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ERX1906442: Illumina MiSeq sequencing; qiita_ptid_52:1715.McG.NF3
1 ILLUMINA (Illumina MiSeq) run: 27,077 spots, 4.1M bases, 2.3Mb downloads

Design: Sampling was conducted at 21 plantations of various land use histories, coffee plantation ages, and soil treatments in the Union de Cooperativas Agropecuarias (UCA) Miraflor, a union of small agricultural cooperatives located within the Miraflor Nature Reserve, 30 km from the city of Esteli. Three 10 x 10 m plots were set up in each plantation, and three soil cores (20 cm depth) were obtained from random points within them. Densiometry measurements were made at dbh level, and all trees with canopies overlapping with the plot were identified. Plantation owners were surveyed for the land use history and soil treatments. All samples were extracted following the EMP protocol.
Submitted by: University of California San Diego Microbiome Initiative (University of California San Diego Microbiome Init)
Study: McGuire Nicaragua coffee soil
show Abstracthide Abstract
Coffee plantations in northern Latin America coincide with areas of extremely rich biodiversity. Recent advances by fair trade organizations have stimulated sustainable agriculture in the form of shade coffee plantations as a way of reconciling economic and conservation targets; however, the shade management techniques vary between sites and result in different canopy assemblies across farms over time. The effect of differing canopy regimes on microbial communities are poorly understood but guide nutrient cycling, crucial for both agriculture and the maintenance of ecosystem diversity. The goal of this project is to explore the relationship between managed canopies, land use history, and soil microbial communities in Nicaraguan shade-coffee plantations, and use this information to develop a set of guidelines for soil management to improve soil quality.
Sample: qiita_sid_1715:1715.McG.NF3
SAMEA93915418 • ERS1563335 • All experiments • All runs
Organism: soil metagenome
Library:
Name: 1715.McG.NF3
Instrument: Illumina MiSeq
Strategy: OTHER
Source: METAGENOMIC
Selection: PCR
Layout: SINGLE
Construction protocol: EMP V4 515f,806rbc protocol
Experiment attributes: (show all 15 attributes...) (hide...)
barcode: GACAGAGGTGCA
center_name: CCME
center_project_name: mcguire_nicaragua_soil
illumina_technology: MiSeq
linker: GT
pcr_primers: FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT
primer: GTGTGCCAGCMGCCGCGGTAA
run_center: CCME
run_date: 3/2/12
run_prefix: McGuire_S0_L001
samp_size: .1,g
sample_center: McGuire Lab, New York NY
sequencing_meth: sequencing by synthesis
target_gene: 16S rRNA
target_subfragment: V4
Runs: 1 run, 27,077 spots, 4.1M bases, 2.3Mb
Run# of Spots# of BasesSizePublished
ERR184446527,0774.1M2.3Mb2017-02-21

ID:
3736735

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