The rhizosphere soil bacterial community dieversity of Sea Rice 86 under different salinities
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA772703 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16548700_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR16548701_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR16548702_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR16548703_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR16548704_subreads.fastq.gz | Fastqsanger.gz |
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Project description:Introduction: A major economic impediment to the aquaculture of marine finfish in land-based recirculating systems is maintaining the system salinity at a range for optimal growth. Florida Pompano (Trachinotus carolinus) are warm water, euryhaline, marine finfish shown to be a suitable candidate for low-salinity culture. Due to its popularity among sport and commercial fishers, high market value, and ability to readily consume pelleted feeds, the Florida Pompano has become a renewed target for commercialized aquaculture. Although the Florida Pompano has been successfully grown at various salinities, its optimal growth salinity has not yet been established. Studies have shown culturing at different salinities has an effect on digestion rates, feed utilization, and lipid biosynthesis. Identifying the optimal salinity for growth would result in decreased energy expenditure on maintaining homeostasis, since osmoregulation is a highly demanding process. This would allow for energy to be spent on the efficient use of nutrients. Methods: Our study was designed to determine how Florida Pompano larviculture at various salinities affects fish health with transcriptomics (RNA-seq) and fatty acid analysis. RNA-seq was used to identify genes actively transcribed and expressed at the time of sampling. After hatching in a salinity of ~ 30 ppt, larvae were reared in 345 L tanks at one of three salinities (10, 20, 30 ppt) in triplicate. Larvae samples for RNA-seq and fatty acid analysis were collected every three days until weaning. Samples for fatty acid composition were analyzed using a gas chromatography-mass spectrometry (GC/MS). RNA was extracted from homogenized whole-body samples using the Qiagen RNeasy Mini kit. Total RNA was sequenced on the Illumina HiSeq 4000 System. Raw sequences were filtered for low-quality sequences, aligned to the S. dumerili reference genome (NCBI Genome: 12614), and quantified. Each sampling day was compared across salinities to establish the differentially expressed genes (DEGs) between salinities. Results & Discussion: The numbers of DEGS in pooled samples was minimal (less than 15 total in each comparison) and the number of DEGS at each dph was variable. There were no significant differences between pooled samples or at each dph according to PERMANOVA analysis, but each dph was statistically different on pairwise analysis. Gene set enrichment analysis revealed that there was a downregulation of immune related genes in lower salinities versus higher salinities suggesting larvae may be dealing with less stress at lower salinities. Most osmoregulation, fatty acid, and immune related genes tested were not significantly different across salinities. This is likely be cause the Florida pompano is euryhaline and has a tolerance to the salinities selected. There was an increase in the expression levels of several immune related genes that may indicate an increase exposure to pathogens at later days post hatch likely related to feeding schedule. There was also an increase in fatty acid biosynthesis genes that corresponded with levels of fatty acids indicating a possible synthesis of essential fatty acids from precursors. Conclusions: From a transcriptomics perspective, the larvae did not show a negative response to lower salinities in comparison to higher salinities, which in fact showed upregulation of immune related genes. Further exploration of Florida pompano’s ability to biosynthesize essential fatty acids is necessary. This study will help enable the optimization of Florida Pompano larviculture using information on the optimal salinity and fatty acid content for growth and facilitate more cost-effective rearing methods.
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Project description:consortium CY-1 cultured under different salinities Raw sequence reads
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Project description:Rhizosphere microorganisms are closely associated with phosphorus (P) uptake in plants and are considered potential agents to mitigate P shortage. However, the mechanisms of rhizospheric microbial community assembly under P deficiency have yet to be elucidated. In this study, bacterial and fungal communities in rice rhizosphere and their P mobilization potential under high (+P) and low (-P) concentrations of P were investigated. Bacterial and fungal community structures were significantly different between -P and +P treatments. And both bacterial and fungal P-mobilizing taxa were enriched in-P treatment; however, the proportion of P-mobilizing agents in the fungal community was markedly greater than that in the bacterial community. A culture experiment confirmed that microbial phosphate solubilizing capacity was significantly higher in -P treatment compared with that in +P treatment. -P treatment lowered bacterial diversity in rice rhizosphere but increased fungal diversity. Further analysis demonstrated that the contribution of deterministic processes in governing bacterial community assembly was strengthened under P deficiency but was largely weakened in shaping the fungal community. These results highlighted that enriching P-mobilizing microbes in the rhizosphere is a vital way for rice to cope with P deficiency, and that fungi contribute considerably to P mobilization in rice rhizosphere. Findings from the study provide novel insights into the assembly of the rhizosphere microbiome under P deficiency and this will facilitate the development of rhizosphere microbial regulation strategies to increase nutrient uptake in plants.
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Project description:RNA sequencing was used to measure global gene expression in wild caught threespine sticklebacks. Native freshwater and marine fish were acclimated in water of different salinities before the gene expression in kidney was measured. The comparative transcriptomic analysis allowed the identification of salt-responsive genes.
