Soil microbiome data of two apple orchards in the UK.

The microbial communities in two apple orchards were characterised using amplicon-based metabarcoding. Samples were taken from tree station locations along a linear transect and from adjacent grass aisles, at both orchards. Comparison was made between the communities occurring at tree station locations and the grass aisles, and between orchards. Further discussion of these datasets is given in https://doi.org/10.1016/j.apsoil.2018.05.015 (Deakin et al., 2018).

Specifications table

Value of the data

These microbiome data include both fungal and bacterial communities from two long standing apple orchards in the U.K. As such they offer a wealth of future opportunities to:

Aid in identifying common microbial communities between apple orchards.

Make comparison of microbial communities under different soil management practices, for example, long-term perennial crops vs. annual crops.

Help identify best management practices for enhancing soil microbial communities.

Data

This datasets contain an abundance of and a comparative analyses of bacterial and fungal communities found in U.K. dessert apple and cider apple orchards. The data contain fungal and bacterial operational taxonomic units (OTUs) found at tree stations and adjacent (approx. 2 m) grass aisle between tree rows, further context to these data (e.g., soil description and management practice) are given in [1]. Table 1 provides a summary of the sequencing data, Table 2 a summary of the OTU taxonomic data, Table 3 and Table 4 show the top 20 by abundance fungal and bacterial OTUs, respectively, which differed significantly between tree station and grass aisle. Table 5, Table 6, Table 7, Table 8 list the numbers of OTUs aggregated at the phylum and class ranks which differed between (1) tree station and grass aisle, (2) orchards and (3) tree station, and grass aisle at each orchard. Supplementary files 1, 2, and 3 contain OTU sequence information, OTU taxonomy and raw sample abundance for the OTUs, respectively, for fungal communities and Supplementary files 4, 5, and 6 present the same for bacterial communities. The column headers in Supplementary files 3 and 6 provide sample metadata (C/D cider or dessert, Y/N tree station or grass aisle, 1–24 sample location, a/b/c sample replicate).

Table 1

The number of raw reads, reads aligned to OTUs and OTUs from each kingdom, summed for all samples and for each orchard.

		Total reads per sample	Reads aligned to OTUs	Total OTUs	OTUs > 5 reads
All	Fungi	12,456,087	7,016,415 (56.3%)	2,132	2,067
	Bacteria	13,562,736	9,734,624 (71.8%)	6,392	6,167
Cider	Fungi	5,357,051	3,069,449 (57.3%)	1,552	1,394
	Bacteria	7,000,356	5,069,312 (72.4%)	5,786	4,752
Dessert	Fungi	7,099,036	3,946,966 (55.6%)	1,638	1,371
	Bacteria	6,562,380	4,665,312 (71.1%)	4,984	4,472

Table 2

The percentage of OTUs which could be classified at the given taxonomic rank by the UTAX algorithm at the confidence level of 0.65.

	Kingdom	Phylum	Class	Order	Family	Genus	Species
Fungi	100	63.7	44.7	36.8	28.3	17.2	6.1
Bacteria	95.8	76.7	51.1	21.4	12.7	14.7	NA

Table 3

The top 20 (by abundance) fungal OTUs with higher abundance in grass aisles (positive fold change) or tree stations (negative fold change) and with absolute fold change > 2 and Benjamini–Hochberg corrected P ≤ 0.05.

