ampliconflow
Archive records ENA PRJNA630593 SRA PRJNA630593 BioProject PRJNA630593

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

PRJNA630593 released 25 Sept 2026

PRJNA630593

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 27 released samples and 27 runs.

Samples
27
Runs
27
Collection
2007-06 to 2007-06

Linked publication

Soil microbial community structure and functionality changes in response to long-term metal and radionuclide pollution.

10.1111/1462-2920.15394 · 2021 · via europepmc

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

abstract

Microbial communities are essential for a healthy soil ecosystem. Metals and radionuclides can exert a persistent pressure on the soil microbial community. However, little is known on the effect of long-term co-contamination of metals and radionuclides on the microbial community structure and functionality. We investigated the impact of historical discharges of the phosphate and nuclear industry on the microbial community in the Grote Nete river basin in Belgium. Eight locations were sampled along a transect to the river edge and one location further in the field. Chemical analysis demonstrated a metal and radionuclide contamination gradient and revealed a distinct clustering of the locations based on all metadata. Moreover, a relation between the chemical parameters and the bacterial community structure was demonstrated. Although no difference in biomass was observed between locations, cultivation-dependent experiments showed that communities from contaminated locations survived better on singular metals than communities from control locations. Furthermore, nitrification, a key soil ecosystem process seemed affected in contaminated locations when combining metadata with microbial profiling. These results indicate that long-term metal and radionuclide pollution impacts the microbial community structure and functionality and provides important fundamental insights into microbial community dynamics in co-metal-radionuclide contaminated sites.

Linked by the enrich stage from europepmc.

Location

sampling sites from the release coordinates
27sampling sites · drag to pan, scroll or pinch to zoom

Place name hierarchy

  1. ▸ België / Belgique / Belgien
  2. › Antwerpen
  3. › Mechelen

Districts named on the samples

  • Mechelen 1

Latitude 51.13515 to 51.13569, longitude 4.60992 to 4.61159. 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

27 samples, 2007-06 to 2007-06

51.1351 to 51.1357 N, 4.6099 to 4.6116 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, region V3

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

Illumina MiSeq

27 runs; PAIRED 301.0 bp reads; the linked paper's text supports MiSeq

07 this release

Denoising

dada2 1.38.0

7,000 ASVs from 304,356 reads

ampliconflow branches off at step 6, Sequencing

this release

ampliconflow starts here: 304,356 reads from 27 runs, QC to 90.8% 16S identity and 83.8% above Q30, primers trimmed, dada2 1.38.0 to 7,000 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 15,587 characters. It supports: platform, subfragment.

Conflict on sequencing platform: the release has Illumina MiSeq, the linked paper's text supports MiSeq.

27

Samples

27 runs

7k

Features

OTUs at 97%

304.4k

Reads

mapped total

124 MB

Release size

85 files

Depth floor

1,000 reads

no samples below

QC warnings

27

100% of runs warned

Reads per sample

log scale
min
7,750
median
10,978
max
17,012

Feature detection

100.0% non-zero

7,000 / 7,000 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 91,863 (30.2%)
  • Acidobacteriota 87,638 (28.8%)
  • Bacteroidota 28,574 (9.4%)
  • Verrucomicrobiota 20,989 (6.9%)
  • Actinomycetota 18,327 (6.0%)
  • Gemmatimonadota 11,941 (3.9%)
  • Myxococcota 11,795 (3.9%)
  • Nitrospirota 9,576 (3.1%)
  • Chloroflexota 6,698 (2.2%)
  • Thermodesulfobacteriota 4,883 (1.6%)
  • Planctomycetota 3,563 (1.2%)
  • Methylomirabilota 2,509 (0.8%)
  • Latescibacterota 1,553 (0.5%)
  • Patescibacteria 638 (0.2%)
  • Bacillota 554 (0.2%)
  • MBNT15 419 (0.1%)
  • RCP2-54 319 (0.1%)
  • Candidatus Kryptonia 312 (0.1%)
  • Cyanobacteriota 308 (0.1%)
  • Spirochaetota 290 (0.1%)

