Archive records ENA PRJNA1031540 SRA PRJNA1031540 BioProject PRJNA1031540

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

PRJNA1031540 released 25 Sept 2026

PRJNA1031540

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

Study

The study record carries no description, and its registered title is the accession itself. The figures below are computed from the 33 released samples and 32 runs.

Samples: 33
Runs: 32
Collection: 2021-10 to 2022-04

Linked publication

Inhibition profile of three biological nitrification inhibitors and their response to soil pH modification in two contrasting soils.

10.1093/femsec/fiae072 · 2024 · via europepmc

Linked by the enrich stage. Fields taken from the paper: primers, subfragment.

abstract

Up to 70% of the nitrogen (N) fertilizer applied to agricultural soils is lost through microbially mediated processes, such as nitrification. This can be counteracted by synthetic and biological compounds that inhibit nitrification. However, for many biological nitrification inhibitors (BNIs), the interaction with soil properties, nitrifier specificity, and effective concentrations are unclear. Here, we investigated three synthetic nitrification inhibitors (SNIs) (DCD, DMPP, and nitrapyrin) and three BNIs [methyl 3(4-hydroxyphenyl) propionate (MHPP), methyl 3(4-hydroxyphenyl) acrylate (MHPA), and limonene] in two agricultural soils differing in pH and nitrifier communities. The efficacies of SNIs and BNIs were resilient to short-term pH changes in the neutral pH soil, whereas the efficacy of some BNIs increased by neutralizing the alkaline soil. Among the BNIs, MHPA showed the highest inhibition and was, together with MHPP, identified as a putative AOB/comammox-selective inhibitor. Additionally, MHPA and limonene effectively inhibited nitrification at concentrations comparable to those used for DCD. Moreover, we identified the effective concentrations at which 50% and 80% of inhibition is observed (EC50 and EC80) for the BNIs, and similar EC80 values were observed in both soils. Overall, our results show that these BNIs could potentially serve as effective alternatives to SNIs currently used.

Linked by the enrich stage from europepmc.

Location

sampling sites from the release coordinates

33sampling sites · drag to pan, scroll or pinch to zoom colour by

Place name hierarchy

▸ Österreich
› Niederösterreich
› Bezirk Gänserndorf

Districts named on the samples

Bezirk Gänserndorf 1

Latitude 48.21589 to 48.21589, longitude 16.61836 to 16.61836. 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

33 samples, 2021-10 to 2022-04

48.2159 to 48.2159 N, 16.6184 to 16.6184 E

02 not reported

Storage

not reported

neither the archive nor the linked paper states storage conditions

03 https://europepmc.org/article/MED/38702852

Processing

DNeasy PowerSoil

extraction kit named in the linked paper

04 per-run QC and the linked paper

PCR

16S rRNA V4, primers 806R, U515F, region V3

primers: trimmed

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

32 runs; PAIRED 253.8485 bp reads; the linked paper's text supports MiSeq

07 this release

Denoising

dada2 1.38.0

13,440 ASVs from 524,002 reads

ampliconflow branches off at step 6, Sequencing

this release

ampliconflow starts here: 524,002 reads from 32 runs, QC to 93.0% 16S identity and 91.0% above Q30, primers trimmed, dada2 1.38.0 to 13,440 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 15,146 characters. It supports: extraction_kit, platform, primers, subfragment.

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

Samples

32 runs

13.4k

Features

OTUs at 97%

524k

Reads

mapped total

53 MB

Release size

99 files

Depth floor

1,000 reads

no samples below

QC warnings

97% of runs warned

Reads per sample

log scale

min: 5,859
median: 16,173
max: 35,368

Feature detection

99.5% non-zero

13,369 / 13,440 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 83,973 (16.0%)
Actinomycetota 76,183 (14.5%)
Acidobacteriota 67,645 (12.9%)
Thermoproteota 58,440 (11.2%)
Bacillota 42,840 (8.2%)
Verrucomicrobiota 39,938 (7.6%)
Planctomycetota 39,738 (7.6%)
Bacteroidota 31,749 (6.1%)
Cyanobacteriota 24,873 (4.7%)
Chloroflexota 24,483 (4.7%)
Myxococcota 13,729 (2.6%)
Gemmatimonadota 5,560 (1.1%)
Thermodesulfobacteriota 4,516 (0.9%)
Nitrospirota 4,440 (0.8%)
Latescibacterota 1,246 (0.2%)
Armatimonadota 1,244 (0.2%)
Methylomirabilota 1,114 (0.2%)
Bdellovibrionota 670 (0.1%)
Entotheonellaeota 484 (0.1%)
NB1-j 357 (0.1%)

