Search

Previous studies demonstrated that EV71-infected cells secrete extracellular vesicles (EVs), facilitating the transfer of viral components to recipient cells and thereby promoting virus spread. Considering lipid signaling plays a crucial role in EVs-mediated cell-to-cell communication, we compared the lipid profile of EVs secreted from uninfected and EV71-infected cells (EVs-Mock and EVs-EV71) using the human rhabdomyosarcoma (RD) cell model. These two groups of EVs were purified by using size exclusion chromatography (SEC), respectively, and evaluated by transmission electron microscopy (TEM), nanoparticle tracking technology (NTA), and Western blotting (WB). In-depth lipidomic analysis of EVs identified 1705 lipid molecules belonging to 43 lipid classes. The data showed a significant increase in the lipid content of EVs after EV71 infection. Meanwhile, we deeply analyzed the changes in lipids and screened for lipid molecules with significant differences compared EVs-EV71 with EVs-Mock EVs. Altogether, we report the alterations in the lipid profile of EVs derived from RD-cells after EV71 infection, which may affect the function of the EVs in the recipient cells.

Background and aims:Intercropping, a widely used planting pattern, could affect soil physicochemical properties, microbial community diversity, and further crop yields. However, its impacts on soil microbial diversity and ecosystem functioning and further soil sustainability are poorly understood.Methods:We conducted field experiments by intercropping maize with four important crops (i.e., sesame, peanut, soybean, and sweet potato), and examined soil microbial community diversity and ecosystem functioning such as microbial biomass and enzyme activities under monocropping and intercropping. We quantified their intercropping effects on microbial diversity and ecosystem functions with effect size metric Cohen d by comparing to the monocropping of maize.Results:We found that the four intercropping systems significantly increased soil aggregates in respective of the 2–0.25 mm grain size. Intercropping consistently elevated ecosystem functioning, such as soil enzyme activities of urease, phosphatase, and catalase, soil microbial biomass carbon and soil microbial biomass nitrogen. The Cohen d of bacterial richness also increased from 0.39 to 2.36, the latter of which was significant for maize/peanut intercropping. Notably, these ecosystem functions were strongly associated with the diversity of bacteria and fungi and the relative abundance of their ecological clusters identified with network analysis.Conclusion:Together, our findings indicate that intercropping generally affected soil physicochemical properties, ecosystem functions, and promoted microbial community diversity. More importantly, our findings highlight the important roles of microbial diversity of ecological clusters (that is, network modules) in maintaining ecosystem functioning after intercropping. These results will help to better understand the microbial diversity and ecosystem function in intercropping systems and guide agricultural practice.

Microbial beta diversity has been recently studied along the water depth in aquatic ecosystems, however its turnover and nestedness components remain elusive especially for multiple taxonomic groups. Based on the beta diversity partitioning developed by Baselga and Local Contributions to Beta Diversity (LCBD) partitioning by Legendre, we examined the water-depth variations in beta diversity components of bacteria, archaea and fungi in surface sediments of Hulun Lake, a semi-arid lake in northern China, and further explored the relative importance of environmental drivers underlying their patterns. We found that the relative abundances of Proteobacteria, Chloroflexi, Euryarchaeota, and Rozellomycota increased toward deep water, while Acidobacteria, Parvarchaeota, and Chytridiomycota decreased. For bacteria and archaea, there were significant (p

Saline lakes possess substantial carbon storage and play essential roles in global carbon cycling. Benthic microorganisms mine and decompose sediment organic matter via extracellular enzymes to acquire limiting nutrients and thus meet their element budgets, which ultimately causes variations in sediment carbon storage. However, current knowledge about microbial nutrient limitation and the associated organic carbon changes especially in saline lake remains elusive. Therefore, we took Qinghai Lake, the largest saline lake of China, as an example to identify the patterns and drivers of microbial metabolic limitations quantified by the vector analyses of extracellular enzyme stoichiometry. Benthic microorganisms were dominantly colimited by carbon (C) and nitrogen (N). Such microbial C limitation was aggravated upon the increases in water salinity and sediment total phosphorus, which suggests that sediment C loss would be elevated when the lake water is concentrated (increasing salinity) and phosphorus becomes enriched under climate change and nutrient pollution, respectively. Microbial N limitation was predominantly intensified by water total nitrogen and inhibited by C limitation. Among the microbial drivers of extracellular enzyme investments, bacterial community structure consistently exerted significant effects on the C, N, and P cycles and microbial C and N limitations, while fungi only altered the P cycle through species richness. These findings advance our knowledge of microbial metabolic limitation in saline lakes, which will provide insights towards a better understanding of global sediment C storage dynamics under climate warming and intensified human activity.