Top genera

  • Incertae Sedis 157,067 (51.6%)
  • Candidatus Solibacter 14,028 (4.6%)
  • Nitrospira 9,050 (3.0%)
  • MND1 8,452 (2.8%)
  • Bryobacter 6,743 (2.2%)
  • Candidatus Udaeobacter 6,366 (2.1%)
  • Flavobacterium 5,470 (1.8%)
  • Acidibacter 4,939 (1.6%)
  • Bradyrhizobium 4,623 (1.5%)
  • Chryseotalea 4,518 (1.5%)
  • GOUTA6 4,327 (1.4%)
  • Candidatus Koribacter 4,172 (1.4%)
  • Ellin6067 3,281 (1.1%)
  • Massilia 2,996 (1.0%)
  • Rhodanobacter 2,628 (0.9%)
  • ADurb.Bin063-1 2,381 (0.8%)
  • IS-44 2,189 (0.7%)
  • Acidothermus 2,122 (0.7%)
  • Gemmatimonas 2,025 (0.7%)
  • Gaiella 1,955 (0.6%)

Rank-abundance

log-log
1 10 100 1k 1 10 100 ASV_1 · Nitrospira: 2612 reads ASV_2 · Candidatus Udaeobacter: 1524 reads ASV_3 · Nitrospira: 1170 reads ASV_4 · Rhodanobacter: 1118 reads ASV_5 · Candidatus Solibacter: 1050 reads ASV_6 · Incertae Sedis: 966 reads ASV_7 · Incertae Sedis: 912 reads ASV_8 · Candidatus Udaeobacter: 857 reads ASV_9 · Incertae Sedis: 855 reads ASV_10 · Incertae Sedis: 852 reads ASV_11 · Incertae Sedis: 852 reads ASV_12 · Candidatus Solibacter: 826 reads ASV_13 · Massilia: 825 reads ASV_14 · Incertae Sedis: 770 reads ASV_15 · Incertae Sedis: 753 reads ASV_16 · Bradyrhizobium: 698 reads ASV_17 · Candidatus Solibacter: 695 reads ASV_18 · Incertae Sedis: 687 reads ASV_19 · Incertae Sedis: 687 reads ASV_20 · Nitrospira: 656 reads ASV_21 · Incertae Sedis: 649 reads ASV_22 · Incertae Sedis: 640 reads ASV_23 · MND1: 638 reads ASV_24 · Bryobacter: 634 reads ASV_25 · Incertae Sedis: 629 reads ASV_26 · Nitrospira: 615 reads ASV_27 · Nitrospira: 610 reads ASV_28 · Bryobacter: 598 reads ASV_29 · Incertae Sedis: 596 reads ASV_30 · Incertae Sedis: 559 reads ASV_31 · Incertae Sedis: 548 reads ASV_32 · Incertae Sedis: 545 reads ASV_33 · Incertae Sedis: 544 reads ASV_34 · Candidatus Solibacter: 541 reads ASV_35 · GOUTA6: 539 reads ASV_36 · Incertae Sedis: 535 reads ASV_37 · IS-44: 534 reads ASV_38 · Incertae Sedis: 532 reads ASV_39 · Candidatus Solibacter: 529 reads ASV_40 · Candidatus Udaeobacter: 522 reads ASV_41 · Incertae Sedis: 518 reads ASV_42 · Candidatus Udaeobacter: 505 reads ASV_43 · Candidatus Solibacter: 504 reads ASV_44 · Ellin516: 503 reads ASV_45 · Incertae Sedis: 498 reads ASV_46 · Candidatus Solibacter: 495 reads ASV_47 · Ellin516: 486 reads ASV_48 · Incertae Sedis: 482 reads ASV_49 · Pelotalea: 481 reads ASV_50 · Incertae Sedis: 479 reads ASV_51 · Ellin6067: 471 reads ASV_52 · Incertae Sedis: 471 reads ASV_53 · Incertae Sedis: 451 reads ASV_54 · Occallatibacter: 450 reads ASV_55 · Bradyrhizobium: 450 reads ASV_56 · Rhodanobacter: 447 reads ASV_57 · Incertae Sedis: 444 reads ASV_58 · Candidatus Koribacter: 438 reads ASV_59 · Nitrospira: 436 reads ASV_60 · Incertae Sedis: 435 reads ASV_61 · Incertae Sedis: 432 reads ASV_62 · Incertae Sedis: 430 reads ASV_63 · Candidatus Koribacter: 430 reads ASV_64 · Bryobacter: 429 reads ASV_65 · Candidatus Koribacter: 427 reads ASV_66 · MND1: 426 reads ASV_67 · CL500-29 marine group: 423 reads ASV_68 · GOUTA6: 418 reads ASV_69 · Candidatus Solibacter: 414 reads ASV_70 · Candidatus Solibacter: 412 reads ASV_71 · GOUTA6: 410 reads ASV_72 · Candidatus Solibacter: 407 reads ASV_73 · Bradyrhizobium: 406 reads ASV_74 · Incertae Sedis: 404 reads ASV_75 · Incertae Sedis: 403 reads ASV_76 · Incertae Sedis: 403 reads ASV_77 · Candidatus Koribacter: 400 reads ASV_78 · Incertae Sedis: 398 reads ASV_79 · Bryobacter: 397 reads ASV_80 · Incertae Sedis: 396 reads ASV_81 · Bradyrhizobium: 392 reads ASV_82 · Incertae Sedis: 387 reads ASV_83 · Incertae Sedis: 386 reads ASV_84 · Incertae Sedis: 385 reads ASV_85 · Incertae Sedis: 383 reads ASV_86 · MND1: 382 reads ASV_87 · Incertae Sedis: 381 reads ASV_88 · Incertae Sedis: 381 reads ASV_89 · Incertae Sedis: 379 reads ASV_90 · Candidatus Udaeobacter: 378 reads ASV_91 · GOUTA6: 377 reads