ampliconflow
Archive records ENA PRJDB7978 SRA PRJDB7978 BioProject PRJDB7978

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

PRJDB7978 released 25 Sept 2026

PRJDB7978

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 65 released samples and 65 runs.

Samples
65
Runs
65
Collection
2014-06 to 2014-07

Linked publication

Microbiome analysis of the restricted bacteria in radioactive element-containing water at the Fukushima Daiichi Nuclear Power Station.

10.1128/aem.02113-23 · 2024 · via europepmc

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

abstract

A major incident occurred at the Fukushima Daiichi Nuclear Power Station following the tsunami triggered by the Tohoku-Pacific Ocean Earthquake in March 2011, whereby seawater entered the torus room in the basement of the reactor building. Here, we identify and analyze the bacterial communities in the torus room water and several environmental samples. Samples of the torus room water (1 × 10<sup>9</sup> Bq<sup>137</sup>Cs/L) were collected by the Tokyo Electric Power Company Holdings from two sampling points between 30 cm and 1 m from the bottom of the room (TW1) and the bottom layer (TW2). A structural analysis of the bacterial communities based on 16S rRNA amplicon sequencing revealed that the predominant bacterial genera in TW1 and TW2 were similar. TW1 primarily contained the genus <i>Limnobacter</i>, a thiosulfate-oxidizing bacterium. γ-Irradiation tests on <i>Limnobacter thiooxidans</i>, the most closely related phylogenetically found in TW1, indicated that its radiation resistance was similar to ordinary bacteria. TW2 predominantly contained the genus <i>Brevirhabdus</i>, a manganese-oxidizing bacterium. Although bacterial diversity in the torus room water was lower than seawater near Fukushima, ~70% of identified genera were associated with metal corrosion. Latent environment allocation-an analytical technique that estimates habitat distributions and co-detection analyses-revealed that the microbial communities in the torus room water originated from a distinct blend of natural marine microbial and artificial bacterial communities typical of biofilms, sludge, and wastewater. Understanding the specific bacteria linked to metal corrosion in damaged plants is important for advancing decommissioning efforts.<h4>Importance</h4>In the context of nuclear power station decommissioning, the proliferation of microorganisms within the reactor and piping systems constitutes a formidable challenge. Therefore, the identification of microbial communities in such environments is of paramount importance. In the aftermath of the Fukushima Daiichi Nuclear Power Station accident, microbial community analysis was conducted on environmental samples collected mainly outside the site. However, analyses using samples from on-site areas, including adjacent soil and seawater, were not performed. This study represents the first comprehensive analysis of microbial communities, utilizing meta 16S amplicon sequencing, with a focus on environmental samples collected from the radioactive element-containing water in the torus room, including the surrounding environments. Some of the identified microbial genera are shared with those previously identified in spent nuclear fuel pools in countries such as France and Brazil. Moreover, our discussion in this paper elucidates the correlation of many of these bacteria with metal corrosion.

Linked by the enrich stage from europepmc.

Location

sampling sites from the release coordinates

No sample coordinates in this release

The study reports no latitude or longitude, and its metadata carries no lat_lon text field either, so no map or place-name hierarchy can be drawn. Every other panel is computed from the count table and the sample metadata.

How the sequences were obtained

sample to release
01 study metadata

Sample collection

65 samples, 2014-06 to 2014-07

02 not reported

Storage

not reported

no storage statement in the study metadata

03 not reported

Processing

not reported

no extraction kit or lysis protocol recorded

04 per-run QC

PCR

16S rRNA V4

primers: trimmed

05 not reported

Sequencing preparation

not reported

no library kit or index strategy recorded

06 study metadata

Sequencing

Illumina MiSeq

65 runs; PAIRED 151.0 bp reads

07 this release

Denoising

dada2 1.38.0

40,327 ASVs from 1,822,004 reads

ampliconflow branches off at step 6, Sequencing

this release

ampliconflow starts here: 1,822,004 reads from 65 runs, QC to 82.5% 16S identity and 92.1% above Q30, primers trimmed, dada2 1.38.0 to 40,327 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.