Declining soil quality and microecological imbalances were evaluated in larch plantations in this study. One potential solution to this problem is the cultivation of mixed coniferous and broad-leaved plantations. However, it is unclear whether and how soil microbial community structure and nutrient cycling function would be affected by mixed plantations and soil depths. In this study, we used high-throughput sequencing technology to investigate bacterial 16S and fungal ITS regions for comparisons of soil microbial diversity among plantation types (a Larix gmelinii pure plantation, a Fraxinus mandshurica pure plantation, a Larix–Fraxinus mixed plantation within the Larix row, the Fraxinus row, and between the Larix and Fraxinus rows) and soil depths (0–10, 10–20, and 20–40 cm). These data were used to evaluate variations in microbial communities and nutrient cycling function with the determining environmental factors. Our results indicated that bacteria had a stronger spatial dependence than did fungi, while plantation types significantly affected the fungal community. The relative abundance of Gaiellaceae, as well as bacterial ligninolysis, nitrate ammonification, and nitrite ammonification functions significantly increased with increasing soil depth. Compared with other plantations, the relative abundance of Inocybaceae was significantly higher in the Larix plantation. Distance-based redundancy analysis (db-RDA) showed that Gaiellaceae and Inocybaceae abundances were positively correlated with ammonium nitrogen content, available phosphorus content, and phosphatase activity. Our findings indicate that variations in soil available phosphorus are closely related to the relative abundances of Gaiellaceae at different soil depths and Inocybaceae in different plantation types. Mixed plantations might change the availability of soil phosphorus by controlling the relative abundance of Inocybaceae. We recommend that fungal community changes be considered in the sustainable management of mixed plantations.

Biological migration is usually associated with disturbances and environmental changes that are key drivers in determining the diversity, community compositions, and function of gut microbiome. However, little is known about how gut microbiome is affected by disturbance such as salinity changes during migration from seawater to freshwater. Here, we tracked the gut microbiome succession of Chinese mitten crabs (Eriocheir sinensis) during their migrations from seawater to freshwater and afterward using 16S rDNA sequencing for 127 days, and explored the temporal patterns in microbial diversity and the underlying environmental factors. The species richness of gut microbiome showed a hump-shaped trend over time during seawater–freshwater migration. The community dissimilarities of gut microbiome increased significantly with day change. The turnover rate of gut microbiome community was higher during seawater–freshwater transition (1–5 days) than that in later freshwater conditions. Salinity was the major factor leading to the alpha diversity and community dissimilarity of gut microbiome during seawater–freshwater transition, while the host selection showed dominant effects during freshwater stage. The transitivity, connectivity, and average clustering coefficient of gut microbial co-occurrence networks showed decreased trends, while modularity increased during seawater–freshwater migration. For metabolic pathways, “Amino Acid Metabolism” and “Lipid Metabolism” were higher during seawater–freshwater transition than in freshwater. This study advances our mechanistic understanding of the assembly and succession of gut microbiota, which provides new insights into the gut ecology of other aquatic animals.

Although mycobacterial proteins in exosomes from peripheral serum of patients with tuberculosis (TB) have been identified, other exact compositions of exosomes remain unknown. In the present study, a comprehensive proteomics analysis of serum exosomes derived from patients with active TB (ATB) was performed. Exosomes from patients with ATB were characterized using nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM), and western blotting analysis. Then identified protein components were quantified by label-free proteomics and were determined via bioinformatics analysis. A total of 123 differential proteins were identified in ATB serum exosomes and analyzed with Gene Ontology (GO) analysis. Among these proteins heat shock protein70 (HSP70), CD81, major histocompatibility complex-I (MHC-I ) and tumor susceptibility gene101 (TSG101) were present in exosomes of ATB and normal individuals confirmed via western blotting. In addition, among identified exosomal proteins lipopolysaccharide binding protein (LBP) increased significantly, but CD36 and MHC-I decreased significantly in ATB exosomes. Meanwhile, MHC-I was down-expressed in serum and peripheral blood mononuclear cells (PBMCs) of ATB, but interestingly CD36 was down-regulated in serum and up-expressed in PBMCs of ATB patients validated with ELISA and flow cytometry. CD36 was up-regulated by M. tuberculosis H37Ra infection in macrophages and suppressed in exosomes from H37Ra infected macrophages detected by western blotting. This study provided a comprehensive description of the exosome proteome in the serum of patients with ATB and revealed certain potential biomarkers associated with TB infection.