ASV_92 · Incertae Sedis: 376 reads ASV_93 · GOUTA6: 375 reads ASV_94 · Incertae Sedis: 375 reads ASV_95 · Incertae Sedis: 373 reads ASV_96 · Acidothermus: 370 reads ASV_97 · Acidibacter: 369 reads ASV_98 · Incertae Sedis: 368 reads ASV_99 · GOUTA6: 365 reads ASV_100 · Candidatus Solibacter: 362 reads ASV_101 · Incertae Sedis: 362 reads ASV_102 · Nitrospira: 359 reads ASV_103 · Incertae Sedis: 359 reads ASV_104 · Incertae Sedis: 358 reads ASV_105 · Incertae Sedis: 358 reads ASV_106 · Candidatus Koribacter: 357 reads ASV_107 · Incertae Sedis: 354 reads ASV_108 · Incertae Sedis: 350 reads ASV_109 · Thiobacillus: 348 reads ASV_110 · Candidatus Solibacter: 345 reads ASV_111 · Afipia: 338 reads ASV_112 · Incertae Sedis: 337 reads ASV_113 · MND1: 335 reads ASV_114 · Incertae Sedis: 333 reads ASV_115 · Incertae Sedis: 333 reads ASV_116 · MND1: 331 reads ASV_117 · Incertae Sedis: 328 reads ASV_118 · Ellin6067: 328 reads ASV_119 · Bradyrhizobium: 328 reads ASV_120 · Incertae Sedis: 327 reads ASV_121 · Pelotalea: 324 reads ASV_122 · Incertae Sedis: 323 reads ASV_123 · Incertae Sedis: 321 reads ASV_124 · MND1: 317 reads ASV_125 · Geobacter: 313 reads ASV_126 · Candidatus Koribacter: 311 reads ASV_127 · Incertae Sedis: 311 reads ASV_128 · Incertae Sedis: 311 reads ASV_129 · Incertae Sedis: 310 reads ASV_130 · Candidatus Solibacter: 308 reads ASV_131 · Incertae Sedis: 308 reads ASV_132 · Incertae Sedis: 307 reads ASV_133 · Incertae Sedis: 303 reads ASV_134 · Incertae Sedis: 303 reads ASV_135 · Incertae Sedis: 302 reads ASV_136 · Flavobacterium: 300 reads ASV_137 · Incertae Sedis: 300 reads ASV_138 · Bradyrhizobium: 299 reads ASV_139 · Acidibacter: 297 reads ASV_140 · Gaiella: 294 reads ASV_141 · Incertae Sedis: 293 reads ASV_142 · Candidatus Solibacter: 292 reads ASV_143 · Incertae Sedis: 289 reads ASV_144 · Candidatus Solibacter: 289 reads ASV_145 · Incertae Sedis: 287 reads ASV_146 · Candidatus Solibacter: 285 reads ASV_147 · Incertae Sedis: 284 reads ASV_148 · Incertae Sedis: 282 reads ASV_149 · CL500-29 marine group: 280 reads ASV_150 · Massilia: 279 reads ASV_151 · Incertae Sedis: 279 reads ASV_152 · Incertae Sedis: 278 reads ASV_153 · Incertae Sedis: 277 reads ASV_154 · Incertae Sedis: 277 reads ASV_155 · MND1: 276 reads ASV_156 · Puia: 275 reads ASV_157 · Candidatus Udaeobacter: 275 reads ASV_158 · Incertae Sedis: 275 reads ASV_159 · Incertae Sedis: 274 reads ASV_160 · Incertae Sedis: 272 reads ASV_161 · Incertae Sedis: 272 reads ASV_162 · Candidatus Koribacter: 269 reads ASV_163 · Occallatibacter: 269 reads ASV_164 · MND1: 268 reads ASV_165 · Incertae Sedis: 263 reads ASV_166 · Candidatus Solibacter: 261 reads ASV_167 · ADurb.Bin063-1: 261 reads ASV_168 · Incertae Sedis: 261 reads ASV_169 · Candidatus Koribacter: 260 reads ASV_170 · Incertae Sedis: 259 reads ASV_171 · Flavobacterium: 258 reads ASV_172 · Incertae Sedis: 257 reads ASV_173 · Incertae Sedis: 257 reads ASV_174 · Acidibacter: 255 reads ASV_175 · Incertae Sedis: 255 reads ASV_176 · Incertae Sedis: 254 reads ASV_177 · MND1: 254 reads ASV_178 · Pelotalea: 253 reads ASV_179 · Acidibacter: 253 reads ASV_180 · Incertae Sedis: 253 reads ASV_181 · Incertae Sedis: 252 reads ASV_182 · Incertae Sedis: 252 reads ASV_183 · Incertae Sedis: 252 reads ASV_184 · Incertae Sedis: 250 reads ASV_185 · Nitrospira: 249 reads ASV_186 · Incertae Sedis: 249 reads ASV_187 · Incertae Sedis: 247 reads ASV_188 · Incertae Sedis: 247 reads ASV_189 · MND1: 247 reads ASV_190 · Puia: 246 reads ASV_191 · Incertae Sedis: 246 reads ASV_192 · Incertae Sedis: 245 reads ASV_193 · Acidibacter: 245 reads ASV_194 · Incertae Sedis: 244 reads ASV_195 · Bryobacter: 243 reads ASV_196 · Candidatus Solibacter: 243 reads ASV_197 · Nitrospira: 243 reads ASV_198 · Incertae Sedis: 242 reads ASV_199 · Candidatus Solibacter: 242 reads ASV_200 · Incertae Sedis: 241 reads rank reads