Species/taxaa	Base mean	Fold change	P value
Eurotiomycetes(c)	7488.35	20.87	1.55×10-6
Eurotiomycetes(c)	903.59	15.27	1.85×10-4
Eurotiomycetes(c)	797.77	9.48	4.16×10-3
Mortierellaceae(f)	664.58	4.74	4.88×10-7
Fungi(k)	627.46	4.69	2.42×10-2
Monodictys(g)	328.51	3.07	1.44×10-2
Fungi(k)	371.91	2.88	1.06×10-2
Mortierella exigua	1523.28	2.25	1.30×10-2
Cryptococcus aerius	1048.08	−2.37	4.39×10-3
Ilyonectria macrodidyma	1439.95	−2.51	1.30×10-4
Tetracladium(g)	668.40	−2.74	2.03×10-3
Trichoderma(g)	423.53	−2.88	2.01×10-2
Ascomycota(p)	536.66	−2.93	7.11×10-3
Ascomycota(p)	2940.50	−3.48	1.05×10-2
Ascomycota(p)	510.30	−3.91	8.78×10-4
Pyronemataceae(f)	672.12	−5.3	3.52×10-4
Pichia(g)	406.19	−7.23	1.61×10–11
Mrakia frigida	417.63	−7.74	3.40×10-8
Pyronemataceae(f)	1418.61	−8.03	2.93×10-10
Dothideomycetes(o)	378.39	−10.38	3.40×10-10

The lowest assignable taxonomic rank with a UTAX confidence ≥ 0.65.

Table 4

The top 20 (by abundance) bacterial OTUs with higher abundance in grass aisles (positive fold change) or tree stations (negative fold change) and with absolute fold change > 2 and Benjamini–Hochberg corrected P ≤ 0.05.

Genus/taxaa	Base mean	Fold Change	P value
Deltaproteobacteria(c)	151.68	6.90	3.64×10–29
Acidobacteria group3(c)	315.87	2.76	9.69×10−8
Myxococcales(o)	121.44	2.39	1.06×10−13
Gammaproteobacteria(c)	421.41	2.16	4.06×10−10
Bacteroidetes incertae sedis(c)	364.51	2.15	1.64×10−6
Acidobacteria Group5(c)	110.04	2.12	3.97×10−7
Acidobacteria Group1(c)	910.60	2.11	2.79×10−2
Terrimonas	529.47	2.11	2.00×10−3
Rhizobiales(c)	113.99	2.10	3.77×10−9
Betaproteobacteria	132.13	2.06	4.40×10−8
Acidobacteria Group6(c)	105.82	2.05	8.31×10−4
Acidobacteria Group6	150.35	2.03	1.58×10−5
Xanthobacteraceae(f)	146.35	−2.06	3.95×10−7
Flavobacterium	254.87	−2.16	4.59×10−4
Skermanella	151.03	−2.30	6.61×10−6
Gemmatimonadetes(p)	106.09	−2.30	6.74×10−9
Novosphingobium	236.82	−2.53	2.20×10−8
Pseudomonas	899.89	−2.57	1.44×10−8
Flavobacterium	166.80	−3.35	3.83×10−7
Flavobacterium	130.38	−4.13	1.50×10−10

The lowest assignable taxonomic rank with a UTAX confidence ≥ 0.65.

Table 5

The number of fungal OTUs with differential abundance (Benjamini–Hochberg corrected P ≤ 0.05), aggregated at the phylum rank.

Taxaa	Vegetation typeb (tree station vs. grass aisle)	Orchardc (cider vs. dessert)	Interactiond
Ascomycota	177; 103	447	54
Basidiomycota	25; 36	117	6
Chytridiomycota	6; 11	31	3
Fungi	101; 98	278	17
Glomeromycota	1; 15	18	1
Rozellomycota	3; 3	11	3
Zygomycota	5; 8	39	3
Blastocladiomycota	0; 1	1	0
Total	318; 275	942	87

Starting from the phylum rank—the lowest level of taxon with a UTAX confidence ≥ 0.65.

The number of OTUs in each taxon which had higher abundance in tree station (before semicolon) and higher abundance in grass aisle samples (after semicolon).

The number of OTUs in each taxon which had different abundances between the two orchards.

The number of OTUs in each taxon which had different abundances between tree station compared to grass aisle samples at each orchard.

Table 6

The number of bacterial OTUs with differential abundance (Benjamini–Hochberg corrected P ≤ 0.05), aggregated at the phylum rank.