Many species of seed-borne fungi are closely allied with seed varieties and growing regions, including many seed-borne pathogens, but their species richness and distribution remain largely unknown. This study was conducted to explore the seed-borne fungal composition, abundance and diversity in Avena sativa (B7) and A. nuda (B2) seed samples collected from Baicheng (BB), Dingxi (DB) and Haibei (HB) city, using Illumina sequencing techniques. Our results show that a total of 543,707 sequences were obtained and these were assigned to 244 operational taxonomic units (OTUs) with 97% similarity. Oat varieties and growing locations had a significant difference on seed-borne fungal diversity. HB had a higher fungal diversity than BB and DB, Shannon diversity and ACE richness index of fungal in HB seeds was significantly higher than in BB and DB (P < 0.05). In different varieties, both taxon richness and evenness of B7 seeds was significantly higher than B2 (P < 0.05). A total of 4 fungal phyla and 26 fungal genera were detected. Ascomycota was the dominant phylum and Alternaria sp. was the most abundant genus in B2 and B7 oat seeds from different regions. Mycosphaerella sp. had a higher abundance in HB7 and DB7, respectively, Epicoccum sp. had a higher abundance in HB7 and BB7. The results of alpha and beta diversity analysis revealed the presence of different effects in fungal communities of different varieties and regions of oat, especially in seed pathogenic fungi distribution. Structural equation modeling also explained oat varieties and growing regions have significant influences on seed-borne fungal abundance, composition and diversity. This study demonstrated that the differences of varieties and regions are the main factors resulting in the changes of seed-borne fungal community of oat.

Dissolved organic matter (DOM) provides carbon substrates and energy sources for sediment microbes driving benthic biogeochemical processes. The interactions between microbes and DOM are dynamic and complex and require the understanding based on fine-scale microbial community and physicochemical profiling. In this study, we characterized the porewater DOM composition in a 300-cm sediment core from the Pearl River estuary, China, and examined the interactions between DOM and archaeal and bacterial communities. DOM composition were highly stratified and associated with changing microbial communities. Compared to bacteria, the amplicon sequence variants of archaea showed significant Pearson correlations (r ≥ 0.65, P < 0.01) with DOM molecules of low H/C ratios, high C number and double bond equivalents, indicating that the distribution of archaea was closely correlated to recalcitrant DOM while bacteria were associated with relatively labile compounds. This was supported by the presence of auxiliary enzyme families essential for lignin degradation and bcrABCD, UbiX genes for anaerobic aromatic reduction in metagenome-assembled genomes of Bathyarchaeia. Our study demonstrates that niche differentiation between benthic bacteria and archaea may have important consequences in carbon metabolism, particularly for the transformation of recalcitrant organic carbon that may be predominant in aged marine sediments.

Water-depth biodiversity gradient, one of the typical biogeographical patterns on Earth, is understudied for bacteria in freshwater ecosystems, and thus left the underlying mechanisms poorly understood especially for benthic bacteria. Here, we investigated the water-depth distribution of surface sediment bacterial phyla and their driving factors in Lake Lugu, a plateau lake in Southwest China. Our results revealed that the relative abundance of 11 dominant bacterial phyla showed various water-depth patterns, such as increasing, decreasing, hump-shaped, and U-shaped patterns. These patterns across phyla were consistent with their different niche positions of water depth, while the occupancy-abundance relationships were not dependent on phylum attributes. Consistently, phylum abundance was best explained by water depth; other physical and chemical factors, such as metal ion concentrations, SiO2, and pH, can also explain the variations in some bacterial phyla. Chemical variables were the main drivers of the dominant bacterial phyla. However, biotic variables also showed substantial importance for some phyla, such as Planctomycetes, Actinobacteria, and WS3. This work could provide new insights into the general water-depth patterns and underlying mechanisms of the relative abundance of bacterial phyla in freshwater ecosystems.

The Epichloë endophyte-Festuca sinensis association produces alkaloids which can protect the host plant from biotic and abiotic stresses. Alkaloid concentrations depend on the genetic predisposition of grass and endophyte, and are affected by the environment. Endophyte infected F. sinensis of six ecotypes were grown in experimental field and greenhouse for 2 years. Their aboveground plant tissues were collected each season to test for peramine, lolitrem B, and ergot concentrations. The results showed that seasonal changes affected the peramine, lolitrem B and ergot concentrations of Epichloë endophyte-F. sinensis associations; and these three different alkaloids responded differently to seasonal variation. The peramine concentration of six ecotypes of F. sinensis decreased significantly (p < 0.05) from spring to autumn. The lolitrem B concentration of F. sinensis was higher in autumn than in other seasons. Ergot concentrations of five ecotypes (41, 57, 84, 99, and 141) of F. sinensis peaked in the summer, and lowered in spring and autumn. In addition, the ecotype has insignificant effect (p > 0.05) on the peramine and lolitrem B concentrations of F. sinensis, but it has a significant impact (p < 0.05) on the ergot concentrations. We concluded that the seasonal variation and ecotypes can influence the alkaloids produced by the F. sinensis-endophyte associations, but the effects of seasonal conditions on the alkaloid concentrations are more pronounced than ecotypes.