65

Samples

65 runs

40.3k

Features

OTUs at 97%

1.8M

Reads

mapped total

70 MB

Release size

163 files

Depth floor

1,000 reads

no samples below

QC warnings

65

100% of runs warned

Reads per sample

log scale
min
20,050
median
26,979
max
39,268

Feature detection

100.0% non-zero

40,327 / 40,327 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 497,374 (27.3%)
  • Acidobacteriota 314,304 (17.3%)
  • Actinomycetota 281,967 (15.5%)
  • Planctomycetota 149,875 (8.2%)
  • Bacteroidota 117,440 (6.4%)
  • Chloroflexota 96,683 (5.3%)
  • Verrucomicrobiota 91,095 (5.0%)
  • Myxococcota 80,674 (4.4%)
  • Gemmatimonadota 45,061 (2.5%)
  • Bacillota 38,070 (2.1%)
  • Methylomirabilota 17,276 (0.9%)
  • Latescibacterota 16,338 (0.9%)
  • Thermodesulfobacteriota 15,446 (0.8%)
  • Bdellovibrionota 9,896 (0.5%)
  • Thermoproteota 6,072 (0.3%)
  • Nitrospirota 5,969 (0.3%)
  • Armatimonadota 5,615 (0.3%)
  • Chlamydiota 4,931 (0.3%)
  • Cyanobacteriota 4,862 (0.3%)
  • MBNT15 3,916 (0.2%)

Top genera

  • Incertae Sedis 997,235 (54.7%)
  • Candidatus Udaeobacter 43,411 (2.4%)
  • Bradyrhizobium 34,985 (1.9%)
  • Ellin6067 31,415 (1.7%)
  • Acidibacter 23,625 (1.3%)
  • Acidiferrimicrobium 18,666 (1.0%)
  • Gemmatimonas 18,398 (1.0%)
  • Candidatus Solibacter 17,991 (1.0%)
  • Rhizobacter 15,846 (0.9%)
  • Acidothermus 14,452 (0.8%)
  • Ferruginibacter 13,929 (0.8%)
  • Nocardioides 13,857 (0.8%)
  • Chthoniobacter 13,837 (0.8%)
  • Gaiella 13,819 (0.8%)
  • Bryobacter 12,679 (0.7%)
  • Mycobacterium 12,262 (0.7%)
  • Puia 12,205 (0.7%)
  • Sphingomonas 10,720 (0.6%)
  • Pseudolabrys 9,443 (0.5%)
  • mle1-7 9,411 (0.5%)

