opens the authoritative record at ENA, SRA or BioSample; this page never replaces it
PRJEB3386
Pipeline 0.1.0 Contract v0.1 Licence CC-BY-4.0
Tags
- 16S rRNA
- V4
- amplicon
- selection pcr
- single-end
- 454 GS FLX
- primers present
- CC-BY-4.0
derived from the release metadata, not hand-written
Study
The study record carries no description, and its registered title is the accession itself. The figures below are computed from the 22 released samples and 22 runs.
- Samples
- 22
- Runs
- 22
- Collection
- 2011-06 to 2011-06
Linked publication
Effect of metal oxide nanoparticles on microbial community structure and function in two different soil types.10.1371/journal.pone.0084441 · 2013 · via europepmc
Linked by the enrich stage. Fields taken from the paper: primers.
abstract
Increased availability of nanoparticle-based products will, inevitably, expose the environment to these materials. Engineered nanoparticles (ENPs) may thus find their way into the soil environment via wastewater, dumpsters and other anthropogenic sources; metallic oxide nanoparticles comprise one group of ENPs that could potentially be hazardous for the environment. Because the soil bacterial community is a major service provider for the ecosystem and humankind, it is critical to study the effects of ENP exposure on soil bacteria. These effects were evaluated by measuring bacterial community activity, composition and size following exposure to copper oxide (CuO) and magnetite (Fe3O4) nanosized (<50 nm) particles. Two different soil types were examined: a sandy loam (Bet-Dagan) and a sandy clay loam (Yatir), under two ENP concentrations (1%, 0.1%). Results indicate that the bacterial community in Bet-Dagan soil was more susceptible to change due to exposure to these ENPs, relative to Yatir soil. More specifically, CuO had a strong effect on bacterial hydrolytic activity, oxidative potential, community composition and size in Bet-Dagan soil. Few effects were noted in the Yatir soil, although 1% CuO exposure did cause a significant decreased oxidative potential and changes to community composition. Fe3O4 changed the hydrolytic activity and bacterial community composition in Bet-Dagan soil but did not affect the Yatir soil bacterial community. Furthermore, in Bet-Dagan soil, abundance of bacteria annotated to OTUs from the Bacilli class decreased after addition of 0.1% CuO but increased with 1% CuO, while in Yatir soil their abundance was reduced with 1% CuO. Other important soil bacterial groups, including Rhizobiales and Sphingobacteriaceae, were negatively affected by CuO addition to soil. These results indicate that both ENPs are potentially harmful to soil environments. Furthermore, it is suggested that the clay fraction and organic matter in different soils interact with the ENPs and reduce their toxicity.
Linked by the enrich stage from europepmc.
Location
sampling sites from the release coordinatesPlace name hierarchy
- ▸ ישראל
- › מחוז המרכז
Latitude 31.98333 to 31.98333, longitude 34.81667 to 34.81667. Names resolved with OpenStreetMap Nominatim from the release's own coordinates; Coordinates parsed from the released lat_lon text field, which the pipeline keeps but does not split into latitude/longitude columns.
How the sequences were obtained
sample to releaseSample collection
22 samples, 2011-06 to 2011-06
31.9833 to 31.9833 N, 34.8167 to 34.8167 E
Storage
not reported
neither the archive nor the linked paper states storage conditions
Processing
not reported
no extraction kit or lysis protocol in the archive or the linked paper
PCR
16S rRNA V4, primers 1100R, 530F, 907R
primers: present
Sequencing preparation
not reported
no library kit or index strategy in the archive or the linked paper
Sequencing
454 GS FLX
22 runs; SINGLE 356.4545 bp reads; the linked paper's text supports 454
Denoising
dada2 1.38.0
2,846 ASVs from 31,500 reads
ampliconflow branches off at step 6, Sequencing
this releaseampliconflow starts here: 31,500 reads from 22 runs, QC to 89.2% 16S identity and 65.3% above Q30, primers trimmed, dada2 1.38.0 to 2,846 ASVs, taxonomy against a SINTAX reference, then the release (CC-BY-4.0).
Steps 1 to 6 are how the sequences were obtained, from the study's own archive metadata. Step 7 is what the authors report doing with the sequences in the linked paper. ampliconflow starts at the deposited reads rather than repeating the wet lab.
Taxonomy assigned with SILVA 138.2 (SINTAX).