Top genera

Incertae Sedis 265,748 (50.7%)
Candidatus Udaeobacter 16,786 (3.2%)
Sphingomonas 13,719 (2.6%)
Paenibacillus 10,525 (2.0%)
Nocardioides 8,549 (1.6%)
Candidatus Nitrososphaera 7,703 (1.5%)
Pirellula 7,150 (1.4%)
Chthoniobacter 7,115 (1.4%)
Mycobacterium 6,869 (1.3%)
Niallia 6,803 (1.3%)
Peribacillus 6,470 (1.2%)
Massilia 6,312 (1.2%)
Bryobacter 5,461 (1.0%)
Candidatus Solibacter 5,331 (1.0%)
Pseudarthrobacter 4,954 (0.9%)
Neobacillus 4,923 (0.9%)
Gaiella 4,905 (0.9%)
Nitrospira 4,436 (0.8%)
Bacillus 4,254 (0.8%)
Blastococcus 4,241 (0.8%)

Rank-abundance

log-log

13,369 ranked features, top 200 shown. A steep drop means a few taxa carry most of the reads.

Per-sample reads

32 samples

min: 5,859
median: 16,173
max: 35,368

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

Expected richness when 32 samples are subsampled to a common depth, resampled 31 draws. Median 598 features observed at full depth.

Depth against richness

log depth

One point per sample. Correlation of log reads with observed features is 0.676, so the depth floor is doing most of the work of deciding how many features a sample shows.

Per-run QC

16S identity 93.0% alignment call per run
Q30 rate 91.0% mean Q 35.8
Amplicon V4 primers trimmed
PhiX 0.0% control spike-in

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

Diversity

Shannon: 5.96
Simpson: 0.996
Evenness: 0.938
Chao1: 603

Median across samples. Observed richness ranges 0 to 1,020.

Feature prevalence

0 of 13,440 features

present in at least half of the 33 samples (0.0%). 11,005 features appear in one sample only, which is the long tail rarefaction is fighting.

Ordination

x y colour

One point per sample, 33 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 · 16.8%

evenness 14.3%
chao1 2.2%
shannon 2.0%
observed 0.7%

pc2 · 12.0%

evenness 7.3%
year 5.2%
chao1 2.7%
shannon 1.4%

pc3 · 6.7%

pH 4.2%
observed 3.5%
reads 3.3%
chao1 2.7%

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

Median Shannon 5.961 across the release; observed richness runs 0 to 1020.

Bray-Curtis dissimilarity

33 x 33, darker is closer

Sample order is the release order, 33 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 0.583

state 0 3 samples
state 1 16 samples
state 2 8 samples
state 3 6 samples

Clustered on the centred log-ratio of the top 200 features; 33 samples.

Batch-bias audit

states against

adjusted Rand 0.0289 p = 0.2630

no strong evidence that the states are the batch

999 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

year 0.018

Joint R2 0.018, 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 2021 (n=16) and 2022 (n=16)

Cohen's d: 2.346 (large)
Cliff's delta: 0.938
log2 fold change: 0.131

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

Taxa against year

kruskal with bh

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

Nothing survives. The smallest q is 1.000, which is the honest answer for a study whose samples are spread across three years with two to thirteen samples per year.

16s-v4:ASV_1 H 0.06 · p 0.811 · q 1.000
16s-v4:ASV_2 H 0.08 · p 0.774 · q 1.000
16s-v4:ASV_3 H 0.01 · p 0.924 · q 1.000
16s-v4:ASV_4 H 0.02 · p 0.886 · q 1.000
16s-v4:ASV_5 H 0.05 · p 0.830 · q 1.000

Group difference and spread

Bray-Curtis, 999 permutations

PERMANOVA pseudo-F: 1.002 · p 0.397
PERMDISP F: 2.15 · p 0.445
Distance decay (Mantel r): n/a · p n/a

202116
202217

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 0.029p 0.540

Hellinger-scaled, 1 dummy predictors over 33 samples. The constraint explains 2.9% of the community inertia, -0.003 adjusted.

CCA · p 0.899

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

Co-occurrence network

100 nodes · 3,564 edges

positive: 3,564
negative: 0
density: 0.720
components: 1
mean degree: 71.3

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

Hubs by degree

Differential abundance

wilcoxon · bh

13,369 features tested, 0 survive q ≤ 0.05

2021 against 2022, {"2021":17,"2022":16}. Nothing separates the two classes after correction, so the contamination signal is a community-level shift rather than a handful of marker taxa.

