ampliconflow
Archive records ENA PRJNA338649 SRA PRJNA338649 BioProject PRJNA338649

opens the authoritative record at ENA, SRA or BioSample; this page never replaces it

PRJNA338649 released 25 Sept 2026

PRJNA338649

Pipeline 0.1.0 Contract v0.1 Licence CC-BY-4.0

Tags

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 16 released samples and 16 runs.

Samples
16
Runs
16
Collection
2012-10 to 2012-10

Linked publication

Amplicon Sequencing Reveals Microbiological Signatures in Spent Nuclear Fuel Storage Basins.

10.3389/fmicb.2018.00377 · 2018 · via europepmc

Linked by the enrich stage. Fields taken from the paper: primers, subfragment. No per-sample coordinates in the paper.

abstract

Water quality is an important determinant for the structural integrity of alloy cladded fuels and assemblies during long-term wet storage. Detailed characterization of a water filled storage basin for spent nuclear reactor fuel was performed following the formation and proliferation of an amorphous white flocculent. White precipitant was sampled throughout the storage basin for chemical and spectroscopic characterization, and environmental DNA was extracted for 454 pyrosequencing of bacterial 16S rRNA gene diversity. Accordingly, spectroscopic analyses indicated the precipitant to be primarily amorphous to crystalline aluminum (oxy) hydroxides with minor associated elemental components including Fe, Si, Ti, and U. High levels of organic carbon were co-localized with the precipitant relative to bulk dissolved organic concentrations. Bacterial densities were highly variable between sampling locations and with depth within the water filled storage basin; cell numbers ranged from 4 × 10<sup>3</sup>to 4 × 10<sup>4</sup> cells/mL. Bacterial diversity that was physically associated with the aluminum (oxy) hydroxide complexes exceeded an estimated 4,000 OTUs/amplicon library (3% cutoff) and the majority of sequences were aligned to the families <i>Burkholderiaceae</i> (23%), <i>Nitrospiraceae</i> (23%), <i>Hyphomicrobiaceae</i> (17%), and <i>Comamonadaceae</i> (6%). We surmise that episodic changes in the physical and chemical properties of the basin contribute to the polymerization of aluminum (oxy) hydroxides, which in turn can chemisorb nutrients, carbon ligands and bacterial cells from the surrounding bulk aqueous phase. As such, these precipitants should establish favorable microhabitats for bacterial colonization and growth. Comparative analyses of 16S rRNA gene amplicon libraries across a selection of natural and engineered aquatic ecosystems were performed and microbial community and taxonomic signatures unique to the spent nuclear fuel (SNF) storage basin environment were revealed. These insights could spur the development of tractable bio-indicators that are specific of and diagnostic for water quality at discrete locations and finer scales of resolution, marking an important contribution for improved water quality and management of SNF storage facilities.

Linked by the enrich stage from europepmc.

Location

sampling sites from the release coordinates
16sampling sites · drag to pan, scroll or pinch to zoom

Place name hierarchy

  1. ▸ United States
  2. › Tennessee
  3. › Cheatham County

Districts named on the samples

  • Cheatham County 1

Latitude 36.34 to 36.34, longitude -87.03 to -87.03. 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 release
01 study metadata

Sample collection

16 samples, 2012-10 to 2012-10

36.3400 to 36.3400 N, -87.0300 to -87.0300 E

02 not reported

Storage

not reported

neither the archive nor the linked paper states storage conditions

03 not reported

Processing

not reported

no extraction kit or lysis protocol in the archive or the linked paper

04 per-run QC and the linked paper

PCR

16S rRNA V3-V4, 35 cycles, primers 338, region V1-V2

primers: present

05 not reported

Sequencing preparation

not reported

no library kit or index strategy in the archive or the linked paper

06 study metadata

Sequencing

454 GS FLX Titanium

16 runs; SINGLE 452.6875 bp reads; the linked paper's text supports 454

07 this release

Denoising

dada2 1.38.0

2,909 ASVs from 243,304 reads

ampliconflow branches off at step 6, Sequencing

this release

ampliconflow starts here: 243,304 reads from 16 runs, QC to 65.2% 16S identity and 74.6% above Q30, primers trimmed, dada2 1.38.0 to 2,909 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 9,925 characters. It supports: pcr_cycles, platform, primers, subfragment.

Conflict on sequencing platform: the release has 454 GS FLX Titanium, the linked paper's text supports 454.

16

Samples

16 runs

2.9k

Features

OTUs at 97%

243.3k

Reads

mapped total

136 MB

Release size

64 files

Reads per sample

log scale
min
5,179
median
14,539
max
27,759

Feature detection

100.0% non-zero

2,909 / 2,909 features

Features with at least one observed read. The remainder are present in the reference set but not detected in these samples.