The linked paper's methods run to 17,176 characters. It supports: platform, primers.
Conflict on sequencing platform: the release has 454 GS FLX, the linked paper's text supports 454.
22
Samples
22 runs
2.8k
Features
OTUs at 97%
65.9k
Reads
mapped total
135 MB
Release size
73 files
Depth floor
1,000 reads
no samples below
QC warnings
22
100% of runs warned
Reads per sample
log scale- min
- 1,132
- median
- 2,417
- max
- 6,700
Feature detection
100.0% non-zero2,846 / 2,846 features
Features with at least one observed read. The remainder are present in the reference set but not detected in these samples.
Composition
Top phyla
- Pseudomonadota 22,974 (34.9%)
- Actinomycetota 11,795 (17.9%)
- Bacillota 8,982 (13.6%)
- Bacteroidota 7,363 (11.2%)
- Gemmatimonadota 5,015 (7.6%)
- Acidobacteriota 3,827 (5.8%)
- Chloroflexota 2,182 (3.3%)
- Myxococcota 1,163 (1.8%)
- Verrucomicrobiota 740 (1.1%)
- Armatimonadota 507 (0.8%)
- Bdellovibrionota 403 (0.6%)
- Planctomycetota 273 (0.4%)
- Patescibacteria 201 (0.3%)
- Cyanobacteriota 132 (0.2%)
- Methylomirabilota 101 (0.2%)
- Candidatus Kapabacteria 75 (0.1%)
- Thermodesulfobacteriota 41 (0.1%)
- Nitrospirota 18 (0.0%)
- Latescibacterota 9 (0.0%)
- MBNT15 8 (0.0%)
Top genera
- Incertae Sedis 17,502 (26.6%)
- Sphingomonas 3,397 (5.2%)
- Massilia 2,767 (4.2%)
- Microvirga 2,625 (4.0%)
- Flavisolibacter 2,431 (3.7%)
- Neobacillus 2,332 (3.5%)
- Noviherbaspirillum 2,271 (3.4%)
- Nocardioides 1,823 (2.8%)
- Daejeonella 1,693 (2.6%)
- Lysinibacillus 1,688 (2.6%)
- Lysobacter 1,629 (2.5%)
- Blastococcus 1,422 (2.2%)
- Caenimonas 1,378 (2.1%)
- Rubrobacter 1,068 (1.6%)
- Bacillus 1,002 (1.5%)
- Solirubrobacter 858 (1.3%)
- Azohydromonas 819 (1.2%)
- Pontibacter 791 (1.2%)
- Mesobacillus 786 (1.2%)
- Phenylobacterium 754 (1.1%)
Rank-abundance
log-log2,846 ranked features, top 200 shown. A steep drop means a few taxa carry most of the reads.
Per-sample reads
22 samples- min
- 1,132
- median
- 2,417
- max
- 6,700
Downstream QC and analysis
computed from the released tablesEleven modules, computed from the released count table, the sample metadata and the per-run QC reports. Each panel states its own n and the test it used; a module that cannot run on this release is shown as a flagged gap rather than an empty frame.
Rarefaction
median with p10 to p90Expected richness when 11 samples are subsampled to a common depth, resampled 31 draws. Median 36 features observed at full depth.
Depth against richness
log depthOne point per sample. Correlation of log reads with observed features is 0.913, so the depth floor is doing most of the work of deciding how many features a sample shows.
Per-run QC
- 16S identity 89.2% alignment call per run
- Q30 rate 65.3% mean Q 31
- Amplicon V4 primers present
- PhiX 0.0% control spike-in
22 run report(s), n/a GC, 0.0% ambiguous bases.
Diversity
- Shannon
- 4.34
- Simpson
- 0.983
- Evenness
- 0.916
- Chao1
- 118
Median across samples. Observed richness ranges 0 to 222.
Feature prevalence
0 of 2,846 features
present in at least half of the 22 samples (0.0%). 1,435 features appear in one sample only, which is the long tail rarefaction is fighting.
Ordination
One point per sample, 22 plotted. Choose the axes and the colour variable; hover a point for its sample id. The legend below the axes names the levels or the numeric range.