16s-v4:ASV_1000p 0.090 · q 0.406 · log2FC 2.72
16s-v4:ASV_10000p 0.332 · q 0.406 · log2FC -0.70
16s-v4:ASV_10001p 0.332 · q 0.406 · log2FC -0.70
16s-v4:ASV_10002p 0.332 · q 0.406 · log2FC -0.70
16s-v4:ASV_10003p 0.332 · q 0.406 · log2FC -0.70
16s-v4:ASV_10004p 0.332 · q 0.406 · log2FC -0.70

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

Feature ranking and power

by mean

16s-v4:ASV_1mean 71.73
16s-v4:ASV_2mean 65.61
16s-v4:ASV_3mean 54.30
16s-v4:ASV_4mean 51.52
16s-v4:ASV_5mean 46.58
16s-v4:ASV_6mean 43.73
16s-v4:ASV_7mean 41.97
16s-v4:ASV_8mean 41.00

Power: 3 samples per group for 2.35 SD at 0.8 power, alpha 0.05. The study was sufficiently sized for a moderate effect; the effect it actually found is small.

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.

Similar studies

composition, metadata, location, shared authors

PRJDB797875%

taxonomy 79% similar (genus)
same region (V4)
shared author(s): h, t

65 samples

PRJNA36104657%

taxonomy 73% similar (genus)
same region (V4)

60 samples

PRJNA30759653%

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.

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

11 files · sha256 in manifest

Files are served from https://huggingface.co/datasets/hmacgregor/ampliconflow-releases/resolve/main/PRJNA1031540-20260926/ once hosting is wired. Until then the links point at a placeholder base URL.

Samples

33 samples

Sample	Collected	Reads	Features	Shannon	State
SAMN38046997	2022-04	11,318	488	5.891	3
SAMN38046998	2022-04	9,483	402	5.628	3
SAMN38046999	2022-04	5,859	282	5.316	0
SAMN38047000	2022-04	15,837	598	5.929	1
SAMN38047001	2022-04	7,838	357	5.517	3
SAMN38047002	2022-04	6,844	322	5.476	1
SAMN38047003	2022-04	7,340	290	5.153	1
SAMN38047004	2022-04	10,768	420	5.634	2
SAMN38047005	2022-04	11,533	464	5.734	2
SAMN38047006	2022-04	10,026	410	5.599	2
SAMN38047007	2022-04	15,771	607	6	1
SAMN38047008	2022-04	13,360	538	5.862	1
SAMN38047009	2022-04	7,334	340	5.51	1
SAMN38047010	2022-04	10,305	423	5.689	1
SAMN38047011	2022-04	8,758	378	5.621	3
SAMN38047012	2022-04	18,778	662	5.993	2
SAMN38049510	2021-10	18,703	644	6.025	1
SAMN38049511	2021-10	19,274	673	6.084	1
SAMN38049512	2021-10	25,201	834	6.383	1
SAMN38049513	2021-10	17,893	651	6.142	3
SAMN38049514	2021-10	29,645	975	6.52	1
SAMN38049515	2021-10	22,030	770	6.301	0
SAMN38049516	2021-10	24,791	828	6.38	1
SAMN38049517	2021-10	17,556	640	6.133	1
SAMN38049518	2021-10	0	0		1
SAMN38049519	2021-10	24,766	798	6.237	1
SAMN38049520	2021-10	19,036	632	6.012	2
SAMN38049521	2021-10	13,580	501	5.798	2
SAMN38049522	2021-10	16,510	565	5.904	2
SAMN38049523	2021-10	19,990	691	6.116	1
SAMN38049524	2021-10	20,403	679	6.109	2
SAMN38049525	2021-10	28,104	927	6.46	0
SAMN38049526	2021-10	35,368	1,020	6.536	3

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Tags

Study

Linked publication

Location

Place name hierarchy

Districts named on the samples

How the sequences were obtained

ampliconflow branches off at step 6, Sequencing

Reads per sample

Feature detection

Composition

Top phyla

Top genera

Rank-abundance

Per-sample reads

Downstream QC and analysis

Rarefaction

Depth against richness

Per-run QC

Diversity

Feature prevalence

Ordination

Alpha diversity per sample

Bray-Curtis dissimilarity

Phylogenetic diversity

Community states

Batch-bias audit

Variance partitioning

Effect size

Taxa against year

Group difference and spread

Spatial structure

Constrained ordination

Co-occurrence network

Hubs by degree

Differential abundance

Feature ranking and power

Phylogenetic and signal analyses need a tree

Similar studies

Missing or wrong data?

Downloads

Samples