Illumina MiSeq sequencing investigation on the contrasting rhizosphere soil bacterial community structures in tea orchard soil under different content of aluminium

Figures & data

Table 1. The effects of soil pH, invertase activity, urease activity and cellulase activity in different treatments.

Treatment soil	pH	Invertase activity (mg glucose g^−1 soil 24 h^−1)	Urease activity (mg NH3–N g^−1 soil 24 h^−1)	Cellulase activity (mg glucose g^−1 soil 72 h^−1)
N-Soil	5.08 ± 0.59 bc	2.16 ± 0.65 a	0.36 ± 0.05 a	0.07 ± 0.01 a
O-Soil	5.64 ± 0.34 c	5.59 ± 0.64 b	0.57 ± 0.12 a	0.09 ± 0.02 a
F-Soil	4.86 ± 0.45 b	8.93 ± 0.93 d	1.02 ± 0.19 b	0.16 ± 0.03 bc
T-Soil	4.02 ± 0.33 a	9.87 ± 0.22 d	1.18 ± 0.13 b	0.18 ± 0.02 c
R-Soil	3.53 ± 0.26 a	7.68 ± 0.31 c	1.11 ± 0.09 b	0.13 ± 0.01 b

Data are expressed as the means ± SD of the three replications followed by the same letter in the same column are not significantly different (P > .05).

Figure 1. OTU Venn analysis.

Table 2. Comparison of the estimated richness, diversity indexes and Pielou’s evenness at the operational taxonomic unit (OTU) level.

Treatments	Observed OTUs	ACE estimator	Chao1	Shannon
N-Soil	1104.00 ± 116.00 a	1247.92 ± 103.00 a	1274.64 ± 89.00 a	5.32 ± 0.28 a
O-Soil	1623.00 ± 50.00 b	1750.46 ± 20.00 b	1765.23 ± 28.00 b	6.05 ± 0.33 a
F-Soil	1449.00 ± 193.00 ab	1553.16 ± 144.00 b	1580.01 ± 155.00 ab	5.72 ± 1.16 a
T-Soil	1363.00 ± 155.00 ab	1506.93 ± 149.00 ab	1539.51 ± 143.00 ab	5.42 ± 0.57 a
R-Soil	1406.00 ± 288.00 ab	1555.54 ± 260.00 b	1574.06 ± 267.00 ab	5.69 ± 0.31 a

Averages of replicates three standard error; means followed by different letters are significantly different at P < .05.

Figure 2. Comparison of the bacterial communities at the phylum level (‘Other’ means sequences that could not be classified into any known group).

Table 3. The significant different genera among all treatments.

