Ontology highlight
ABSTRACT:
PROVIDER: PRJNA807743 | ENA |
REPOSITORIES: ENA
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Project description:Understanding microbial community diversity is thought to be crucial for improving process functioning and stabilities of wastewater treatment systems. However, current studies largely focus on taxonomic groups based on 16S rRNA, which are not necessarily linked to functioning, or a few selected functional genes. Here we launched a study to profile the overall functional genes of microbial communities in three full-scale wastewater treatment systems. Triplicate activated sludge samples from each system were analyzed using a high-throughput metagenomics tool named GeoChip 4.2, resulting in the detection of 38,507 to 40,647 functional genes. A high similarity of 75.5% to 79.7% shared genes was noted among the nine samples. Moreover, correlation analyses showed that the abundances of a wide array of functional genes were associated with system performances. For example, the abundances of overall nitrogen cycling genes had a strong correlation to total nitrogen (TN) removal rates (r = 0.7647, P < 0.01). The abundances of overall carbon cycling genes were moderately correlated with COD removal rates (r = 0.6515, P < 0.01). Lastly, we found that influent chemical oxygen demand (COD inf) and total phosphorus concentrations (TP inf), and dissolved oxygen (DO) concentrations were key environmental factors shaping the overall functional genes. Together, the results revealed vast functional gene diversity and some links between the functional gene compositions and microbe-mediated processes.
2014-12-31 | GSE53744 | GEO
Project description:The principles governing acquisition and interspecies exchange of nutrients in microbial communities and how those exchanges impact community productivity are poorly understood. Here, we examine energy and macronutrient acquisition in unicyanobacterial consortia for which species-resolved genome information exists for all members, allowing us to use multi-omic approaches to predict species’ abilities to acquire resources and examine expression of resource-acquisition genes during succession. Metabolic reconstruction indicated that a majority of heterotrophic community members lacked the genes required to directly acquire the inorganic nutrients provided in culture medium, suggesting high metabolic interdependency. The sole primary producer in consortium UCC-O, cyanobacterium Phormidium sp. OSCR, displayed declining expression of energy harvest, carbon fixation, and nitrate and sulfate reduction proteins but sharply increasing phosphate transporter expression over 28 days. Most heterotrophic members likewise exhibited signs of phosphorus starvation during succession. Though similar in their responses to phosphorus limitation, heterotrophs displayed species-specific expression of nitrogen acquisition genes. These results suggest niche partitioning around nitrogen sources may structure the community when organisms directly compete for limited phosphate. Such niche complementarity around nitrogen sources may increase community diversity and productivity in phosphate-limited phototrophic communities.
2017-05-24 | GSE99220 | GEO
Project description:This study evaluated glycine as a sole carbon source in an EBPR sequencing batch reactor, demonstrating effective phosphorus removal comparable to systems fed with mixed substrates. Microbial and genome-resolved analyses revealed a community with complementary metabolic roles, highlighting its contribution to phosphorus removal dynamics.
2026-06-07 | PXD077488 | Pride
Project description:A high phosphorus intake has been associated with various metabolic disorders, including chronic kidney disease, cardiovascular disease, and osteoporosis. Recent studies have demonstrated the effects of dietary phosphorus on lipid and glucose metabolism. This study investigated the impact of a high-phosphorus diet on mouse skeletal muscle lipid composition and gene transcription. Adult male mice (n = 12/group) received either a diet with an adequate (0.3%) or a high (1.2%) phosphorus concentration for 6 weeks. The lipidome analysis showed that among the 17 analyzed lipid classes, the concentrations of three classes were reduced in the high phosphorus group compared to the adequate phosphorus group. These classes were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and lysophosphatidylcholine (LPC) (p < 0.05). Out of the three hundred and twenty-three individual lipid species analyzed, forty-nine showed reduced concentrations, while three showed increased concentrations in the high phosphorus group compared to the adequate phosphorus group. The muscle transcriptome analysis identified 142 up- and 222 down-regulated transcripts in the high phosphorus group compared to the adequate phosphorus group. Gene set enrichment analysis identified that genes that were up-regulated in the high phosphorus group were linked to the gene ontology terms “mitochondria” and “Notch signaling pathway”, whereas genes that were down-regulated were linked to the “PI3K-AKT pathway”. Overall, the effects of the high-phosphorus diet on the muscle lipidome and transcriptome were relatively modest, but consistently indicated an impact on lipid metabolism.
2023-09-13 | GSE236311 | GEO
Project description:In the early stages (30 days) of phosphorus deficiency stress, Epimedium pubescens leaves cope with short-term phosphorus deficiency by increasing the expression of related genes such as carbon metabolism, flavonoid synthesis and hormone signal transduction pathways, producing sufficient energy, scavenging ROS, and adjusting plant morphology. However, with the extension of stress duration to 90 days, the expression of genes related to phosphorus cycling and phosphorus recovery (PHT1-4, PHO1 homolog3, PAP) was upregulated, and transcriptional changes and post-transcriptional regulation (miRNA regulation and protein modification) were enhanced to resist long-term phosphorus deficiency stress. In addition, bHLH, MYB, NAC, WRKY and other families also play an important role in regulating gene expression and coping with phosphorus deficiency stress, especially MYB60 negatively regulates flavonoid synthesis pathway, which is significantly down-regulated in leaves treated with phosphorus deficiency for 30 days, thereby promoting the accumulation of flavonoid compounds in leaves.
