimed to analyze the effects of the transformation from natural alpine grassland (NAG) to mixed artificial grassland (MAG) on the characteristics of soil microbial community. We used Illumina Miseq high-throughput sequencing technology to investigate the soil microbial community of natural grassland and mixed artificial grassland. The results showed that plant diversity and the content of soil organic matter decreased significantly from NAG to MAG. In total, 29 and 11 phyla bacteria and fungi were detected, respectively. Compared with that in NAG, the Shannon indexes of the bacterial community increased significantly in MAG (from 9.51 to 9.89), whereas these differences were not significant between the NAG and MAG fungal community. The structure and composition of the soil microbial community showed significant differences between NAG and MAG. In addition, Mantel test results suggested that soil total organic matter, total nitrogen, and soil moisture were significantly correlated with variations in the bacterial community, and soil total organic matter and soil moisture were significantly correlated with variations in fungal community. The results of linear discriminant analysis (LEfSe) indicated that Atribacteria and Ascomycota microorganisms could be considered as the indicator groups for NAG, whereas Gemmata and Trichocomaceae microorganisms could be considered as the indicator groups for MAG. Tax4Fun2 results showed that the transition from NAG to MAG affected the utilization of different carbon sources by bacteria.

The investigation of the physiochemical factors and bacterial communities indicates a low-toxic infectious risk of the Qiujiang River in Shanghai, China.

The overall water quality of urban rivers is closely related to the community structure and the physiochemical factors in them. In this study, the bacterial communities and physiochemical factors of the Qiujiang River, an important urban river in Shanghai, were explored. Water samples were collected from nine sites of the Qiujiang River on November 16, 2020. The water quality and bacterial diversity were studied through physicochemical detection, microbial culture and identification, luminescence bacteria method, and 16S rRNA Illumina MiSeq high-throughput sequencing technology. The water pollution of the Qiujiang River was quite serious with three water quality evaluation indexes, including Cd2+, Pb2+, and NH4+-N, exceeding the Class V standard set by the Environmental Quality Standards for Surface Water (China, GB3838-2002), while the luminescent bacteria test indicated low toxicity of nine sampling sites. Through 16S rRNA sequencing, a total of 45 phyla, 124 classes, and 963 genera were identified, in which Proteobacteria, Gammaproteobacteria, and Limnohabitans were the most abundant phylum, class, and genus, respectively. The Spearman correlation heatmap and redundancy analysis showed that the bacterial communities in the Qiujiang River were correlated with pH; the concentrations of K+, and NH4+-N, and the Limnohabitans were significantly correlated with the concentrations of K+, and NH4+-N in the Zhongyuan Road bridge segment. In addition, opportunistic pathogens Enterobacter cloacae complex and Klebsiella pneumoniae in the samples collected in the Zhongyuan Road bridge segment and Huangpu River segment, respectively, were successfully cultured. The Qiujiang River was a heavily polluted urban river. The bacterial community structure and diversity were greatly affected by the physiochemical factors of the Qiujiang River, and it displayed low toxicity while a relatively high infectious risk of intestinal and lung infectious diseases.

Distribution patterns and driving mechanism of soil protozoan community at the different depths of Larix principis-chinensis forest in the Luya Mountain, China.

To reveal the assembly mechanisms of soil protozoan community in subalpine forest ecosystems, we analyzed the composition and diversity of protozoan communities and their drivers at the six strata (the litter profile, humus profile, 0-10 cm, 10-20 cm, 20-40 cm and 40-80 cm) of soil profiles in subalpine Larix principis-rupprechtii forest in Luya Mountain using Illumina Miseq high-throughput sequencing technology. The results showed that protozoa in the soil profiles belonged to 335 genera, 206 families, 114 orders, 57 classes, 21 phyla, and 8 kingdoms. There were five dominant phyla (relative abundance >1%) and 10 dominant families (relative abundance >5%). The α diversity decreased significantly with increasing soil depth. Results of PCoA analysis showed that the spatial composition and structure of protozoan community differed significantly across soil depths. The results of RDA analysis showed that soil pH and soil water content were important factors driving protozoan community structure across soil profile. Null model analysis suggested that the heterogeneous selection dominated the processes of protozoan community assemblage. Molecular ecological network analysis revealed that the complexity of soil proto-zoan communities decreased continuously with increasing depth. These results elucidate the assembly mechanism of soil microbial community in subalpine forest ecosystem.