Composition

Taxonomy not assigned in this artifact

The count table and metadata are complete, but the reference set in this release carries empty taxonomy labels, so composition cannot be shown. The taxonomy stage of the pipeline has not been run against this build.

ranks present in features.parquet: domain, phylum, class, order, family, genus, species

Downstream QC and analysis

computed from the released tables

Eleven 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 p90
2k 5k 10k 20k 386 0

Expected richness when 16 samples are subsampled to a common depth, resampled 31 draws. Median 180 features observed at full depth.

Depth against richness

log depth
403 0 reads per sample, log scale

One point per sample. Correlation of log reads with observed features is 0.585, so the depth floor is doing most of the work of deciding how many features a sample shows.

Per-run QC

  • 16S identity 65.2% alignment call per run
  • Q30 rate 74.6% mean Q 33.7
  • Amplicon V3-V4 primers present
  • PhiX 0.0% control spike-in

16 run report(s), n/a GC, 0.0% ambiguous bases.

Diversity

Shannon
3.99
Simpson
0.954
Evenness
0.738
Chao1
180

Median across samples. Observed richness ranges 38 to 403.

Feature prevalence

0 of 2,909 features

present in at least half of the 16 samples (0.0%). 2,908 features appear in one sample only, which is the long tail rarefaction is fighting.

Ordination

pc1 pc2

One point per sample, 16 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 · 6.7%

  • evenness 60.9%
  • shannon 44.1%
  • observed 18.2%
  • chao1 18.2%

pc2 · 6.7%

  • observed 5.3%
  • chao1 5.3%
  • reads 1.6%
  • shannon 1.1%

pc3 · 6.7%

  • reads 5.5%
  • observed 2.6%
  • chao1 2.6%
  • shannon 0.4%

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

Shannon
5.0 16 samples

Median Shannon 3.988 across the release; observed richness runs 38 to 403.

Bray-Curtis dissimilarity

16 x 16, darker is closer

Sample order is the release order, 16 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 silhouette

k = 2 silhouette 0.175

  • state 0 1 samples
  • state 1 15 samples

Clustered on the centred log-ratio of the top 200 features; 16 samples.

Batch-bias audit

states against

adjusted 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, CLR

Joint 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

with

features 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 distance

    the study's coordinates fall on a single site (no spread), so spatial autocorrelation is not defined

    Co-occurrence network

    100 nodes · 307 edges

    positive
    307
    negative
    0
    density
    0.062
    components
    16
    mean degree
    6.1

    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 tree

      No tree in this release.

      ASV panel

      no sequence file

      The representative sequences are not in this release, so length and GC cannot be drawn.

      Most abundant ASVs

      ASVphylumgenusmeanprev.
      ASV_1PseudomonadotaParacandidimonas735.06%
      ASV_2PseudomonadotaParacandidimonas656.86%
      ASV_3PseudomonadotaParacandidimonas381.46%
      ASV_4Candidatus EremiobacterotaIncertae Sedis315.96%
      ASV_5PseudomonadotaParacandidimonas290.56%
      ASV_6AcidobacteriotaIncertae Sedis220.86%
      ASV_7BacillotaDesulfosporosinus202.36%
      ASV_8AcidobacteriotaIncertae Sedis193.46%
      ASV_9PseudomonadotaRhodanobacter191.36%
      ASV_10AcidobacteriotaIncertae Sedis189.76%
      ASV_11BacillotaDesulfosporosinus167.66%
      ASV_12PseudomonadotaRhodanobacter167.16%

      Similar studies

      composition, metadata, location, shared authors
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      PRJNA36104654%
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      PRJNA25474254%
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      31 samples

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      23 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.

      Contribute to PRJNA338649

      Validated automatically where it can be, reviewed by a person where it cannot.

      Downloads

      0 files · sha256 in manifest

      Files are served from https://huggingface.co/datasets/hmacgregor/ampliconflow-releases/resolve/main/PRJNA338649-20260926/ once hosting is wired. Until then the links point at a placeholder base URL.

      Samples

      16 samples
      Sample Collected group Reads Features Shannon State
      SAMN05560345 2012-10-03 12,566 248 4.443 1
      SAMN05560346 2012-10-03 18,161 259 4.299 1
      SAMN05560347 2012-10-03 16,092 43 1.371 1
      SAMN05560348 2012-10-03 5,530 38 2.049 1
      SAMN05560349 2012-10-03 10,032 156 3.561 1
      SAMN05560350 2012-10-03 16,788 62 1.82 1
      SAMN05560351 2012-10-03 11,036 63 2.706 1
      SAMN05560352 2012-10-03 19,969 239 4.063 1
      SAMN05560353 2012-10-03 11,540 204 4.278 1
      SAMN05560354 2012-10-03 20,294 103 2.938 1
      SAMN05560355 2012-10-03 10,092 209 4.471 1
      SAMN05560356 2012-10-03 5,179 105 3.913 1
      SAMN05560357 2012-10-03 20,560 364 4.914 1
      SAMN05560358 2012-10-03 24,719 403 4.954 0
      SAMN05560359 2012-10-03 27,759 331 4.252 1
      SAMN05560360 2012-10-03 12,987 83 2.549 1

      click a column head to sort