Search Results (352)

This research aimed to study changes in the diversity of the soil bacterial community in a jujube forest with different years of abandonment. To this end, we took the mountain jujube forest with different abandoned years (1 a, 3 a, 6a and 20 a) in the Qijiashan jujube experimental demonstration base in Yanchuan County as the research object; we used Illumina Miseq high-throughput sequencing technology to analyze the changes in the soil bacterial community structure and reveal the key environmental drivers of bacterial community variation in the abandoned jujube forest in the study area. The results showed the following findings: (1) Phylum Actinomycetota (34%), Proteobacteria (29%), and Acidobacteriota (13%) were the dominant phyla of the soil bacterial community in the abandoned jujube forest. (2) Abandonment altered the composition of soil bacteria at the OTU level in jujube plantations. (3) There are differences in the soil bacterial community structure across different periods of abandonment in the jujube forest. (4) Soil water content is the main factor affecting the bacterial community structure of the abandoned jujube forest. There are differences in the soil water content of abandoned woodlands, which affects the community structure of soil microorganisms. Full article

Excessive fertilizer input and low output are currently problems for peach production in China. Sugar alcohols such as sorbitol and mannitol represent promising eco-friendly fertilization strategies to improve fruit quality and optimize nutrient management. Our research explored the effect of sorbitol and mannitol on the rhizosphere environment and peach growth from the rhizosphere micro-ecology perspective. Potted peach seedlings were used as materials. Without adding or adding different sorbitol and mannitol concentration gradients (100, 200, 400) combined with potassium dihydrogen phosphate (KH₂PO₄), the physicochemical properties of rhizosphere soil, leaf nutrition, photosynthetic and growth index were determined, and the rhizosphere bacterial community was analyzed via Illumina Miseq high-throughput sequencing. Both sorbitol and mannitol altered the rhizosphere environment, effectively improved leaf photosynthesis, and promoted peach seedling growth; particularly, M100 had optimal affection. Sorbitol and mannitol altered the bacterial structure and reduced bacterial diversity, which observably correlated with soil organic matter and available potassium. For the rhizosphere bacterial composition, sorbitol and mannitol increased specific bacterial OTUs and induced changes in bacterial composition, among which chemoheterotrophic and nitrogen-transforming bacteria increased with the addition of sorbitol and mannitol. Association network analysis and a structural equation model showed that S100 and M100 mainly enriched Vicinamibacteraceae to regulate peach seedling growth. Overall, low-concentration sorbitol and mannitol showed the best effect in peach seedling growth through regulating the rhizosphere environment. Full article

The Qinghai-Xizang Plateau is among the most ecologically vulnerable and responsive areas worldwide. Studying the characteristics of soil microbial communities along altitudinal gradients on plateaus and revealing the response mechanisms and vertical distribution patterns of microbial communities in alpine ecosystems is of significant academic value for assessing the ecological stability of the Qinghai-Xizang Plateau. This research examines the Lhasa River Basin by employing Illumina NovaSeq high-throughput sequencing to investigate how soil bacterial and fungal communities shift across elevation gradients in the Duilong Qu subbasin. This study also explored the key environmental drivers behind these microbial distribution patterns. The results indicate the following: (1) Key bacterial groups in the Duilong Qu Basin soil include Proteobacteria, Acidobacteria, and Actinobacteria, with Ascomycota, Mortierellomycota, and Basidiomycota as the prevalent fungal phyla. (2) Soil bacterial richness fluctuates with increasing elevation, and diversity exhibits a V-shaped distribution; fungal richness increases monotonically with elevation, whereas diversity shows no altitudinal dependence. (3) Principal coordinate analysis (PCoA) revealed that bacterial community structures exhibit separation trends across different elevations, with high intragroup consistency; fungal community structures at mid-elevations (4000–5000 m) show clustering similarity, whereas those at 3650–5000 m and 5500 m remain highly distinct from those at other elevations. (4) RDA reveals that factors such as accessible phosphorus, potassium, and organic content have a major effect on how bacterial communities are arranged. On the other hand, soil conductivity, along with available and total phosphorus levels, as well as pH, plays a key role in shaping fungal communities. (5) Functional prediction analysis suggests that soil bacteria shift from aerobic and biofilm-forming to facultatively anaerobic, stress-tolerant, and pathogenic traits with increasing elevation. Fungi are predominantly undefined saprotrophs, transitioning from ectomycorrhizal and pathogenic functions to saprotrophic functions at relatively high elevations. Full article