Rank-abundance

log-log
1 10 100 1k 1 10 100 ASV_1 · Bradyrhizobium: 7844 reads ASV_2 · Bradyrhizobium: 7564 reads ASV_3 · Candidatus Udaeobacter: 7200 reads ASV_4 · Rhizobacter: 4213 reads ASV_5 · Incertae Sedis: 4110 reads ASV_6 · Bradyrhizobium: 3916 reads ASV_7 · Incertae Sedis: 3912 reads ASV_8 · Candidatus Udaeobacter: 3865 reads ASV_9 · Incertae Sedis: 3807 reads ASV_10 · Incertae Sedis: 3547 reads ASV_11 · Incertae Sedis: 3423 reads ASV_12 · Incertae Sedis: 3422 reads ASV_13 · Ellin6067: 3304 reads ASV_14 · Incertae Sedis: 3035 reads ASV_15 · Incertae Sedis: 3019 reads ASV_16 · Incertae Sedis: 2907 reads ASV_17 · Incertae Sedis: 2763 reads ASV_18 · Incertae Sedis: 2707 reads ASV_19 · Incertae Sedis: 2655 reads ASV_20 · Incertae Sedis: 2655 reads ASV_21 · Incertae Sedis: 2649 reads ASV_22 · Incertae Sedis: 2584 reads ASV_23 · mle1-7: 2573 reads ASV_24 · Pseudolabrys: 2525 reads ASV_25 · Pseudarthrobacter: 2512 reads ASV_26 · Incertae Sedis: 2504 reads ASV_27 · Candidatus Udaeobacter: 2495 reads ASV_28 · Rhizobacter: 2407 reads ASV_29 · Incertae Sedis: 2394 reads ASV_30 · Bradyrhizobium: 2342 reads ASV_31 · Sphingomonas: 2293 reads ASV_32 · Incertae Sedis: 2289 reads ASV_33 · Solirubrobacter: 2274 reads ASV_34 · Incertae Sedis: 2164 reads ASV_35 · Aetherobacter: 2094 reads ASV_36 · Bradyrhizobium: 2031 reads ASV_37 · Hyphomicrobium: 2016 reads ASV_38 · Incertae Sedis: 2009 reads ASV_39 · Incertae Sedis: 1991 reads ASV_40 · Incertae Sedis: 1953 reads ASV_41 · Ramlibacter: 1920 reads ASV_42 · Incertae Sedis: 1821 reads ASV_43 · Incertae Sedis: 1817 reads ASV_44 · Ellin6067: 1809 reads ASV_45 · Bradyrhizobium: 1785 reads ASV_46 · Incertae Sedis: 1783 reads ASV_47 · Incertae Sedis: 1773 reads ASV_48 · Nocardioides: 1773 reads ASV_49 · Incertae Sedis: 1766 reads ASV_50 · Incertae Sedis: 1763 reads ASV_51 · Variovorax: 1762 reads ASV_52 · P3OB-42: 1739 reads ASV_53 · Incertae Sedis: 1701 reads ASV_54 · Acidibacter: 1691 reads ASV_55 · Incertae Sedis: 1690 reads ASV_56 · Incertae Sedis: 1688 reads ASV_57 · Ellin6067: 1646 reads ASV_58 · Incertae Sedis: 1619 reads ASV_59 · Incertae Sedis: 1581 reads ASV_60 · Massilia: 1580 reads ASV_61 · Incertae Sedis: 1572 reads ASV_62 · Candidatus Solibacter: 1560 reads ASV_63 · Acidibacter: 1557 reads ASV_64 · Acidothermus: 1556 reads ASV_65 · Bradyrhizobium: 1555 reads ASV_66 · Candidatus Udaeobacter: 1555 reads ASV_67 · Incertae Sedis: 1545 reads ASV_68 · Bacillus: 1533 reads ASV_69 · Incertae Sedis: 1528 reads ASV_70 · Sphingomonas: 1509 reads ASV_71 · Incertae Sedis: 1498 reads ASV_72 · Priestia: 1495 reads ASV_73 · Ellin6067: 1494 reads ASV_74 · Incertae Sedis: 1487 reads ASV_75 · Candidatus Udaeobacter: 1477 reads ASV_76 · Incertae Sedis: 1467 reads ASV_77 · Puia: 1461 reads ASV_78 · Incertae Sedis: 1460 reads ASV_79 · Incertae Sedis: 1454 reads ASV_80 · Mycobacterium: 1447 reads ASV_81 · Incertae Sedis: 1441 reads ASV_82 · Incertae Sedis: 1438 reads ASV_83 · Pseudolabrys: 1435 reads ASV_84 · Incertae Sedis: 1420 reads ASV_85 · Incertae Sedis: 1398 reads ASV_86 · Devosia: 1396 reads ASV_87 · Candidatus Udaeobacter: 1389 reads ASV_88 · Incertae Sedis: 1377 reads ASV_89 · Incertae Sedis: 1375 reads ASV_90 · Ramlibacter: 1362 reads ASV_91 · Acidiferrimicrobium: 1361 reads ASV_92 · Ellin6067: 1347 reads ASV_93 · Incertae Sedis: 1343 reads ASV_94 · Mycobacterium: 1335 reads ASV_95 · Ramlibacter: 1332 reads ASV_96 · Acidothermus: 1331 reads ASV_97 · Incertae Sedis: 1325 reads ASV_98 · Acidiferrimicrobium: 1319 reads ASV_99 · Incertae Sedis: 1312 reads ASV_100 · Nakamurella: 