7,000 ranked features, top 200 shown. A steep drop means a few taxa carry most of the reads.

Per-sample reads

27 samples
min
7,750
median
10,978
max
17,012

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 305 0

Expected richness when 27 samples are subsampled to a common depth, resampled 31 draws. Median 270 features observed at full depth.

Depth against richness

log depth
361 0 reads per sample, log scale

One point per sample. Correlation of log reads with observed features is 0.283, so the depth floor is doing most of the work of deciding how many features a sample shows.

Per-run QC

  • 16S identity 90.8% alignment call per run
  • Q30 rate 83.8% mean Q 34.2
  • Amplicon V3-V4 primers present
  • PhiX 0.0% control spike-in

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

Diversity

Shannon
4.74
Simpson
0.986
Evenness
0.858
Chao1
270

Median across samples. Observed richness ranges 160 to 361.

Feature prevalence

0 of 7,000 features

present in at least half of the 27 samples (0.0%). 6,864 features appear in one sample only, which is the long tail rarefaction is fighting.

Ordination

pc1 pc2

One point per sample, 27 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 · 5.5%

  • reads 29.6%
  • evenness 8.9%
  • shannon 3.2%
  • observed 0.0%

pc2 · 4.9%

  • evenness 22.9%
  • shannon 16.6%
  • reads 3.8%
  • observed 0.0%

pc3 · 4.7%

  • reads 7.4%
  • shannon 3.6%
  • evenness 2.5%
  • observed 0.9%

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
5.1 27 samples

Median Shannon 4.744 across the release; observed richness runs 160 to 361.