Routine aquaculture practices such as capture, transportation, and handling can disrupt the relationship between commensal and opportunistic bacteria in the fish skin microbiome. Anesthetic baths are a common welfare practice in aquaculture to reduce stress during handling. However, to date, no studies assessed the effect of anesthetics on bacterial communities in fish skin mucus. This study is the first to evaluate the influence of benzocaine, a widely used anesthetic, on the skin mucus bacterial microbiome of Atlantic salmon reared in a recirculating aquaculture system (RAS). Using Illumina high-throughput 16S rRNA gene sequencing, we found that bacterial richness and diversity were significantly reduced in skin mucus samples from fish with anesthesia (ANE) when compared with those without anesthesia (CTR). The predominant bacterial classes in both groups were Gammaproteobacteria (54.1–62.6%) and Betaproteobacteria (22.6–22.9%). However, significant dissimilarities in beta diversity were observed between the bacterial community structure of salmon skin mucus samples from ANE and CTR. These findings demonstrate that benzocaine exposure alters skin mucus microbiome of Atlantic salmon potentially leading to dysbiosis. This study also provides baseline information on the bacterial communities of Atlantic salmon skin mucus microbiome in an RAS. As no temporal resampling was performed, the duration and persistence of these changes remain unknown and warrant further investigation. Full article

To study the effects of different microbial agents on the microbial community structure of continuously cropped strawberry soil after soil fumigation, seven treatments were applied: T1 (Trichoderma harzianum + Bacillus subtilis + actinomycetes), T2 (Trichoderma harzianum + Bacillus subtilis), T3 (Trichoderma harzianum + actinomycetes), T4 (CK) (water control), T5 (Bacillus subtilis), T6 (actinomycetes) and T7 (Trichoderma harzianum). A high-throughput sequencing platform (Illumina HiSeq 2500) was used to analyze the soil bacterial and fungal communities and their compositions. Compared with the T4 (CK) treatment, the application of microbial agents increased the richness and diversity of soil bacteria and fungi, and the effects of single microbial agents and compound microbial agents differed. The richness, diversity indices and population sizes of bacteria and fungi in the T6 treatment were the highest. The Chao1, observed species and Shannon indices of bacteria were 22.51%, 23.56% and 5.61% greater, respectively, than those of T4 (CK). The Chao1, observed species, Shannon and Simpson indices of fungi were 41.28%, 41.83%, 128.02% and 88.65% higher, respectively, than those of T4 (CK). At the genus level, the bacterial community compositions of T2 and T6 were the most similar, and the fungal community compositions of T1 and T5 were the most similar. Analysis of the genera in the dominant communities revealed that the application of microbial agents after dazomet fumigation increased the numbers and recovery rates of soil bacteria and fungi, especially the beneficial fungal genera, Lecanicillium, Cladosporium, Saccharomyces and Aspergillus. An investigation of strawberry growth and yield-related indicators revealed that the T6 treatment resulted in the lowest seedling mortality and the highest yield. In summary, adding microbial agents to soil with continuous cropping of strawberry after fumigation with dazomet is a scientifically sound and effective method for reconstructing the balance of the soil microbial flora and overcoming the obstacles associated with continuous cropping. In this study, the T6 (actinomycetes) treatment presented the best performance. Full article