1310 reads ASV_101 · Incertae Sedis: 1309 reads ASV_102 · Incertae Sedis: 1308 reads ASV_103 · Candidatus Udaeobacter: 1307 reads ASV_104 · Incertae Sedis: 1303 reads ASV_105 · Nocardioides: 1301 reads ASV_106 · Incertae Sedis: 1288 reads ASV_107 · Incertae Sedis: 1287 reads ASV_108 · Incertae Sedis: 1276 reads ASV_109 · Incertae Sedis: 1268 reads ASV_110 · Incertae Sedis: 1267 reads ASV_111 · Gaiella: 1264 reads ASV_112 · Pedomicrobium: 1252 reads ASV_113 · Incertae Sedis: 1249 reads ASV_114 · Bradyrhizobium: 1247 reads ASV_115 · Ellin6067: 1241 reads ASV_116 · Acidothermus: 1238 reads ASV_117 · Incertae Sedis: 1224 reads ASV_118 · Phenylobacterium: 1214 reads ASV_119 · Incertae Sedis: 1214 reads ASV_120 · Incertae Sedis: 1213 reads ASV_121 · Reyranella: 1198 reads ASV_122 · Gaiella: 1185 reads ASV_123 · Incertae Sedis: 1163 reads ASV_124 · Incertae Sedis: 1150 reads ASV_125 · Aquincola: 1146 reads ASV_126 · Incertae Sedis: 1141 reads ASV_127 · Incertae Sedis: 1138 reads ASV_128 · Incertae Sedis: 1132 reads ASV_129 · Incertae Sedis: 1121 reads ASV_130 · Mycobacterium: 1117 reads ASV_131 · Incertae Sedis: 1104 reads ASV_132 · Incertae Sedis: 1104 reads ASV_133 · Incertae Sedis: 1104 reads ASV_134 · Conexibacter: 1104 reads ASV_135 · Incertae Sedis: 1100 reads ASV_136 · Candidatus Udaeobacter: 1088 reads ASV_137 · Puia: 1087 reads ASV_138 · Ellin6067: 1086 reads ASV_139 · Flavobacterium: 1082 reads ASV_140 · Rhizobacter: 1081 reads ASV_141 · Flavobacterium: 1080 reads ASV_142 · Candidatus Udaeobacter: 1074 reads ASV_143 · Cellulomonas: 1068 reads ASV_144 · Gemmatimonas: 1068 reads ASV_145 · mle1-7: 1065 reads ASV_146 · Incertae Sedis: 1050 reads ASV_147 · Nakamurella: 1045 reads ASV_148 · Pseudolabrys: 1043 reads ASV_149 · Conexibacter: 1034 reads ASV_150 · Incertae Sedis: 1032 reads ASV_151 · Incertae Sedis: 1025 reads ASV_152 · Incertae Sedis: 1022 reads ASV_153 · Incertae Sedis: 1022 reads ASV_154 · Incertae Sedis: 1019 reads ASV_155 · Incertae Sedis: 1016 reads ASV_156 · Incertae Sedis: 1005 reads ASV_157 · Aquisphaera: 1003 reads ASV_158 · Incertae Sedis: 1002 reads ASV_159 · Acidibacter: 1001 reads ASV_160 · Incertae Sedis: 998 reads ASV_161 · Gemmatimonas: 997 reads ASV_162 · Incertae Sedis: 992 reads ASV_163 · Bradyrhizobium: 987 reads ASV_164 · Acidiferrimicrobium: 986 reads ASV_165 · Pseudarthrobacter: 980 reads ASV_166 · Incertae Sedis: 980 reads ASV_167 · Acidiferrimicrobium: 968 reads ASV_168 · Arenimonas: 966 reads ASV_169 · Incertae Sedis: 958 reads ASV_170 · Solirubrobacter: 958 reads ASV_171 · Candidatus Udaeobacter: 956 reads ASV_172 · Incertae Sedis: 955 reads ASV_173 · Incertae Sedis: 954 reads ASV_174 · Aquisphaera: 951 reads ASV_175 · Luedemannella: 950 reads ASV_176 · Incertae Sedis: 948 reads ASV_177 · Priestia: 943 reads ASV_178 · Ellin6067: 942 reads ASV_179 · Incertae Sedis: 941 reads ASV_180 · oc32: 941 reads ASV_181 · mle1-7: 937 reads ASV_182 · Incertae Sedis: 932 reads ASV_183 · Gaiella: 930 reads ASV_184 · Incertae Sedis: 925 reads ASV_185 · Ellin6067: 924 reads ASV_186 · Ellin6067: 920 reads ASV_187 · Incertae Sedis: 917 reads ASV_188 · Reyranella: 917 reads ASV_189 · Incertae Sedis: 912 reads ASV_190 · Incertae Sedis: 910 reads ASV_191 · Incertae Sedis: 903 reads ASV_192 · Incertae Sedis: 902 reads ASV_193 · Acidibacter: 899 reads ASV_194 · Incertae Sedis: 896 reads ASV_195 · Incertae Sedis: 895 reads ASV_196 · Incertae Sedis: 895 reads ASV_197 · Incertae Sedis: 887 reads ASV_198 · Baekduia: 885 reads ASV_199 · Acidibacter: 884 reads ASV_200 · Rhizobacter: 875 reads rank reads