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Project description:Streptococcus sp. zg-86 isolate:zg-86 Genome sequencing
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Project description:Transcriptome analysis of NTHi 86-028NPrpsL, NTHi 86-028NPrpsL∆fur, and NTHi 86-028NPrpsL∆fur(pT-fur) strains Nontypeable Haemophilus influenzae (NTHi) is a commensal microorganism of the normal human nasopharyngeal flora, yet also an opportunistic pathogen of the upper and lower respiratory tracts. Changes in gene expression patterns in response to host microenvironments are likely critical for survival. One such system of gene regulation is the ability to carefully regulate iron uptake. A central regulatory system that controls iron uptake, mediated by the ferric uptake regulator Fur, is present in multiple bacteria, including NTHi. To understand the regulation of iron homeostasis in NTHi, fur was deleted in the NTHi strain 86-028NPrpsL. Using RNA-Seq, we identified both protein-encoding and small RNA genes whose expression was repressed or activated by Fur. Overall design: These data comprise transcriptional anaylses of an rpsL mutant of 86-028NP, an isogenic fur mutant of 86-028NPrpsL and a complemented fur mutant strain. All strains were grown in defined medium containing 10 µg/ml human hemoglobin to mid-log phase. Cells were then harvested and RNA extracted. A total of three biological replicates were generated for these analyses.
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Project description:Nitrification at different salinities: biofilm community composition and physiological plasticity
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Project description:Transcriptome analysis of NTHi 86-028NPrpsL, NTHi 86-028NPrpsL∆fur, and NTHi 86-028NPrpsL∆fur(pT-fur) strains Nontypeable Haemophilus influenzae (NTHi) is a commensal microorganism of the normal human nasopharyngeal flora, yet also an opportunistic pathogen of the upper and lower respiratory tracts. Changes in gene expression patterns in response to host microenvironments are likely critical for survival. One such system of gene regulation is the ability to carefully regulate iron uptake. A central regulatory system that controls iron uptake, mediated by the ferric uptake regulator Fur, is present in multiple bacteria, including NTHi. To understand the regulation of iron homeostasis in NTHi, fur was deleted in the NTHi strain 86-028NPrpsL. Using RNA-Seq, we identified both protein-encoding and small RNA genes whose expression was repressed or activated by Fur. Overall design: These data comprise transcriptional anaylses of an rpsL mutant of 86-028NP, an isogenic fur mutant of 86-028NPrpsL and a complemented fur mutant strain. All strains were grown in defined medium containing 10 µg/ml human hemoglobin to mid-log phase. Cells were then harvested and RNA extracted. A total of three biological replicates were generated for these analyses. Analysis of transcriptomes using the Illumina HiSeq 2000 of three strains of nontypeable Haemophilus influenzae which include NTHi 86-028NPrpsL, NTHi 86-028NPrpsL∆fur, and NTHi 86-028NPrpsL∆fur(pT-fur) strains. For each strain three biological replicates were analyzed
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Project description:Nontypeable Haemophilus influenzae (NTHi) is a commensal microorganism of the normal human nasopharyngeal flora, yet also an opportunistic pathogen of the upper and lower respiratory tracts. Changes in gene expression patterns in response to host microenvironments are likely critical for survival. One such system of gene regulation is the ability to carefully regulate iron uptake. A central regulatory system that controls iron uptake, mediated by the ferric uptake regulator Fur, is present in multiple bacteria, including NTHi. Previous work has identified a small RNA, HrrF, that is Fur-regulated in NTHi 86-028NPrpsL.To understand the contribution made by HrrF to gene regulation in NTHi, hrrF was deleted in the NTHi strain 86-028NPrpsLM-bM-^HM-^Ffur. Using RNA-Seq, we identified protein-encoding genes whose expression was repressed or activated by HrrF. These data comprise transcriptional anaylses of an rpsL mutant of 86-028NP, an isogenic fur mutant of 86-028NPrpsL, an isogenic fur mutant of 86-028NPrpsL also containing a full deletion of hrrF, and an isogenic fur mutant of 86-028NPrpsL also containing a deletion of only the 3' portion of hrrF. All strains were grown in defined medium containing 10 M-BM-5g/ml human hemoglobin to mid-log phase. Cells were then harvested and RNA extracted. A total of three biological replicates were generated for these analyses. Analysis of transcriptomes using the Illumina HiSeq 2000 of four strains of nontypeable Haemophilus influenzae which include NTHi 86-028NPrpsL, NTHi 86-028NPrpsLM-bM-^HM-^Ffur, NTHi 86-028NPrpsLM-bM-^HM-^FfurM-bM-^HM-^FhrrF, and NTHi 86-028NPrpsLM-bM-^HM-^FfurM-bM-^HM-^FhrrF3' strains. For each strain three biological replicates were analyzed.
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