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SRX1294673: SOIL MICROBIAL COMMUNITY RESISTANCE TO NPK FERTILIZATION AND RESILIANCE TO FERTILIZATION WITH DICYANDIAMIDE-TREATED SWINE SLURRY
1 ION_TORRENT (Ion Torrent PGM) run: 3.8M spots, 781M bases, 581.8Mb downloads

Design: The experiment was carried out in the Federal University of Santa Maria (UFSM), Rio Grande do Sul State, Brazil (29°43’ S, 53°43’ W, altitude 105). The field was cultivated during 2 years before soil sampling (2011 and 2012) with a corn/cereal succession (corn/oat/corn/wheat) under a no-tillage system. a composite soil sample (mixture of 8 random points in each plot to form a single composite sample) was taken of the top soil (0-5 cm) from the triplicate plots. Pre-experiment soil samples were collected one day before application of treatments, when there were 6.1 t ha-1 of wheat residues (Triticum aestivum L.; cv. Quartz) on the soil surface. Four days after treatment application, maize (Zea mays L.; hibrid 32R22 Herculex) was sown manually, with an interrow distance of 0.7 m. After maize was sown, soil samples were taken on days 3, 6, 11, 25 and 50 after maize seedling for molecular analyses. The samples were immediately placed in liquid nitrogen and stored at -80ºC until total RNA extraction. The PowerSoil Total RNA Isolation Kit (MO-BIO Laboratories, Inc., CA) was used to extract the total RNA from two grams of soil per sample (n = 72) by following the manufacturer’s instructions. The V4 region of the 16S rRNA gene was amplified and sequenced using the PGM Ion Torrent (Life Technologies) using archaeal/bacterial primers 515F and 806R. Multiple samples were PCR-amplified using barcoded primers linked with the Ion adapter “A” sequence (5′-CCATCTCATCCCTGCGTGTCTCCGACTCAG-3′) and Ion adapter “P1” sequence (5′-CCTCTCTATGGGCAGTCGGTGAT-3′) to obtain a sequence of primer composed for A-barcode-806R and P1-515F adapter and primers. Five runs were performed. The raw sequences and the barcodes used are provided as follow: Chp1.fastq (TCCCTTGTCTCC-Control_0; ACGAGACTGATT-Control_0; GCTGTACGGATT-Control_0; ATCACCAGGTGT-NPK_0; TGGTCAACGATA-NPK_0; ATCGCACAGTAA-NPK_0; GTCGTGTAGCCT-Slurryswine_0; AGCGGAGGTTAG-Slurryswine_0; ATCCTTTGGTTC-Slurryswine_0; TACAGCGCATAC-Slurryswine_DCD_0; ACCGGTATGTAC-Slurryswine_DCD_0; AATTGTGTCGGA-Slurryswine_DCD_0; TGCATACACTGG-Control_3; AGTCGAACGAGG-Control_3; ACCAGTGACTCA-Control_3; GAATACCAAGTC-NPK_3; GTAGATCGTGTA-NPK_3; TAACGTGTGTGC-NPK_3; CATTATGGCGTG-Slurryswine_3; CCAATACGCCTG-Slurryswine_3); Chip2.fastq (TCCCTTGTCTCC-Slurryswine_3; ACGAGACTGATT-Slurryswine_DCD_3; GCTGTACGGATT-Slurryswine_DCD_3; ATCACCAGGTGT-Slurryswine_DCD_3; GTCGTGTAGCCT-Control_6; TACAGCGCATAC-NPK_6; ACCGGTATGTAC-Slurryswine_6; AATTGTGTCGGA-Slurryswine_6; TGCATACACTGG-Slurryswine_6; AGTCGAACGAGG-Slurryswine_DCD_6; ACCAGTGACTCA-Slurryswine_DCD_6; GTAGATCGTGTA-Control_12; TAACGTGTGTGC-Control_12) Chip3.fastq (TCCCTTGTCTCC-NPK_12; ACGAGACTGATT-NPK_12; GCTGTACGGATT-Slurry_swine_12; ATCACCAGGTGT-Slurry_swine_12; TGGTCAACGATA-Slurry_swine_12; ATCGCACAGTAA-Slurry_swine_DCD_12; GTCGTGTAGCCT-Slurry_swine_DCD_12; AGCGGAGGTTAG-Slurry_swine_DCD_12; ATCCTTTGGTTC-Control_25; TACAGCGCATAC-Control_25; ACCGGTATGTAC-Control_25; AATTGTGTCGGA-NPK_25; TGCATACACTGG-NPK_25; AGTCGAACGAGG-NPK_25; ACCAGTGACTCA-Slurry_swine_25; GAATACCAAGTC-Slurry_swine_25; GTAGATCGTGTA-Slurry_swine_25; TAACGTGTGTGC-Slurry_swine_DCD_25; CATTATGGCGTG-Slurry_swine_DCD_25; CCAATACGCCTG-Slurry_swine_DCD_25) Chip4.fastq (TCCCTTGTCTCC-Control_50; ACGAGACTGATT-Control_50; GCTGTACGGATT-Control_50; ATCACCAGGTGT-NPK_50; TGGTCAACGATA-NPK_50; ATCGCACAGTAA-NPK_12; GTCGTGTAGCCT-Slurry swine_50; AGCGGAGGTTAG-Slurry swine_50; ATCCTTTGGTTC-Slurry swine_50; TACAGCGCATAC-Slurry swine _ DCD_50; ACCGGTATGTAC-Slurry swine _ DCD_50; AATTGTGTCGGA-Slurry swine _ DCD_50; TGCATACACTGG-Slurry_input; AGTCGAACGAGG-Slurry_input; ACCAGTGACTCA-Slurry_input; GAATACCAAGTC-Slurry_input_DCD; GTAGATCGTGTA-Slurry_input_DCD; TAACGTGTGTGC-Slurry_input_DCD) Chip5.fastq (TGGTCAACGATA-Control_6; ATCGCACAGTAA-Control_6; AGCGGAGGTTAG-NPK_6; ATCCTTTGGTTC-NPK_6; ACCGGTATGTAC-Slurry swine _ DCD_0; AATTGTGTCGGA-NPK_25; TGCATACACTGG-NPK_25; ACCAGTGACTCA-Slurry swine_25; GAATACCAAGTC-Slurry swine _ DCD_6; TAACGTGTGTGC-Control_12; CATTATGGCGTG-Control_12; CCAATACGCCTG-NPK_12)
Submitted by: FEDERAL UNIVERSITY OF PAMPA
Study: Recent History of Land Use Buffers the Shifts of Soil Bacterial Community
show Abstracthide Abstract
The interaction among plants, soil and microorganisms is considered to be the major driver of the ecosystem functions and any modification on plant cover and/or soil properties might affect the microbial structure, which, in turn, will influence the ecological processes. Assuming that soil properties are the major drivers of soil bacterial diversity and structure, within the same soil type, can the plant cover cause significant shifts on soil bacterial community composition? To address this question we used 16S rRNA pyrosequencing to detect differences in diversity, composition and/or relative abundance of bacterial taxa from an area covered by pristine forest and eight years old grassland surrounded by this forest. After removing the natural forest, the soil bacterial community did not suffer a great differentiation. Sixty nine percent of the operational taxonomic unities (OTUs) were shared between environments. Overall, forest samples and grassland samples presented the same diversity and the clustering analysis did not show the occurrence of very distinctive bacterial communities between environments. However, we detected eleven OTUs in statistically significantly higher abundance in the forest samples but in lower abundance in the grassland samples and twelve OTUs in statistically significantly higher abundance in the grassland samples but in lower abundance in the forest samples. Those results illustrate that as long as the soil chemical and physical conditions do not suffer great alterations, the recent history of land use buffers the shifts of soil bacterial community.
Sample: Pampa Microbiome
SAMN00996358 • SRS334046 • All experiments • All runs
Organism: soil metagenome
Library:
Name: Swine slurry fertilization
Instrument: Ion Torrent PGM
Strategy: AMPLICON
Source: METAGENOMIC
Selection: PCR
Layout: SINGLE
Spot descriptor:
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Runs: 1 run, 3.8M spots, 781M bases, 581.8Mb
Run# of Spots# of BasesSizePublished
SRR25337583,848,704781M581.8Mb2015-10-01

ID:
1850753

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