40,327 ranked features, top 200 shown. A steep drop means a few taxa carry most of the reads.

Per-sample reads

65 samples
min
20,050
median
26,979
max
39,268

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 1,428 0

Expected richness when 65 samples are subsampled to a common depth, resampled 31 draws. Median 1,275 features observed at full depth.

Depth against richness

log depth
1,566 0 reads per sample, log scale

One point per sample. Correlation of log reads with observed features is 0.755, so the depth floor is doing most of the work of deciding how many features a sample shows.

Per-run QC

  • 16S identity 82.5% alignment call per run
  • Q30 rate 92.1% mean Q 35.8
  • Amplicon V4 primers trimmed
  • PhiX 0.1% control spike-in

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

Diversity

Shannon
6.73
Simpson
0.998
Evenness
0.94
Chao1
1,275

Median across samples. Observed richness ranges 985 to 1,566.

Feature prevalence

0 of 40,327 features

present in at least half of the 65 samples (0.0%). 29,003 features appear in one sample only, which is the long tail rarefaction is fighting.

Ordination

pc1 pc2

One point per sample, 65 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 · 24.1%

  • site 45.9%
  • reads 15.0%
  • pH 12.9%
  • evenness 7.3%

pc2 · 9.9%

  • site 39.9%
  • reads 8.2%
  • habitat 2.3%
  • evenness 1.5%

pc3 · 5.0%

  • site 11.3%
  • observed 2.4%
  • chao1 2.4%
  • shannon 2.3%

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
6.9 65 samples

Median Shannon 6.729 across the release; observed richness runs 985 to 1566.

Bray-Curtis dissimilarity

65 x 65, darker is closer

Sample order is the release order, 65 labels, and the matrix itself ships as beta_distance.tsv beside the analysis.

Phylogenetic diversity

Faith's PD median n/a

From tree.nwk, range to .

Community states

CLR, k by silhouette

k = 2 silhouette 0.510

  • state 0 49 samples
  • state 1 16 samples

Clustered on the centred log-ratio of the top 200 features; 65 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
  • habitat 0.004
  • site 0.446
  • pH 0.104

Joint R2 0.463, so the metadata explains a modest slice of the feature variation, and the two variables are not independent of one another.

Effect size

Shannon diversity between rhizosphere (n=33) and surface (n=32)

Cohen's d
-0.769 (medium)
Cliff's delta
-0.426
log2 fold change
-0.015

Means n/a and n/a. The difference is small and the spread is wide, which is what the delta says too.

Taxa against habitat

kruskal with bh

200 features tested, 0 survive the correction at q ≤ 0.05

Nothing survives. The smallest q is 0.811, which is the honest answer for a study whose samples are spread across three years with two to thirteen samples per year.

  • ASV_1 H 0.67 · p 0.414 · q 0.811
  • ASV_2 H 0.57 · p 0.450 · q 0.811
  • ASV_3 H 0.45 · p 0.504 · q 0.811
  • ASV_4 H 0.72 · p 0.396 · q 0.811
  • ASV_5 H 0.48 · p 0.490 · q 0.811

Group difference and spread

Bray-Curtis, 999 permutations
PERMANOVA pseudo-F
0.731 · p 0.809
PERMDISP F
8.40 · p 0.096
Distance decay (Mantel r)
n/a · p n/a
  • rhizosphere32
  • surface33

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

Constrained ordination

contamination class as the constraint

RDA · R2 0.322p 0.001

Hellinger-scaled, 12 dummy predictors over 65 samples. The constraint explains 32.2% of the community inertia, 0.166 adjusted.

CCA · p 0.001

Chi-square weighted SVD. Not significant here, which is the honest reading at this sample size and predictor count.

Co-occurrence network

100 nodes · 4,631 edges

positive
4,568
negative
63
density
0.936
components
1
mean degree
92.6

Spearman on log1p proportions, 100 features, |r| ≥ 0.50, FDR 0.05.

Hubs by degree

    Differential abundance

    wilcoxon · bh

    40,327 features tested, 0 survive q ≤ 0.05

    rhizosphere against surface, {"rhizosphere":33,"surface":32}. Nothing separates the two classes after correction, so the contamination signal is a community-level shift rather than a handful of marker taxa.

    • ASV_10000p 0.340 · q 0.415 · log2FC 1.00
    • ASV_10001p 0.340 · q 0.415 · log2FC 1.00
    • ASV_10002p 0.340 · q 0.415 · log2FC 1.00
    • ASV_10003p 0.340 · q 0.415 · log2FC 1.00
    • ASV_10004p 0.340 · q 0.415 · log2FC 1.00
    • ASV_10005p 0.154 · q 0.415 · log2FC -1.02

    R-backed alternatives kept external: ancombc, deseq2, aldex2, linda, corncob.

    Feature ranking and power

    by mean
    • ASV_1mean 120.68
    • ASV_2mean 116.37
    • ASV_3mean 110.77
    • ASV_4mean 64.82
    • ASV_5mean 63.23
    • ASV_6mean 60.25
    • ASV_7mean 60.18
    • ASV_8mean 59.46

    Power: n/a samples per group for n/a SD at power, alpha . The study was sufficiently sized for a moderate effect; the effect it actually found is small.

