Okara Vermicompost
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB80376 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR13699374.fastq.gz | Fastqsanger.gz | |||
| ERR13699375.fastq.gz | Fastqsanger.gz | |||
| ERR13699376.fastq.gz | Fastqsanger.gz | |||
| ERR13699377.fastq.gz | Fastqsanger.gz | |||
| ERR13699378.fastq.gz | Fastqsanger.gz |
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Project description:Vermicompost application has been shown to promote plant growth, alter the rhizosphere microbiome, and suppress plant pathogens. These beneficial properties are often attributed to the activity of vermicompost-associated microorganisms. However, little is known about the microbial shifts that occur in the rhizosphere after vermicompost application. To better understand the impact of vermicompost treatments on the assembly of rhizosphere bacterial communities, 16S rDNA communities of vermicompost and rhizospheres of each peat- and soil-grown tomatoes were profiled after conventional fertigation, irrigation without additional nutrients, and addition of three different vermicompost-extracts. The full dataset consisted of 412 identified genera, of which 317 remained following stringent quality filtration. Tomato rhizosphere microbiome responses to treatments were complex and unique between peat and soil growth substrates. Direct colonization of vermicompost-origin taxa into rhizospheres was limited, with genera Photobacterium and Luteimonas colonizing peat rhizospheres, genera Truepera, Phenylobacterium, and Lysinibacillus colonizing soil rhizospheres, and genus Pelagibius appearing in both soil and peat rhizospheres. Further patterns of differential abundance and presence/absence between treatments highlight vermicompost-mediated effects on rhizosphere microbiome assembly as an interplay of rhizosphere medium, direct colonization of vermicompost-origin taxa and vermicompost-induced shifts in the rhizosphere microbial community. This exploratory analysis is intended to provide an initial look at 16S community composition of vermicompost and the effects of vermicompost treatment on the rhizosphere microbiome assembly to highlight interactions of potential merit for subsequent investigations.
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Project description:Bacterial root communities in sugar beets grown in potting soil and vermicompost
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Project description:Deciphering synergistic effect of indigenous and polymer-degrading bacteria in vermicomposting via metagenomic sequencing for sustainable strategies of plastic waste management
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Project description:The study of microbial communities or microbiotas in animals and environments is important because of their impact in a broad range of industrial applications, diseases and ecological roles. High throughput sequencing (HTS) is the best strategy to characterize microbial composition and function. Microbial profiles can be obtained either by shotgun sequencing of genomes, or through amplicon sequencing of target genes (e.g., 16S rRNA for bacteria and ITS for fungi). Here, we compared both HTS approaches at assessing taxonomic and functional diversity of bacterial and fungal communities during vermicomposting of white grape marc. We applied specific HTS workflows to the same 12 microcosms, with and without earthworms, sampled at two distinct phases of the vermicomposting process occurring at 21 and 63 days. Metataxonomic profiles were inferred in DADA2, with bacterial metabolic pathways predicted via PICRUSt2. Metagenomic taxonomic profiles were inferred in PathoScope, while bacterial functional profiles were inferred in Humann2. Microbial profiles inferred by metagenomics and metataxonomics showed similarities and differences in composition, structure, and metabolic function at different taxonomic levels. Microbial composition and abundance estimated by both HTS approaches agreed reasonably well at the phylum level, but larger discrepancies were observed at lower taxonomic ranks. Shotgun HTS identified ~1.8 times more bacterial genera than 16S rRNA HTS, while ITS HTS identified two times more fungal genera than shotgun HTS. This is mainly a consequence of the difference in resolution and reference richness between amplicon and genome sequencing approaches and databases, respectively. Our study also revealed great differences and even opposite trends in alpha- and beta-diversity between amplicon and shotgun HTS. Interestingly, amplicon PICRUSt2-imputed functional repertoires overlapped ~50% with shotgun Humann2 profiles. Finally, both approaches indicated that although bacteria and fungi are the main drivers of biochemical decomposition, earthworms also play a key role in plant vermicomposting. In summary, our study highlights the strengths and weaknesses of metagenomics and metataxonomics and provides new insights on the vermicomposting of white grape marc. Since both approaches may target different biological aspects of the communities, combining them will provide a better understanding of the microbiotas under study.