What explains each axis
pc1 · 37.6%
- observed 77.0%
- reads 61.2%
- evenness 17.9%
- chao1 7.3%
pc2 · 6.7%
- evenness 17.9%
- chao1 7.3%
- reads 4.4%
- shannon 2.0%
pc3 · 6.3%
- evenness 20.3%
- shannon 12.7%
- chao1 8.0%
- observed 1.8%
Categorical variables use eta-squared (between-group share of the axis), numeric ones the squared Pearson correlation. Computed from the released sample metadata.
Alpha diversity per sample
ShannonMedian Shannon 4.344 across the release; observed richness runs 0 to 222.
Bray-Curtis dissimilarity
22 x 22, darker is closerSample order is the release order, 22 labels, and the matrix itself ships as beta_distance.tsv beside the analysis.
Phylogenetic diversity
Not available for this release: no Newick tree beside the table; run the tree stage, then re-run analyze. The legacy analysis computed Faith's PD when the container carried a tree, and this one reports the absence instead of an empty column.
Community states
CLR, k by silhouettek = 2 silhouette 0.566
- state 0 21 samples
- state 1 1 samples
Clustered on the centred log-ratio of the top 200 features; 22 samples.
Batch-bias audit
states againstadjusted Rand n/a p = n/a
not enough levels to test
permutations. Every sample here carries both MiSeq and MiniSeq runs, so the batch variable used is the one with two levels, here .
Variance partitioning
mean R2 per feature, CLRJoint R2 n/a, so the metadata explains a modest slice of the feature variation, and the two variables are not independent of one another.
Effect size
No two-level comparison available.
Taxa against all samples
withfeatures tested, 0 survive the correction at q ≤ 0.05
Nothing survives. The smallest q is n/a, which is the honest answer for a study whose samples are spread across three years with two to thirteen samples per year.
Group difference and spread
Bray-Curtis, 999 permutations- PERMANOVA pseudo-F
- n/a · p n/a
- PERMDISP F
- n/a · p n/a
- Distance decay (Mantel r)
- n/a · p n/a
The contamination class separates the communities beyond the spread within each class (PERMANOVA) with no evidence that the spread itself differs (PERMDISP). Distance decay runs over n/a to n/a km.
Spatial structure
observed richness over distancethe study's coordinates fall on a single site (no spread), so spatial autocorrelation is not defined
Co-occurrence network
100 nodes · 506 edges
- positive
- 506
- negative
- 0
- density
- 0.102
- components
- 9
- mean degree
- 10.1
Spearman on log1p proportions, 100 features, |r| ≥ 0.50, FDR 0.05.
Hubs by degree
Phylogenetic and signal analyses need a tree
no Newick tree beside the table; run the tree stage, then re-run analyze. The tree stage aligns the ASVs with MAFFT and builds with FastTree, both detected as external tools; neither is installed on the machine this page was built on, so Faith's PD, UniFrac, Pagel's lambda and Blomberg's K are left flagged rather than guessed.
ASV phylogeny
0 most abundant of the treeNo tree in this release.
ASV panel
no sequence fileThe representative sequences are not in this release, so length and GC cannot be drawn.
Most abundant ASVs
| ASV | phylum | genus | mean | prev. |
|---|---|---|---|---|
| 16s-v4:ASV_1 | Pseudomonadota | Massilia | 18.6 | 5% |
| 16s-v4:ASV_2 | Pseudomonadota | Microvirga | 11.0 | 5% |
| 16s-v4:ASV_3 | Bacteroidota | Daejeonella | 10.0 | 5% |
| 16s-v4:ASV_4 | Bacteroidota | Pontibacter | 9.8 | 5% |
| 16s-v4:ASV_5 | Bacillota | Sporosarcina | 8.0 | 5% |
| 16s-v4:ASV_6 | Bacillota | Bacillus | 7.9 | 5% |
| 16s-v4:ASV_7 | Bacillota | Neobacillus | 7.6 | 5% |
| 16s-v4:ASV_8 | Bacillota | Neobacillus | 7.4 | 5% |
| 16s-v4:ASV_9 | Pseudomonadota | Massilia | 6.6 | 5% |
| 16s-v4:ASV_10 | Pseudomonadota | Massilia | 6.5 | 5% |
| 16s-v4:ASV_11 | Actinomycetota | Nocardioides | 6.3 | 5% |
| 16s-v4:ASV_12 | Pseudomonadota | Noviherbaspirillum | 6.3 | 5% |
Similar studies
composition, metadata, location, shared authors- taxonomy 52% similar (genus)
- same region (V4)
- shared author(s): t
33 samples
- taxonomy 58% similar (genus)
- same region (V4)
- shared author(s): s
16 samples
- taxonomy 46% similar (genus)
- shared author(s): t
27 samples
- taxonomy 48% similar (genus)
- same region (V4)
- shared author(s): i, s, t
65 samples
- taxonomy 45% similar (genus)
- same region (V4)
- shared author(s): d
60 samples
- taxonomy 42% similar (genus)
- shared author(s): d
16 samples
Ranked from the released tables: genus composition as Bray-Curtis similarity, shared environment and method terms, the distance between sample centroids, and authors shared with the linked publication.