Petroleum pollution has become a substantial challenge in soil ecology. The soil bacterial consortia play a major role in the biodegradation of petroleum hydrocarbons. The main objective of this study was to assess changes in bacterial composition and diversity in oil-contaminated dryland soils. The Illumina MiSeq high-throughput sequencing technique was used to study the bacterial diversity and structural change in hyper-arid oil-contaminated soil in the Arava Valley of Israel. The diversity and abundance of soil bacteria declined significantly following oil pollution. The dominant phyla in the petroleum-contaminated soils were Proteobacteria (~33% higher vs. control soil) and Patescibacteria (~2.5% higher vs. control soil), which are oil-associated and hydrocarbon-degrading bacteria. An opposite trend was found for the Actinobacteria (~8%), Chloroflexi (12%), Gemmatimonadetes (3%), and Planctomycetes (2%) phyla, with the lower abundances in contaminated soil vs. control soil. Investigation of long-term contaminated sites revealed significant genus-level taxonomic restructuring in soil bacterial communities. The most evident changes were observed in Mycobacterium, Alkanindiges, and uncultured bacterium-145, which showed marked abundance shifts between spill and control soils across decades. Particularly, hydrocarbon-degrading genera such as Pseudoxanthomonas demonstrated persistent dominance in contaminated sites. While some genera (e.g., Frigoribacterium, Leifsonia) declined over time, others—particularly Nocardioides and Streptomyces—exhibited substantial increases by 2014, suggesting potential ecological succession or adaptive selection. Minor but consistent changes were also detected in stress-tolerant genera like Blastococcus and Quadrisphaera. The effect of oil contamination on species diversity was greater at the 1975 site compared to the 2014 site. These patterns highlight the dynamic response of bacterial communities to chronic contamination, with implications for bioremediation and ecosystem recovery. The study results provide new insights into oil contamination-induced changes in soil bacterial community and may assist in designing appropriate biodegradation strategies to alleviate the impacts of oil contamination in drylands. Full article

Sulfur cycling is a fundamental biogeochemical process, yet its microbial underpinnings in environments like the Isinuka sulfur pool remain poorly understood. Using high-throughput Illumina 16S rRNA sequencing and PICRUSt-based functional inference, we analyzed bacterial diversity and metabolic potential in sediment and water samples. Sediments, characterized by high sulfide/sulfate/thiosulfate, salinity, alkalinity, and organic matter content under anoxic conditions, supported diverse sulfur-reducing and organic-degrading bacteria, primarily from the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria phyla. In contrast, the anoxic water column harbored a less diverse community dominated by α-, γ-, and β-Proteobacteria, including Thiocapsa and Lutimaribacter. Sulfur oxidation genes (soxABCXYZ, sqr) were abundant in water, while sulfate reduction genes (dsrAB, aprAB, and sat/met3) were concentrated in sediments. Core microbiome analysis identified Thiocapsa, Lutimaribacter, and Delftia as functional keystones, integrating sulfur oxidation and nutrient recycling. Sediments supported dissimilatory sulfate-reducing bacteria (unclassified Desulfobacteraceae, Desulfosarcina, Desulfococcus, Desulfotignum, and Desulfobacter), while water samples were enriched in sulfur-oxidizing bacteria like Thiocapsa. Metabolic profiling revealed extensive sulfur, nitrogen, and carbon cycling pathways, with sulfur autotrophic denitrification and anoxygenic photosynthesis coupling sulfur–nitrogen and sulfur–carbon cycles. This study provides key theoretical insights into the microbial dynamics in sulfur-rich environments, highlighting their roles in biogeochemical cycling and potential applications in environmental management. Full article

Soil microorganisms are essential for maintaining the function and health of agricultural ecosystems. However, the responses of microbial communities to long-term changes in land use have been insufficiently explored. Hence, based on a 15 years of field experiments in the northeast Mollisol region of China, we applied the Illumina high-throughput sequencing technology to study the effects of different land use types, including conventional tillage (CT), bare land (BL), no tillage (NT), natural vegetation restoration (NVR), and afforestation (AF), on bacterial communities along the soil profile (0–5 cm, 5–10 cm, 10–20 cm, and 20–30 cm) and co-occurrence networks and identified their relationships with soil physicochemical properties. The findings indicated that the land use type as well as soil depth affected the diversity and structure of bacterial communities significantly. There was no marked difference in the diversity of bacterial communities between CT and NT at different soil depths, except for a depth of 20–30 cm. In NT, NVR, and AF, the relative abundance of Actinomycetota and Firmicutes was higher than that in CT. Conversely, CT showed a remarkably higher abundance of Proteobacteria and Acidobacteriota than BL, NT, NVR, and AF. Compared with CT and BL, increased stability and complexity of the community co-occurrence networks was identified for NT, NVR, and AF. Additionally, the diversity and composition of bacterial communities were correlated with the soil’s total nitrogen (TN), pH as well as total organic carbon (TOC). Our study revealed the potential mechanism by which long-term land use changes affected the distribution of soil bacterial communities, which was of high importance for sustainable development of agriculture and optimal management of land resources. Full article