Taxaa	Vegetation typeb (tree station vs. grass aisle)	Orchardc (cider vs. dessert)	Interactiond
Acidobacteria	54; 61	445	82
Actinobacteria	19; 38	219	28
Armatimonadetes	3; 0	12	2
Bacteria	76; 73	603	63
Bacteroidetes	63; 40	248	45
candidate division WPS-1	1; 7	34	1
candidate division WPS-2	1; 8	20	2
Candidatus Saccharibacteria	11; 8	47	8
Chlamydiae	23; 2	54	11
Chloroflexi	7; 3	77	7
Cyanobacteria/Chloroplast	8; 0	3	4
Euryarchaeota	1; 0	3	0
Firmicutes	26; 5	68	19
Gemmatimonadetes	17; 1	61	11
Hydrogenedentes	1; 0	2	1
Latescibacteria	8; 5	35	7
Nitrospirae	5; 0	10	3
Parcubacteria	11; 2	62	13
Planctomycetes	10; 55	288	17
Proteobacteria	233; 130	911	177
Verrucomicrobia	22; 51	196	43
Elusimicrobia	0; 2	8	1
Fibrobacteres	0; 5	5	2
Spirochaetes	0; 3	5	2
Tenericutes	0; 3	3	2
Aminicenantes	0; 0	1	1
BRC1	0; 0	6	0
Ignavibacteriae	0; 0	1	0
Pacearchaeota	0; 0	1	0
Poribacteria	0; 0	2	0
Thaumarchaeota	0; 0	1	1
Woesearchaeota	0; 0	3	0
Total	600; 502	3434	553

Starting from the phylum rank—the lowest level of taxon with a UTAX confidence ≥ 0.65.

The number of OTUs in each taxon which had higher abundance in tree station (semicolon) and higher abundance in grass aisle samples (after semicolon).

The number of OTUs in each taxon which had different abundances between the two orchards.

The number of OTUs in each taxon which had different abundances between tree station compared to grass aisle samples at each orchard.

Table 7

The number of fungal OTUs with differential abundance (Benjamini–Hochberg corrected P ≤ 0.05), aggregated at the class rank.

Taxaa	Vegetation typeb (tree station vs. grass aisle)	Orchardc (cider vs. dessert)	Interactiond
Agaricomycetes	10; 26	72	1
Agaricostilbomycetes	1; 0	0	0
Ascomycota	35; 32	120	8
Basidiomycota	4; 5	19	0
Chytridiomycetes	4; 3	12	0
Chytridiomycota	1; 8	18	3
Dothideomycetes	33; 13	56	10
Eurotiomycetes	21; 8	39	4
Exobasidiomycetes	2; 0	1	0
Fungi	101; 98	278	17
Glomeromycota	1; 7	9	0
Lecanoromycetes	2; 1	3	0
Leotiomycetes	26; 9	52	3
Microbotryomycetes	2; 4	8	2
Monoblepharidomycetes	1; 0	1	0
Mortierellomycotina Incertae sedis	3; 6	27	3
Mucoromycotina Incertae sedis	1; 1	1	0
Orbiliomycetes	7; 1	5	1
Pezizomycetes	14; 4	29	6
Rozellomycota	3; 3	11	3
Saccharomycetes	1; 3	4	1
Sordariomycetes	38; 31	130	19
Tremellomycetes	6; 1	15	3
Zygomycota	1; 1	10	0
Blastocladiomycota	0; 1	1	0
Glomeromycetes	0; 8	9	1
Pezizomycotina Incertae sedis	0; 1	6	1
Geoglossomycetes	0; 0	3	1
Pucciniomycotina Incertae sedis	0; 0	1	0
Ustilaginomycetes	0; 0	1	0
Zygomycota Incertae sedis	0; 0	1	0
Total	318; 275	942	87

Starting from the phylum rank—the lowest level of taxon with a UTAX confidence ≥ 0.65.

The number of OTUs in each taxon which had higher abundance in tree station (before semicolon) and higher abundance in grass aisle samples (after semicolon).

The number of OTUs in each taxon which had different abundances between the two orchards.

The number of OTUs in each taxon which had different abundances between tree station compared to grass aisle samples at each orchard.