Understanding the effects of environmental factors on microbial communities is critical for microbial ecology, but it remains challenging. In this study, we examined the diversity (alpha diversity) and community compositions (beta diversity) of prokaryotes and fungi in hypersaline sediments and salinized soils from northern China. Environmental variables were highly correlated, but they differed significantly between the sediments and saline soils. The compositions of prokaryotic and fungal communities in the hypersaline sediments were different from those in adjacent saline–alkaline soils, indicating a habitat-specific microbial distribution pattern. The macroelements (S, P, K, Mg, and Fe) and Ca were, respectively, correlated closely with the alpha diversity of prokaryotes and fungi, while the macronutrients (e.g., Na, S, P, and Ca) were correlated with the prokaryotic and fungal beta-diversity (P ≤ 0.05). And, the nine microelements (e.g., Al, Ba, Co, Hg, and Mn) and micronutrients (Ba, Cd, and Sr) individually shaped the alpha diversity of prokaryotes and fungi, while the six microelements (e.g., As, Ba, Cr, and Ge) and only the trace elements (Cr and Cu), respectively, influenced the beta diversity of prokaryotes and fungi (P < 0.05). Variation-partitioning analysis (VPA) showed that environmental variables jointly explained 55.49% and 32.27% of the total variation for the prokaryotic and fungal communities, respectively. Together, our findings demonstrate that the diversity and community composition of the prokaryotes and fungi were driven by different macro and microelements in saline habitats, and that geochemical elements could more widely regulate the diversity and community composition of prokaryotes than these of fungi.

The elevational diversity pattern for microorganisms has received great attention recently but is still understudied, and phylogenetic relatedness is rarely studied for microbial elevational distributions. Using a bar-coded pyrosequencing technique, we examined the biodiversity patterns for soil bacterial communities of tundra ecosystem along 2000-2500 m elevations on Changbai Mountain in China. Bacterial taxonomic richness displayed a linear decreasing trend with increasing elevation. Phylogenetic diversity and mean nearest taxon distance (MNTD) exhibited a unimodal pattern with elevation. Bacterial communities were more phylogenetically clustered than expected by chance at all elevations based on the standardized effect size of MNTD metric. The bacterial communities differed dramatically among elevations, and the community composition was significantly correlated with soil total carbon (TC), total nitrogen, C:N ratio, and dissolved organic carbon. Multiple ordinary least squares regression analysis showed that the observed biodiversity patterns strongly correlated with soil TC and C:N ratio. Taken together, this is the first time that a significant bacterial diversity pattern has been observed across a small-scale elevational gradient. Our results indicated that soil carbon and nitrogen contents were the critical environmental factors affecting bacterial elevational distribution in Changbai Mountain tundra. This suggested that ecological niche-based environmental filtering processes related to soil carbon and nitrogen contents could play a dominant role in structuring bacterial communities along the elevational gradient. [ABSTRACT FROM AUTHOR]

Bacteria and archaea sustain subsurface cave ecosystems by dominating primary production and fueling biogeochemical cyclings, despite the permanent darkness and shortage of nutrients. However, the heterogeneity and underlying mechanism of microbial diversity in caves, in particular those well connect to surface environment are largely unexplored. In this study, we examined the bacterial abundance and composition in Jinjia Cave, a small and shallow limestone cave located on the western Loess Plateau of China, by enumerating and pyrosequencing small subunit rRNA genes. The results clearly reveal the contrasting bacterial community compositions in relation to cave habitat types, i.e., rock wall deposit, aquatic sediment, and sinkhole soil, which are differentially connected to the surface environment. The deposits on the cave walls were dominated by putative cave-specific bacterial lineages within the γ-Proteobacteria or Actinobacteria that are routinely found on cave rocks around the world. In addition, sequence identity with known functional groups suggests enrichments of chemolithotrophic bacteria potentially involved in autotrophic C fixation and inorganic N transformation on rock surfaces. By contrast, bacterial communities in aquatic sediments were more closely related to those in the overlying soils. This is consistent with the similarity in elemental composition between the cave sediment and the overlying soil, implicating the influence of mineral chemistry on cave microhabitat and bacterial composition. These findings provide compelling molecular evidence of the bacterial community heterogeneity in an East Asian cave, which might be controlled by both subsurface and surface environments. [ABSTRACT FROM AUTHOR]