Podocarpus macrophyllus is an evergreen tree with significant ornamental, economic, and medicinal value, widely used in landscape gardening and bonsai production. However, systematic research on the optimal substrate ratios required for its efficient cultivation remains relatively scarce. This study compared the effects of two cultivation substrates (SJ1: 80% native soil + 20% fine sand and SX2: 25% native soil + 25% coarse sand + 25% peat soil + 25% coconut coir) on the growth of P. macrophyllus. Soil physicochemical properties and plant physiological and biochemical indices were measured, and the rhizosphere microbial community structure was analyzed using Illumina MiSeq high-throughput sequencing. The results show that P. macrophyllus grown in the SX2 substrate exhibited significantly greater ground diameter, plant height, chlorophyll content, and soluble protein content than those in the SJ1 substrate. Microbial community analysis indicates that the two different substrates had little impact on alpha diversity. In the bacterial community, the dominant phylum in the SJ1 substrate was Acidobacteriota, whereas in the SX2 substrate, it was Pseudomonadota. In the fungal community, Ascomycota was the dominant phylum in both SJ1 and SX2. Redundancy analysis (RDA) reveals that water content and total porosity were the primary factors influencing the bacterial community structure. Based on physiological indicators and microbial community composition, the SX2 substrate was more conducive to the growth of P. macrophyllus in terms of plant height and ground diameter. Therefore, this study provides valuable insights for substrate selection and optimization in the cultivation of P. macrophyllus. Full article

The bacterial communities of activated sludge are correlative with influent characteristics, geographical discrepancies, and environmental variables, which are essential for wastewater treatment plants (WWTPs). However, the comprehensive deciphering of bacterial community diversity in high-altitude WWTPs is scarce in Tibet, China. This study collected activated sludge samples from four A²O WWTPs (2980–3650 m above sea level) in Tibet. Illumina NovaSeq high-throughput sequencing revealed that Proteobacteria was the most abundant phylum (46.2–62.9%), followed by Bacteroidetes (14.8–21.8%) and Actinobacteria (3.5–10.9%). Candidatus Accumulibacter (7.2–15.1%) was the dominant denitrifying polyphosphate-accumulating organisms (DPAOs). Moreover, a principal coordinate analysis (PCA) revealed strong correlations between environmental factors and dominant phyla, while Candidatus Accumulibacter as a dominant genus was unaffected by environmental factors. Additionally, the reaction mechanisms were analyzed based on the functional gene abundance of carbon, nitrogen, and phosphorus metabolic pathways in high-altitude WWTPs. The carbon metabolism pathway, especially carbohydrate metabolism (14.52%), has more abundant functional genes in Nyingchi (LZ). Nitrogen metabolism mainly consists of assimilatory nitrate reduction, dissimilatory nitrate reduction, and denitrification; the high abundance of functional genes in phosphorus metabolism ensures efficient phosphorus removal. The obtained microbial information in the WWTPs could provide essential guidance for the sustainable management of wastewater treatment systems in high-altitude environments. Future research should focus on monitoring the seasonal dynamics of bacterial communities in high-altitude WWTPs and responses to environmental disturbances, to optimize treatment efficiency and ensure long-term sustainability. Full article