2024-03-30 | GSE259444 | GEO
Project description:Aeolian soil erosion, exacerbated by anthropogenic perturbations, has become one of the most alarming processes of land degradation and desertification. By contrast, dust deposition might confer a potential fertilization effect. To examine how they affect topsoil microbial community, we conducted a study GeoChip techniques in a semiarid grassland of Inner Mongolia, China. We found that microbial communities were significantly (P<0.039) altered and most of microbial functional genes associated with carbon, nitrogen, phosphorus and potassium cycling were decreased or remained unaltered in relative abundance by both erosion and deposition, which might be attributed to acceleration of organic matter mineralization by the breakdown of aggregates during dust transport and deposition. As a result, there were strong correlations between microbial carbon and nitrogen cycling genes. amyA genes encoding alpha-amylases were significantly (P=0.01) increased by soil deposition, reflecting changes of carbon profiles. Consistently, plant abundance, total nitrogen and total organic carbon were correlated with functional gene composition, revealing the importance of environmental nutrients to soil microbial function potentials. Collectively, our results identified microbial indicator species and functional genes of aeolian soil transfer, and demonstrated that functional genes had higher susceptibility to environmental nutrients than taxonomy. Given the ecological importance of aeolian soil transfer, knowledge gained here are crucial for assessing microbe-mediated nutrient cyclings and human health hazard. The experimental sites comprised of three treatments of control, soil erosion and deposition, with 5 replicates of each treatment.
2015-03-28 | E-GEOD-67347 | biostudies-arrayexpress
Project description:Anthropogenic nutrient inputs alter soil biodiversity; however, it remains largely unknown whether changes in soil microeukaryotes (fungi and protists) are primarily driven by direct effects, such as modifications in soil properties, or by indirect effects, such as plant diversity loss. To disentangle these mechanisms, we investigated the long-term effects (11 years) of fertilization and manipulated plant diversity (1, 2, or 4 plant species) on soil microeukaryote communities in a temperate grassland experiment using long-amplicon rRNA sequencing. Our results indicate that fertilization generally had a stronger influence on microeukaryote communities than plant species richness. Fertilization altered the community composition of fungi and protists, increased OTU richness by 20.8% and 52.7%, respectively, and shifted community dominance from fungi to protists. Regarding plant diversity, we observed an effect exclusively on the protist community. Changes were primarily explained by increased plant biomass (driven by both fertilization and plant diversity) and by higher soil phosphorus and lower soil pH levels (driven exclusively by fertilization). Regarding life strategies, we observed synergistic treatment effects: fertilization primarily enhanced fungal saprophytes (only richness), fungal animal pathogens, and protist consumers, whereas plant diversity affected phototrophic protists (reduction) and protist animal pathogens (enhancement). Notably, fertilization and plant diversity decline together led to a cumulative increase in fungal plant pathogens. In conclusion, we highlight that fertilisation alone has a significant effect on soil microeukaryotes, while the additional decline in plant diversity affects different soil groups that are not directly affected by fertilisation. This synergistic pattern indicates that fertilization can influence the entire microeukaryote community through direct and indirect mechanisms, with a cumulative enhancement on certain groups, such as plant pathogens.
2026-07-06 | E-MTAB-15101 | biostudies-arrayexpress
Project description:Increased root H+ secretion is known as a strategy of plant adaption to low phosphorus (P) stress by enhancing mobilization of sparingly soluble P-sources. However, it remains fragmentarywhether enhanced H+ exudation could reconstruct the plant rhizosphere microbial community under low P stress. The present study found that P deficiency led to enhanced H+ exudation from soybean (Glycine max) roots. Three out of all eleven soybean H+-pyrophosphatases (GmVP) geneswere up-regulated by Pi starvation in soybean roots. Among them, GmVP2 showed the highest expression level under low P conditions. Transient expression of a GmVP2-green fluorescent protein chimera in tobacco (Nicotiana tabacum) leaves, and functional characterization of GmVP2 in transgenic soybean hairy roots demonstrated that GmVP2 encoded a plasma membrane transporter that mediated H+ exudation. Meanwhile, GmVP2-overexpression in Arabidopsis thaliana resulted in enhanced root H+ exudation, promoted plant growth, and improved sparingly soluble Ca-P utilization. Overexpression of GmVP2 also changed the rhizospheric microbial community structures, as reflected by a preferential accumulation of acidobacteria in the rhizosphere soils. These results suggested that GmVP2 mediated Pi-starvation responsive H+ exudation,which is not only involved in plant growth and mobilization of sparingly soluble P-sources, but also affects microbial community structures in soils.
2023-06-01 | GSE205273 | GEO