    Phylogenetic diversity

    40,327 tips · MAFFT alignment + FastTree (GTR+CAT)
    Faith's PD median
    129.53
    Faith's PD range
    108.27 – 150.39
    UniFrac PCo1
    10.7%
    UniFrac PCo2
    8.1%

    Faith's PD over the observed tips of each sample; the axes are a PCoA of unweighted UniFrac across the 65 samples.

    Phylogenetic signal

    top 200 features by abundance; trait is mean abundance
    Pagel's lambda
    0.300 · p 0.795
    Blomberg's K
    0.000 · p n/a

    A lambda near 0 means the trait is phylogenetically independent, near 1 means it tracks the tree. Reported scoped to the abundant features because the covariance is quadratic in the feature count.

    ASV phylogeny

    60 most abundant of the tree
    ASV_7 · Acidobacteriota · Incertae Sedis · mean 60.18ASV_7ASV_39 · Acidobacteriota · Incertae Sedis · mean 30.63ASV_47 · Acidobacteriota · Incertae Sedis · mean 27.28ASV_20 · Acidobacteriota · Incertae Sedis · mean 40.85ASV_55 · Acidobacteriota · Incertae Sedis · mean 26.00ASV_21 · Acidobacteriota · Incertae Sedis · mean 40.75ASV_9 · Acidobacteriota · Incertae Sedis · mean 58.57ASV_9ASV_34 · Acidobacteriota · Incertae Sedis · mean 33.29ASV_53 · Pseudomonadota · Incertae Sedis · mean 26.17ASV_31 · Pseudomonadota · Sphingomonas · mean 35.28ASV_37 · Pseudomonadota · Hyphomicrobium · mean 31.02ASV_58 · Pseudomonadota · Incertae Sedis · mean 24.91ASV_14 · Pseudomonadota · Incertae Sedis · mean 46.69ASV_14ASV_12 · Pseudomonadota · Incertae Sedis · mean 52.65ASV_6 · Pseudomonadota · Bradyrhizobium · mean 60.25ASV_1 · Pseudomonadota · Bradyrhizobium · mean 120.68ASV_2 · Pseudomonadota · Bradyrhizobium · mean 116.37ASV_36 · Pseudomonadota · Bradyrhizobium · mean 31.25ASV_30 · Pseudomonadota · Bradyrhizobium · mean 36.03ASV_30ASV_45 · Pseudomonadota · Bradyrhizobium · mean 27.46ASV_24 · Pseudomonadota · Pseudolabrys · mean 38.85ASV_5 · Pseudomonadota · Incertae Sedis · mean 63.23ASV_40 · Pseudomonadota · Incertae Sedis · mean 30.05ASV_10 · Pseudomonadota · Incertae Sedis · mean 54.57ASV_16 · Pseudomonadota · Incertae Sedis · mean 44.72ASV_16ASV_35 · Myxococcota · Aetherobacter · mean 32.22ASV_52 · Myxococcota · P3OB-42 · mean 26.75ASV_43 · Pseudomonadota · Incertae Sedis · mean 27.95ASV_54 · Pseudomonadota · Acidibacter · mean 26.02ASV_51 · Pseudomonadota · Variovorax · mean 27.11ASV_41 · Pseudomonadota · Ramlibacter · mean 29.54ASV_41ASV_4 · Pseudomonadota · Rhizobacter · mean 64.82ASV_28 · Pseudomonadota · Rhizobacter · mean 37.03ASV_13 · Pseudomonadota · Ellin6067 · mean 50.83ASV_44 · Pseudomonadota · Ellin6067 · mean 27.83ASV_57 · Pseudomonadota · Ellin6067 · mean 25.32ASV_60 · Pseudomonadota · Massilia · mean 24.31ASV_60ASV_23 · Pseudomonadota · mle1-7 · mean 39.58ASV_17 · Methylomirabilota · Incertae Sedis · mean 42.51ASV_26 · Acidobacteriota · Incertae Sedis · mean 38.52ASV_15 · Planctomycetota · Incertae Sedis · mean 46.45ASV_38 · Planctomycetota · Incertae Sedis · mean 30.91ASV_49 · Planctomycetota · Incertae Sedis · mean 27.17ASV_49ASV_3 · Verrucomicrobiota · Candidatus Udaeobacter · mean 110.77ASV_8 · Verrucomicrobiota · Candidatus Udaeobacter · mean 59.46ASV_27 · Verrucomicrobiota · Candidatus Udaeobacter · mean 38.38ASV_59 · Verrucomicrobiota · Incertae Sedis · mean 24.32ASV_32 · Chloroflexota · Incertae Sedis · mean 35.22ASV_11 · Chloroflexota · Incertae Sedis · mean 52.66ASV_11ASV_42 · Chloroflexota · Incertae Sedis · mean 28.02ASV_18 · Chloroflexota · Incertae Sedis · mean 41.65ASV_33 · Actinomycetota · Solirubrobacter · mean 34.98ASV_56 · Actinomycetota · Incertae Sedis · mean 25.97ASV_46 · Actinomycetota · Incertae Sedis · mean 27.43ASV_48 · Actinomycetota · Nocardioides · mean 27.28ASV_48ASV_25 · Actinomycetota · Pseudarthrobacter · mean 38.65ASV_22 · Acidobacteriota · Incertae Sedis · mean 39.75ASV_50 · Acidobacteriota · Incertae Sedis · mean 27.12ASV_29 · Acidobacteriota · Incertae Sedis · mean 36.83ASV_19 · Acidobacteriota · Incertae Sedis · mean 40.85
    Pseudomonadota28Acidobacteriota13Actinomycetota5Verrucomicrobiota4Chloroflexota4Planctomycetota3Myxococcota2Methylomirabilota1