Utilizing high-throughput Illumina sequencing, we examined how small RNA (sRNA) profiles vary in Chinese white poplar (Populus tomentosa) across two pivotal infection stages by the rust fungus Melampsora larici-populina: the biotrophic growth phase (T02; 48 h post infection) and the urediniospore development and dispersal phase (T03; 168 h), both essential for plant colonization and prolonged biotrophic engagement. Far exceeding random expectations, siRNA clusters predominantly arose from transposon regions, with pseudogenes also contributing significantly, and infection-stage-specific variations were notably tied to these transposon-derived siRNAs. As the infection advanced, clusters of 24 nt siRNAs in transposon and intergenic regions exhibited pronounced abundance shifts. An analysis of targets indicated that Populus sRNAs potentially regulate 95% of Melampsora larici-populina genes, with pathogen effector genes showing heightened targeting by sRNAs during the biotrophic and urediniospore phases compared to controls, pointing to selective sRNA-target interactions. In contrast to conserved miRNAs across plant species, Populus-specific miRNAs displayed a markedly greater tendency to target NB-LRR genes. These observations collectively highlight the innovative roles of sRNAs in plant defense, their evolutionary roots, and their dynamic interplay with pathogen coevolution. Full article

Morchella rotation and intercropping is a new and efficient ecological planting mode, which not only contributes to economic growth, but also promotes the sustainable development of agriculture and has high ecological benefits. Morchella sextelata is an edible mushroom that relies on soil-based cultivation. Understanding the composition and dynamics of soil fungal communities under different cropping systems is crucial for optimising its cultivation. This study investigated the fungal community characteristics of Morchella spp. under different rotation and intercropping patterns, together with the associated environmental factors. Using Illumina NovaSeq high-throughput sequencing coupled with ecological and statistical analyses, the relative abundance, alpha diversity index, beta diversity, and intergroup differences in fungal communities were assessed. Additionally, key soil physical and chemical properties were evaluated across four cultivation systems: conventional Morchella spp. cultivation, Morchella sextelata—ginger rotation, vine—Morchella sextelata intercropping, and mulberry tree—Morchella sextelata intercropping. Our results indicate that Morchella spp. cultivation leads to a significant decline in soil fungal diversity compared to uncultivated soils This indicates that cultivation with Morchella spp. simplifies the soil fungal community structure to some extent. Furthermore, distinct variations in fungal community structure were observed across the different cropping systems. Regarding major pathomycete, the relative abundance of Paecilomyces penicillatus increases in vine intercropping soil (VIS), whereas Botryotrichum atrogriseum and Paecilomyces sp. are more abundant in ginger rotation soil (GRS). Similarly, Fusarium solani and Mortierella sp. exhibit higher relative abundance in mulberry tree intercropping soil (MTIS) and fallow soil (FS) compared to natural soil (NS). Functional prediction analysis indicated a general increase in the relative abundance of potential animal and plant pathogenic fungi across all the soil samples, excluding the VIS. This increase was most pronounced in GRS. Further study revealed that the physical and chemical properties of covering soil, including pH, available potassium (AK), available phosphorus (AP), and total phosphorus (TP), significantly influence fungal community diversity and structure. A significant negative correlation was observed between pH and the relative abundance of Fusarium fungi. These findings provide valuable data for further exploration of the ecological mechanisms underlying Morchella spp. cultivation, including rotation constraints and disease dynamics. Ultimately, this research aims to support the development of sustainable and high-quality Morchella spp. production. Full article

Gynaephora qinghaiensis is a major pest in the alpine meadow regions of China. While the females are unable to fly, the males can fly and cause widespread damage. The aim of this study was to use transcriptome analysis to identify and verify genes expressed at different developmental stages of Gynaephora qinghaiensis, with particular emphasis on genes associated with wing development. High-throughput sequencing was performed on an Illumina HiSeqTM2000 platform to assess transcriptomic differences in the wings of male and female pupa and male and female adults of Gynaephora qinghaiensis, and the expression levels of the differentially expressed genes (DEGs) were verified by real-time fluorescence quantitative PCR (RT-qPCR). A total of 60,536 unigenes were identified from the transcriptome data, and 25,162 unigenes were obtained from a comparison with four major databases. Further analysis identified 18 DEGs associated with wing development in Gynaephora qinghaiensis. RT-qPCR verification of the expression levels showed consistency with the RNA sequencing results. Spatio-temporal expression profiling of the 18 genes indicated different levels of expression in the thoraces of male and female pupa, as well as between the wing buds of adult females and the wings of adult males. GO annotation analysis showed that the DEGs were associated with similar categories with no significant enrichment and were involved in cellular processes, cellular anatomical entities, and binding. KEGG analysis indicated that the DEGs were associated with endocytosis and metabolic pathways. The results of this study expand the information on genes associated with Gynaephora qinghaiensis wing development and provide support for further investigations of wing development at the molecular level. Full article