Bray-Curtis dissimilarity

27 x 27, darker is closer

Sample order is the release order, 27 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 = 4 silhouette 0.085

  • state 0 2 samples
  • state 1 1 samples
  • state 2 23 samples
  • state 3 1 samples

Clustered on the centred log-ratio of the top 200 features; 27 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
  • depth 0.000

Joint R2 0.000, 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)
0.384 · p 0.001

    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 0.0 to 0.1 km.

    Spatial structure

    observed richness over distance
    Moran's I
    -0.0374 · p 0.547
    Gradient response (rho)
    -0.185 · p 0.374 (decreasing)

    variogram, 8 distance bins, semivariance of richness

    Co-occurrence network

    100 nodes · 122 edges

    positive
    122
    negative
    0
    density
    0.025
    components
    43
    mean degree
    2.4

    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_1NitrospirotaNitrospira96.737%
      ASV_2VerrucomicrobiotaCandidatus Udaeobacter56.430%
      ASV_3NitrospirotaNitrospira43.315%
      ASV_4PseudomonadotaRhodanobacter41.419%
      ASV_5AcidobacteriotaCandidatus Solibacter38.94%
      ASV_6AcidobacteriotaIncertae Sedis35.811%
      ASV_7AcidobacteriotaIncertae Sedis33.819%
      ASV_8VerrucomicrobiotaCandidatus Udaeobacter31.711%
      ASV_9AcidobacteriotaIncertae Sedis31.715%
      ASV_11AcidobacteriotaIncertae Sedis31.64%
      ASV_10AcidobacteriotaIncertae Sedis31.64%
      ASV_12AcidobacteriotaCandidatus Solibacter30.64%

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      31 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 PRJNA630593

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

      Downloads

      8 files · sha256 in manifest

      Files are served from https://huggingface.co/datasets/hmacgregor/ampliconflow-releases/resolve/main/PRJNA630593-20260926/ once hosting is wired. Until then the links point at a placeholder base URL.

      Samples

      27 samples
      Sample Collected group Reads Features Shannon State
      SAMN14840293 2007-06-07 11,653 313 4.991 2
      SAMN14840294 2007-06-07 9,424 239 4.681 2
      SAMN14840295 2007-06-07 9,805 299 4.796 2
      SAMN14840296 2007-06-07 9,240 300 4.913 2
      SAMN14840297 2007-06-07 9,280 199 4.55 2
      SAMN14840298 2007-06-07 11,728 361 4.959 2
      SAMN14840299 2007-06-07 7,750 262 4.64 2
      SAMN14840300 2007-06-07 8,041 220 4.536 2
      SAMN14840301 2007-06-07 10,018 270 4.658 2
      SAMN14840302 2007-06-07 13,268 305 4.906 2
      SAMN14840303 2007-06-07 15,027 281 4.902 1
      SAMN14840304 2007-06-07 8,100 265 4.616 2
      SAMN14840305 2007-06-07 11,819 315 4.534 2
      SAMN14840306 2007-06-07 11,899 173 4.4 3
      SAMN14840307 2007-06-07 11,379 288 4.622 2
      SAMN14840308 2007-06-07 13,121 331 4.839 0
      SAMN14840309 2007-06-07 10,576 160 4.43 0
      SAMN14840310 2007-06-07 10,568 303 4.721 2
      SAMN14840311 2007-06-07 10,887 259 4.912 2
      SAMN14840312 2007-06-07 8,648 225 4.649 2
      SAMN14840313 2007-06-07 11,922 248 4.767 2
      SAMN14840314 2007-06-07 10,978 264 4.814 2
      SAMN14840315 2007-06-07 12,357 290 5.033 2
      SAMN14840316 2007-06-07 14,201 307 5.113 2
      SAMN14840317 2007-06-07 17,012 280 4.886 2
      SAMN14840318 2007-06-07 14,930 225 4.744 2
      SAMN14840319 2007-06-07 10,725 231 4.542 2

      click a column head to sort