    The tree is the release's FastTree over all ASVs; this is the subtree of its 60 most abundant, drawn as a cladogram. Branch lengths are the tree's; the bar is mean abundance in the release. Hover a tip for its taxonomy.

    ASV panel

    40327 sequences

    ungapped length · median 250 bp (190–252)

    GC content · median 55.6%

    Most abundant ASVs

    ASVphylumgenusmeanprev.
    ASV_1PseudomonadotaBradyrhizobium120.749%
    ASV_2PseudomonadotaBradyrhizobium116.425%
    ASV_3VerrucomicrobiotaCandidatus Udaeobacter110.825%
    ASV_4PseudomonadotaRhizobacter64.845%
    ASV_5PseudomonadotaIncertae Sedis63.249%
    ASV_6PseudomonadotaBradyrhizobium60.345%
    ASV_7AcidobacteriotaIncertae Sedis60.239%
    ASV_8VerrucomicrobiotaCandidatus Udaeobacter59.545%
    ASV_9AcidobacteriotaIncertae Sedis58.645%
    ASV_10PseudomonadotaIncertae Sedis54.649%
    ASV_11ChloroflexotaIncertae Sedis52.749%
    ASV_12PseudomonadotaIncertae Sedis52.625%

    Similar studies

    composition, metadata, location, shared authors
    PRJNA103154075%
    • taxonomy 79% similar (genus)
    • same region (V4)
    • shared author(s): h, t

    33 samples

    PRJNA36104660%
    • taxonomy 80% similar (genus)
    • same region (V4)

    60 samples

    PRJNA30759652%
    • taxonomy 65% similar (genus)
    • same region (V4)

    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.