Table 8

The number of bacterial OTUs with differential abundance (Benjamini–Hochberg corrected P ≤ 0.05), aggregated at the class rank.

Taxaa	Vegetation typeb (tree station vs grass aisle)	Orchardc (cider vs dessert)	Interactiond
Acidobacteria	15; 5	65	9
Acidobacteria Group1	2; 1	30	3
Acidobacteria Group10	1; 6	27	3
Acidobacteria Group13	2; 0	4	2
Acidobacteria Group15	2; 0	5	1
Acidobacteria Group16	4; 4	33	3
Acidobacteria Group17	3; 4	20	4
Acidobacteria Group18	1; 0	2	0
Acidobacteria Group2	4; 0	8	2
Acidobacteria Group20	1; 0	1	1
Acidobacteria Group22	1; 3	20	4
Acidobacteria Group3	6; 7	39	12
Acidobacteria Group4	2; 5	39	6
Acidobacteria Group5	2; 2	10	1
Acidobacteria Group6	5; 19	94	23
Acidobacteria Group7	1; 4	19	5
Actinobacteria	19; 37	218	28
Alphaproteobacteria	50; 18	164	36
Anaerolineae	2; 0	14	3
Armatimonadetes	1; 0	10	1
Armatimonadia	2; 0	2	1
Bacilli	2; 0	25	1
Bacteria(k)	76; 73	603	63
Bacteroidetes	14; 22	94	14
Bacteroidetes incertae sedis	5; 4	25	10
Bacteroidia	5; 0	7	2
Betaproteobacteria	33; 18	102	33
candidate division WPS-1	1; 5	30	1
candidate division WPS-2	1; 8	20	2
Candidatus Saccharibacteria	11; 8	47	8
Chlamydiae	6; 0	14	4
Chlamydiia	17; 2	40	7
Chloroflexi	5; 1	38	2
Chloroplast	8; 0	2	3
Clostridia	20; 1	27	14
Cytophagia	10; 2	18	5
Deltaproteobacteria	34; 48	220	34
Epsilonproteobacteria	1; 0	1	0
Euryarchaeota	1; 0	2	0
Firmicutes	2; 2	12	2
Flavobacteriia	8; 1	16	4
Gammaproteobacteria	92; 16	238	50
Gemmatimonadetes	17; 1	61	11
Holophagae	2; 1	5	2
Hydrogenedentes	1; 0	2	1
Latescibacteria	8; 5	35	7
Negativicutes	2; 0	2	1
Nitrospira	5; 0	8	2
Opitutae	2; 1	8	1
Parcubacteria	7; 1	49	9
Parcubacteria(p)	4; 1	13	4
Planctomycetes	1; 14	51	2
Planctomycetia	9; 38	223	15
Proteobacteria	23; 30	184	24
Spartobacteria	6; 18	61	14
Sphingobacteriia	21; 11	88	10
Subdivision3	4; 24	83	22
Verrucomicrobia	3; 6	26	4
Verrucomicrobiae	7; 2	18	2
Caldilineae	0; 1	10	1
candidate division WPS-1(p)	0; 2	4	0
Elusimicrobia	0; 2	7	1
Erysipelotrichia	0; 2	2	1
Fibrobacteres	0, 5	5	2
Ktedonobacteria	0; 1	13	1
Mollicutes	0; 3	3	2
Phycisphaerae	0; 3	14	0
Spirochaetia	0; 3	4	2
Thermoleophilia	0; 1	1	0
Acidobacteria Group11	0; 0	3	0
Acidobacteria Group12	0; 0	1	0
Acidobacteria Group23	0; 0	1	0
Acidobacteria Group25	0; 0	18	1
Acidobacteria Group9	0; 0	1	0
Aminicenantes(p)	0; 0	1	1
BRC1	0; 0	6	0
Chloroflexia	0; 0	2	0
Cyanobacteria	0; 0	1	1
Endomicrobia	0; 0	1	0
Ignavibacteria	0; 0	1	0
Nitrospirae	0; 0	2	1
Oligoflexia	0; 0	2	0
Pacearchaeota(p)	0; 0	1	0
Poribacteria	0; 0	2	0
Spirochaetes	0; 0	1	0
Thaumarchaeota	0; 0	1	1
Thermoplasmata	0; 0	1	0
Woesearchaeota(p)	0; 0	3	0
Total	600; 502	3,434	553

Starting from the phylum rank—the lowest level of taxon with a UTAX confidence ≥ 0.65.