Taxon	N-Soil (%)	O-Soil (%)	F-Soil (%)	T-Soil (%)	R-Soil (%)
Acidothermus	2.34 ± 0.75 b	1.13 ± 0.34 a	0.34 ± 0.18 a	5.14 ± 1.02 d	3.66 ± 0.86 c
Streptomyces	0.15 ± 0.09 a	0.32 ± 0.15 a	11.63 ± 3.87 b	0.42 ± 0.19 a	0.05 ± 0.02 a
Gemmatimonas	0.49 ± 0.12 a	1.99 ± 0.78 b	0.73 ± 0.23 a	0.10 ± 0.04 a	0.65 ± 0.23 a
Nitrospira	0.42 ± 0.11 a	1.08 ± 0.28 b	0.95 ± 0.18 b	0.20 ± 0.07 a	0.29 ± 0.08 a
Rhizomicrobium	2.01 ± 0.39 b	1.24 ± 0.38 a	1.45 ± 0.87 ab	1.30 ± 0.63 a	2.71 ± 0.32 c
Pseudolabrys	0.78 ± 0.43 ab	0.64 ± 0.42 ab	0.39 ± 0.18 a	0.39 ± 0.23 a	1.25 ± 0.27 b
Acidicaldus	1.35 ± 0.78 b	0.05 ± 0.02 a	0.58 ± 0.41 ab	0.59 ± 0.23 ab	0.70 ± 0.14 ab
Acidiphilium	1.41 ± 0.67 c	0.12 ± 0.06 ab	0.02 ± 0.02 a	1.29 ± 0.45 c	0.77 ± 0.25 bc
Acidisphaera	0.49 ± 0.29 c	0.03 ± 0.01 a	0.02 ± 0.01 a	0.34 ± 0.18 bc	0.19 ± 0.05 ab
Dongia	0.75 ± 0.43 ab	2.97 ± 1.02 c	1.68 ± 0.36 b	0.26 ± 0.15 a	0.84 ± 0.22 ab
Sphingomonas	0.66 ± 0.23 a	3.27 ± 0.47 c	2.22 ± 0.41 b	0.39 ± 0.11 a	1.45 ± 0.38 ab
Haliangium	0.37 ± 0.12 ab	0.78 ± 0.21 bc	1.12 ± 0.35 c	0.03 ± 0.02 a	0.30 ± 0.12 ab
Rhodanobacter	0.41 ± 0.23 a	0.71 ± 0.25 a	7.17 ± 1.32 b	1.46 ± 0.52 a	0.51 ± 0.14 a
Acidobacteriaceae Subgroup	8.51 ± 1.31 c	6.62 ± 1.34 bc	3.78 ± 0.98 a	5.37 ± 1.14 b	8.14 ± 1.95 c
Pseudonocardiacea	0.26 ± 0.15 c	0.18 ± 0.09 a	0.19 ± 0.04 a	0.22 ± 0.09 b	0.27 ± 0.14 c
Cytophagacea	0.13 ± 0.08 a	1.42 ± 0.57 b	0.69 ± 0.14 ab	0.02 ± 0.01 a	0.07 ± 0.04 a
Thermosporotrichaceae	4.65 ± 0.98 b	0.11 ± 0.06 a	0.20 ± 0.01 a	0.46 ± 0.05 a	0.21 ± 0.02 a
Gemmatimonadaceae	1.84 ± 0.46 b	1.82 ± 0.38 b	3.00 ± 0.40 b	0.47 ± 0.15 a	1.62 ± 0.42 b
Planctomycetaceae	0.56 ± 0.26 bc	0.28 ± 0.12 ab	0.11 ± 0.08 a	0.75 ± 0.12 c	0.43 ± 0.11 b
Xanthobacteraceae	1.75 ± 0.44 ab	1.35 ± 0.38 a	1.48 ± 0.36 a	2.34 ± 0.25 b	2.06 ± 0.47 ab
Alphai;g__	1.45 ± 0.38 c	0.16 ± 0.09 a	0.02 ± 0.01 a	0.74 ± 0.15 ab	0.79 ± 0.21 ab
Acetobacteraceae; g__	0.50 ± 0.21 a	0.44 ± 0.19 a	0.27 ± 0.09 a	1.12 ± 0.43 b	1.39 ± 0.26 b
DA111; g__	9.03 ± 2.36 b	2.43 ± 1.02 a	1.24 ± 0.38 a	8.15 ± 1.36 b	9.20 ± 1.52 b
Comamonadaceae; g__	0.16 ± 0.08 a	1.53 ± 0.25 c	0.53 ± 0.07 b	0.32 ± 0.04 ab	0.27 ± 0.07 a
Nitrosomonadaceae; g__	0.13 ± 0.06 a	4.79 ± 1.25 c	2.08 ± 0.34 b	0.03 ± 0.01 a	0.40 ± 0.25 a
Xanthomonadaceae; g__	1.52 ± 0.38 ab	2.72 ± 0.54 c	0.99 ± 0.15 a	2.31 ± 0.23 c	2.16 ± 0.46 bc

Note: Data are presented as means and standard errors. Different letters following data in the same row indicate significant differences at P < .05.

Figure 3. Non-metric multi-dimensional scaling (NMDS) at the genus level.

Figure 4. LEfSe results on soil bacterial communities. (a) Histogram of the LDA scores computed for features differentially abundant on different site of tea soil. LEfSe scores can be interpreted as the degree of consistent difference in relative abundance between features of analysed bacterial communities. The histogram thus identifies which clades among all those detected as statistically and biologically differential explain the greatest differences between communities. (b) Taxonomic representation of statistically and biologically consistent differences in different site of tea soil. Differences are represented in the colour of the most abundant class (yellow non-significant, other significantly different). Each circle’s diameter is proportional to the taxon’s abundance.

Data availability statement

Sequence data are deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database [https://www.ncbi.nlm.nih.gov/sra] (PRJNA851941). More details are provided in Data S1 and Data S2. The data that support the findings of this study are available at the figshare repository (https://figshare.com/) at http://doi.org/10.6084/m9.figshare.17162711.v6.