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    Downloads

    8 files · sha256 in manifest

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    Samples

    65 samples
    Sample Collected habitat Reads Features Shannon State
    SAMD00160688 2014-06-06 surface 31,724 1,423 6.82 0
    SAMD00160689 2014-06-06 surface 31,899 1,344 6.748 0
    SAMD00160690 2014-06-06 surface 39,268 1,534 6.886 0
    SAMD00160691 2014-06-06 rhizosphere 33,926 1,349 6.712 0
    SAMD00160692 2014-06-06 rhizosphere 25,423 1,148 6.618 0
    SAMD00160693 2014-06-06 rhizosphere 27,808 1,243 6.673 0
    SAMD00160694 2014-06-06 surface 33,902 1,379 6.76 1
    SAMD00160695 2014-06-06 surface 37,703 1,483 6.86 1
    SAMD00160696 2014-06-06 surface 35,484 1,394 6.808 1
    SAMD00160697 2014-06-06 rhizosphere 29,118 1,146 6.587 1
    SAMD00160698 2014-06-06 rhizosphere 27,454 1,298 6.706 0
    SAMD00160699 2014-06-06 rhizosphere 33,061 1,258 6.668 1
    SAMD00160700 2014-06-06 surface 35,767 1,345 6.701 1
    SAMD00160701 2014-06-06 surface 36,647 1,304 6.643 1
    SAMD00160702 2014-06-06 surface 36,872 1,395 6.743 1
    SAMD00160703 2014-06-06 rhizosphere 26,965 1,240 6.587 0
    SAMD00160704 2014-06-06 rhizosphere 28,324 1,162 6.526 1
    SAMD00160705 2014-06-06 rhizosphere 30,086 1,161 6.575 1
    SAMD00160706 2014-06-28 surface 25,706 1,332 6.779 0
    SAMD00160707 2014-06-28 surface 29,612 1,479 6.853 0
    SAMD00160708 2014-06-28 surface 20,679 1,044 6.559 0
    SAMD00160709 2014-06-28 rhizosphere 31,331 1,413 6.815 0
    SAMD00160710 2014-06-28 rhizosphere 27,372 1,293 6.74 0
    SAMD00160711 2014-06-28 rhizosphere 26,483 1,176 6.639 1
    SAMD00160712 2014-06-28 surface 31,718 1,513 6.882 0
    SAMD00160713 2014-06-28 surface 24,184 1,142 6.662 0
    SAMD00160714 2014-06-28 surface 26,963 1,250 6.743 0
    SAMD00160715 2014-06-28 rhizosphere 26,154 1,270 6.692 0
    SAMD00160716 2014-06-28 rhizosphere 28,385 1,312 6.766 0
    SAMD00160717 2014-06-28 rhizosphere 26,391 1,319 6.788 0
    SAMD00160718 2014-06-28 surface 26,533 1,275 6.729 0
    SAMD00160719 2014-06-28 surface 25,276 1,272 6.738 0
    SAMD00160720 2014-06-28 surface 32,315 1,493 6.851 0
    SAMD00160721 2014-06-28 rhizosphere 25,016 1,182 6.676 0
    SAMD00160722 2014-06-28 rhizosphere 22,038 1,078 6.61 0
    SAMD00160723 2014-06-28 rhizosphere 21,799 1,092 6.6 0
    SAMD00160724 2014-06-28 surface 25,466 1,293 6.753 0
    SAMD00160725 2014-06-28 surface 25,904 1,210 6.669 0
    SAMD00160726 2014-06-28 surface 25,867 1,137 6.651 1
    SAMD00160727 2014-06-28 rhizosphere 24,182 1,232 6.708 0
    SAMD00160728 2014-06-28 rhizosphere 24,791 1,258 6.742 0
    SAMD00160729 2014-06-28 rhizosphere 25,153 1,294 6.756 0
    SAMD00160730 2014-06-25 surface 27,241 1,238 6.755 1
    SAMD00160731 2014-06-25 surface 28,696 1,498 6.886 0
    SAMD00160732 2014-06-25 surface 29,741 1,371 6.815 1
    SAMD00160733 2014-06-25 rhizosphere 26,979 1,376 6.829 0
    SAMD00160734 2014-06-25 rhizosphere 31,610 1,566 6.92 0
    SAMD00160735 2014-06-25 rhizosphere 29,329 1,260 6.736 1
    SAMD00160736 2014-06-25 surface 30,913 1,357 6.765 0
    SAMD00160737 2014-06-25 surface 24,866 1,133 6.619 0
    SAMD00160738 2014-06-25 surface 30,866 1,366 6.771 0
    SAMD00160739 2014-06-25 rhizosphere 28,806 1,281 6.712 0
    SAMD00160740 2014-06-25 rhizosphere 31,427 1,334 6.731 0
    SAMD00160741 2014-06-25 rhizosphere 26,113 1,181 6.608 0
    SAMD00160742 2014-07-19 surface 23,509 1,220 6.663 0
    SAMD00160743 2014-07-19 surface 22,787 1,231 6.656 0
    SAMD00160745 2014-07-19 rhizosphere 24,910 1,237 6.653 0
    SAMD00160746 2014-07-19 rhizosphere 26,438 1,350 6.744 0
    SAMD00160747 2014-07-19 rhizosphere 24,668 1,208 6.603 0
    SAMD00160748 2014-07-19 surface 25,240 1,285 6.772 0
    SAMD00160749 2014-07-19 surface 21,728 1,046 6.6 0
    SAMD00160750 2014-07-19 surface 28,128 1,417 6.862 0
    SAMD00160751 2014-07-19 rhizosphere 23,967 1,154 6.67 0
    SAMD00160752 2014-07-19 rhizosphere 23,243 1,022 6.553 1
    SAMD00160753 2014-07-19 rhizosphere 20,050 985 6.52 0

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