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Project description:Poor soil organic matter is one of the major causes of the deterioration of soil health. Most soils fertility is also decreased when enough organic carbon is not present in the soil. Maize is most susceptible to this poor soil fertility status. A significant amount of maize growth and yield is lost when it is cultivated in low organic matter and poor fertility soil. To overcome this issue organic amendments can play an imperative role. Biochar and vermicompost are organic amendments that can not only improve organic residues but also increase soil nutrient concentration. The current experiment was conducted to explore the sole and combined application of both organic amendments with recommended NPK fertilizer. Four treatments were tested i.e., control, biochar (BC1), vermicompost (VC1) and VC1+BC1 with and without nitrogen (N), phosphorus (P) and potassium (K) in the experiment. Results showed that VC1+BC1+NPK performed significantly best for improvement in maize plant height (6.25 and 3.00%), 1000 grains weight (30.48 and 29.40%), biological yield (18.86 and 43.12%) and grains yield (30.58 and 39.59%) compared to BC0+VC0+NPK and control respectively. A significant improvement in soil N, P and K also validated the efficacious role of VC1+BC1+NPK over BC0+VC0+NPK and control. Treatment VC1+BC1+NPK is recommended for the achievement of better maize growth and yield in poor organic matter soils. More investigations are suggested in variable climatic conditions to declare VC1+BC1+NPK as the best amendment compared to control for enhancing soil N, P and K status as well as maize productivity.
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Project description:Atrazine causes serious contamination of agricultural soils and groundwater. This study investigated the influence mechanism of sterilized soil (CKs), unsterilized soil (CKn), sterilized soil amended with 45 (SsV1), 60 (SsV2), 75 (SsV3) days of vermicompost (the maturity days of vermicompost), and unsterilized soil amended with 45 (SnV1), 60 (SnV2), 75 (SnV3) days of vermicompost on atrazine catabolism. The atrazine degradation experiment lasted for 40 days. The results showed that the atrazine degradation rates for CKs, CKn, SsV1, SsV2, SsV3, SnV1, SnV2, and SnV3 were 24%, 56.9%, 62.8%, 66.1%, 65.9%, 87.5%, 92.9%, and 92.3%, respectively. Indigenous microorganisms capable of degrading atrazine were present in unsterilized soil, and the addition of vermicompost enhanced atrazine degradation. The humic acid content of SnV2 was the highest, at 4.11 g/kg, which was 71.97% higher than that of CKn. The addition of the vermicompost enhanced the production of hydroxyatrazine, deethylatrazine, and deisopropylatrazine. Vermicompost increased the abundance of atrazine-degrading bacteria (Mycobacterium, Devosia, etc.), and introduced new atrazine-degrading bacteria (Mesorhizobium, Demequina). The above results showed that the best degradation of atrazine was achieved with 60 days of vermicompost addition. This study provides a new, efficient, economical, and environmentally friendly strategy for the remediation of atrazine-contaminated soil.
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Project description:Interaction of microbes affects the growth, metabolism and differentiation of members of the community. While direct and indirect competitions, like spite and nutrient consumption have negative effect on each other, microbes also evolved in nature not only to fight, but in some cases to adapt or support each other while increasing the fitness of the community. Presence of bacteria and fungi in the soil results in interactions and various examples were described, including mutualism. Bacilli attach to the plant root and form complex communities in the rhizosphere. Bacillus subtilis, when grown in the presence of Aspergillus niger interacts with the fungal partner, attaches and grows on the hyphae. Using dual transcriptome experiment, we show that both fungi and bacteria alter their metabolisms during the interaction. Interestingly, the transcription of genes related to the antifungal and antibacterial defense mechanism of B. subtilis and A. niger, respectively, are decreased upon attachment of bacteria to the mycelia. Our microarray experiments provide a novel insight into the mutual interaction of a bacterium and a fungus. Aspergillus niger were grown with and without Bacillus subtilis. Biological triplicates were made for both conditions, Affymetrix microarray experiments were performed on these samples.
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