We investigated the dynamic changes in volatile aroma compound profiles (types and concentrations) and associated gene expression patterns in both the peel and pulp tissues of apples during fruit maturation. This study aimed to elucidate the metabolic regulatory mechanisms underlying volatile aroma biosynthesis in Malus domestica “Ningqiu” apples, thereby providing theoretical support for the comprehensive utilization of aroma resources. Our methodological framework integrated headspace solid-phase microextraction gas chromatography–mass spectrometry (HS-SPME-GC-MS), ultra-high-performance liquid chromatography–orbitrap mass spectrometry (UHPLC-OE-MS), and Illumina high-throughput sequencing to generate comprehensive metabolomic and transcriptomic profiles of peel and pulp tissues. Critical differential aroma compound classes were identified, including esters, aldehydes, alcohols, terpenoids, and ketones, with their metabolic pathways systematically mapped through KEGG functional annotation. Our findings revealed substantial transcriptomic and metabolomic divergence across carotenoid, terpenoid, and fatty acid metabolic pathways. Integrative analysis of multi-omics data revealed 26 and 31 putative biologically significant hub genes in peel and pulp tissues, respectively, putatively associated with the observed metabolic signatures. Among these, five core genes—farnesyl diphosphate synthase (FDPS1.X1), alcohol acyltransferases (AAT1 and AAT3), alcohol dehydrogenase (ADH3), and carotenoid cleavage dioxygenase (CCD3)—were recognized as shared regulatory determinants between both tissue types. Furthermore, terpene synthase (TPS7) emerged as a peel-specific regulatory factor, while hydroperoxide lyase (HPL2), alcohol dehydrogenases (ADH2 and ADH4), and alcohol acyltransferase (AAT2) were identified as pulp-exclusive modulators of metabolic differentiation. The experimental findings provide foundational insights into the molecular basis of aroma profile variation in Malus domestica “Ningqiu” and establish a functional genomics framework for precision breeding initiatives targeting fruit quality optimization through transcriptional regulatory network manipulation. Full article

Background: The COVID-19 pandemic has spurred a global race for a preventive vaccine, with a few becoming available just one year after describing this novel coronavirus disease. Among these are inactivated virus vaccines like CoronaVac (Sinovac Biotech), which are used in several countries to reduce the pandemic’s effects. However, its use was associated with low protection, particularly against novel virus variants that quickly appeared in the following months. Vaccines play a crucial role in activating the immune system to combat infections, with Memory B-cells being a key part of this mechanism, eliciting protective neutralizing antibodies. This work focused on studying B-cell memory repertoire after two consecutive doses of CoronaVac. Methodology: Memory B-cells were isolated from five CoronaVac vaccinated and five pre-pandemic individuals and subsequently stimulated in vitro before high-throughput Illumina sequencing of the Heavy Chain Variable repertoire. Results: We observed a shift in the VH repertoire with increased HCDR3 length and enrichment of IGVH 3-23, 3-30, 3-7, 3-72, and 3-74 for IgA BCRs and IGHV 4-39 and 4-59 for IgG BCRs. A high expansion of IgA-specific clonal populations was observed in vaccinated individuals relative to pre-pandemic controls, accompanied by shared IgA variable heavy chain (VH) sequences among memory B cells across different vaccine recipients of IgA clones was also observed in vaccinated individuals compared to pre-pandemic controls, with several IgA VH sharing between memory B cells from different vaccines. Moreover, a high convergence was observed among vaccinees and SARS-CoV-2 neutralizing antibody sequences found in the CoV-abDab database. Conclusion: These data show the ability of CoronaVac to elicit antibodies with characteristics similar to those previously identified as neutralizing antibodies, supporting its protective efficacy. Furthermore, this analysis of the immunological repertoire in the context of viral infections reinforces the importance of immunization in generating convergent antibodies for the antiviral response. Full article