Missing or wrong data?
Report a field that is empty or mistaken, or associate a paper with this study. No account is needed; the contact email is optional and used only to reply about this submission.
Downloads
14 files · sha256 in manifest- Count table (16S V4-V5) 5.7 KB tables/PRJEB3386.16s-v4-v5.parquet
- Count table (16S V4) 6.0 KB tables/PRJEB3386.16s-v4.parquet
- Count table (16S V5) 1.6 KB tables/PRJEB3386.16s-v5.parquet
- Count table, BIOM (16S V4-V5) 18 KB tables/PRJEB3386.16s-v4-v5.biom.gz
- Count table, BIOM (16S V4) 19 KB tables/PRJEB3386.16s-v4.biom.gz
- Count table, BIOM (16S V5) 3.0 KB tables/PRJEB3386.16s-v5.biom.gz
- Taxonomy 176 KB features.parquet
- Taxonomy (TSV) 184 KB taxonomy.tsv.gz
- Sample metadata 20 KB samples.parquet
- Run metadata 14 KB runs.parquet
- Sequences (fasta) 34 KB sequences/PRJEB3386.16s-v4-v5.fasta.gz
- Sequences (fasta) 39 KB sequences/PRJEB3386.16s-v4.fasta.gz
- Sequences (fasta) 3.9 KB sequences/PRJEB3386.16s-v5.fasta.gz
- Manifest manifest.json
Files are served from https://huggingface.co/datasets/hmacgregor/ampliconflow-releases/resolve/main/PRJEB3386-20260926/ once hosting is wired. Until then the links point at a placeholder base URL.
Samples
| Sample | Collected | group | Reads | Features | Shannon | State |
|---|---|---|---|---|---|---|
| SAMEA1712397 | 2011-06 | 0 | 0 | 0 | ||
| SAMEA1712399 | 2011-06 | 0 | 0 | 0 | ||
| SAMEA1712401 | 2011-06 | 1,243 | 79 | 4.003 | 0 | |
| SAMEA1712403 | 2011-06 | 0 | 0 | 0 | ||
| SAMEA1712405 | 2011-06 | 6,700 | 215 | 4.804 | 1 | |
| SAMEA1712407 | 2011-06 | 0 | 0 | 0 | ||
| SAMEA1712410 | 2011-06 | 0 | 0 | 0 | ||
| SAMEA1712412 | 2011-06 | 1,977 | 96 | 4.039 | 0 | |
| SAMEA1712413 | 2011-06 | 0 | 0 | 0 | ||
| SAMEA1712415 | 2011-06 | 1,544 | 72 | 3.785 | 0 | |
| SAMEA1712418 | 2011-06 | 0 | 0 | 0 | ||
| SAMEA1712420 | 2011-06 | 0 | 0 | 0 | ||
| SAMEA1712422 | 2011-06 | 0 | 0 | 0 | ||
| SAMEA1712424 | 2011-06 | 2,232 | 125 | 4.505 | 0 | |
| SAMEA1712426 | 2011-06 | 0 | 0 | 0 | ||
| SAMEA1712428 | 2011-06 | 2,674 | 178 | 4.765 | 0 | |
| SAMEA1712430 | 2011-06 | 1,507 | 81 | 4.029 | 0 | |
| SAMEA1712432 | 2011-06 | 4,355 | 140 | 4.344 | 0 | |
| SAMEA1712434 | 2011-06 | 2,264 | 115 | 4.399 | 0 | |
| SAMEA1712436 | 2011-06 | 4,705 | 222 | 4.993 | 0 | |
| SAMEA1712438 | 2011-06 | 0 | 0 | 0 | ||
| SAMEA1712440 | 2011-06 | 2,299 | 118 | 4.341 | 0 |
click a column head to sort