The number of OTUs in each taxon which had higher abundance in tree station (before semicolon) and higher abundance in grass aisle samples (after semicolon).

The number of OTUs in each taxon which had different abundances between the two orchards.

The number of OTUs in each taxon which had different abundances between tree station compared to grass aisle samples at each orchard.

Experimental design, materials, and methods

Study design

Soil microbial communities were profiled in soil samples taken from two geographically and agronomically distinct apple orchards. Full information on the location and history of the two orchards is given in [1]. Within each orchard, soils were sampled from two vegetation types, former tree stations and the adjacent grassed aisles; which were divided into three blocks of ca. 20 m long, each with eight consecutive. Three replicate soil cores (2.5 cm diameter, containing soil of 5 cm–20 cm depth) were taken ca. 15 cm apart for each sampling point (grass aisle and tree station).

DNA extraction and sequencing

Total genomic DNA was isolated from 0.25 g of each soil sample using the protocol as described in [1]. PCR amplification of Internal Transcribed Spacer (ITS) regions of ITS1 and ITS2 and the V4 variable region of the 16S rRNA gene was performed and samples sequenced on the Illumina MiSeq. Full PCR conditions and sequencing preparation are given in [1].

Bioinformatics analysis of sequence reads

FASTQ sequences were processed to identify operational taxonomic units (OTUs) and calculate OTU abundances using UPARSE 9.0 OTU clustering pipeline [2].

Assignment of taxonomic rank

The UTAX algorithm (http://drive5.com/usearch/manual/tax_conf.html) assigned each OTU representative sequence to taxonomic ranks by alignment to the reference databases ‘Unite V7’ (ITS) [3] and ‘RDP training set 15’ (16 S) [4].

Statistical analyses

Statistical analyses were carried out in R 3.2.0 [5]. OTU counts were library size normalised using the DESeq. 2 median-of-ratios method [6], [7]. The three samples taken from each sampling point were treated as analytical replicates and the data were pooled. OTUs with fewer than six normalised reads across all samples were excluded from further statistical analysis. All analyses were carried out separately for ITS and 16S data.

Differential OTU abundance

DESeq. 2 was used to detect OTUs with differential relative abundances in relation to vegetation type, orchards and their interactions. The fitted model was: Spatial location within each orchard, vegetation type (grass vs. tree), orchard (cider vs. dessert), and the interaction between vegetation type and orchard. Statistical significance was determined at the 5% level (Benjamini–Hochberg adjusted [8]).

Subject area	Biology
More specific subject area	Soil microbial ecology, metabarcoding, spatial correlation
Type of data	tab separated values (.tsv)
	FASTA sequences (.fa)
How data was acquired	Illumina MiSeq with v3 chemistry
Data format	Raw data and analysed data
Experimental factors	Fungal and bacterial soil communities from two apple orchards from both managed and unmanaged soil
Experimental features	Operation taxonomic units quantitated using metabarcoding of ITS (fungal) and 16 S (bacterial) ribosomal regions. Three samples measured for each sample point and mean used for quantification.
Data source location	Dessert Orchard: UK lat. 51.210596, long. 0.601664
	Cider orchard: UK lat. 52.251020, long. -2.301711
Data accessibility	The data are available with this article
Related research article	Deakin G, Tilston EL, Bennett J, Passey T, Harrison N, Fernández F, Xu X. Spatial structuring of soil microbial communities in commercial apple orchards. Applied Soil Ecology. 2018 130:1–12 [1].