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Effects of Rapeseed Cake Fertilizer On Soil Bacterial Diversity and Community Structure in Peach Orchards
Effects of Rapeseed Cake Fertilizer On Soil Bacterial Diversity and Community Structure in Peach Orchards
In the cultivation process, the application of organic fertilizers instead of chemical fertilizers can effectively improve soil
structure, soil fertility, nutrient absorption, and fruit quality. In this study, the effects of potassium fulvic acid and compound
microbial inoculant in rapeseed cake fertilizer on soil bacteria in peach orchard were investigated. The results showed that the
application of rapeseed cake fertilizer significantly increased the abundance of beneficial bacteria in the soil. The results of
functional prediction showed that rapeseed cake fertilizer and potassium fulvic acid used in conjunction could improve nitrogen
fixation and carbon sequestration rates in soil. This study can provide a theoretical basis for the application of rapeseed cake
fertilizer in peach tree cultivation.
Keywords: Rapeseed cake fertilizer, peach orchard, microbial diversity, high-throughput sequencing, bacterial community.
Sun, P., J. Wu, X. Lin, Y. Wang, J. Zhu, C. Chen, H. Jia, X. Wang and J. Shen. 2023. Effects of rapeseed cake fertilizer on soil bacterial diversity and
community structure in peach orchards. Pakistan Journal of Agricultural Sciences 60:1-8.
[Received 6 Jul 2022; Accepted 27 Dec 2022; Published 31 Mar 2023]
Attribution 4.0 International (CC BY 4.0)
Sun, Wu, Lin, Wang, Zhu, Chen, Jia, Wang & Shen
promote plant growth (Qiao et al., 2021). In recent years, the Tiangen Biochemical Technology Co., Ltd. (Beijing, China)
application of rapeseed cake fertilizer is concentrated in was used to extract DNA from all soil samples. These DNA
tobacco planting, where it has been shown to increase total extracts were sent to Beijing Biomaike Biotechnology Co.,
organic carbon content, soluble organic carbon content, Ltd. for library construction, where an Illumina Novaseq 6000
available phosphorus, available potassium, and soil urease System was used for high-throughput sequencing. PCR
activity (Tian et al., 2017; Wu et al., 2019; Wu et al., 2020). amplification was performed using bacteria-specific primers
In tea leaf production settings, rapeseed cake fertilizer has 338F (5'-ACTCCTACGGGAGGCAGCA-3') and 806R (5'-
been observed to effectively increase soil pH value, NH 4-N GGACTACHVGGGTWTCTAAT-3') in the variable region
content, NO3-N content, and leaching resistance (Xie et al., of 16S rRNA gene V3-V4 to amplify the target gene.
2020). In banana cultivation, the application of rapeseed cake Sequencing libraries were quantified using the Qubit 4.0
fertilizer was also observed to alter the soil’s bacterial Fluorometer (Thermo Fisher Scientific, Shanghai, China).
content, with a corresponding reduction in the incidence of Sequencing with 300-base pair paired-end reads was
banana wilt (Qiao et al., 2021). performed on Illumina Novaseq 6000 System at Biomarker
In this study, the effects of rapeseed cake fertilizer on soil Technologies (Beijing, China).
bacteria in peach orchard were analyzed using 16S rRNA Bioinformatics analysis: Trimmomatic v0.33 software was
gene amplicon sequencing, both with and without potassium used to filter the raw reads obtained by sequencing, and then
fulvic acid and bacterial inoculant. cutadapt 1.9.1 software was used to identify and remove
primer sequences. Usearch v10 software was used to splice
MATERIALS AND METHODS these sequences, with the length of the spliced data then
filtered according to the length range of different regions.
Experimental design and sampling: The experiment was UCHIME v4.2 software (Edgar et al., 2011) was used to
carried out in the peach planting experimental area of identify and remove chimera sequences to obtain the final
Yuandong Township Fruit and Flower (Provincial) effective data. Reads were clustered at a similarity level of
Agricultural Science and Technology Park, Jindong District, 97.0% using Usearch software to obtain OTUs. Species
Jinhua City, from January to July 2020. All tested peach trees annotation and taxonomic analysis of bacteria were
were of the "Yulupantao" variety. A total of four treatments performed using QIIME software, and the alpha diversity
were set up in the experiment: Group 1 (the control group): indices of samples were evaluated using QIIME2 software
1.5 kg ordinary compound fertilizer (N:P:K=15-15-15) plus (Bolyen et al., 2019). Beta diversity analysis was performed
0.5 kg urea; Group 2: 5 kg rapeseed cake(35 percent protein, using QIIME software, using principal coordinate analysis
12 percent crude fiber, 9.7 percent fat, and 8 percent ash); (PCoA) and the unweighted group average method (UPGMA)
Group 3: 5 kg rapeseed cake plus 250 g potassium fulvic acid; to compare the difference and similarity of the composition of
and Group 4: 5 kg rapeseed cake plus 100 g compound different samples’ OTUs. Linear discriminant analysis (LDA)
microbial inoculum(effective viable count >2×10 10 cfu/g). effect size (LEfSe) was employed to identify statistically
Nine trees were selected for each treatment group, five holes different biomarkers among groups. Bacterial functions were
(depth of 15 ± 5 cm and diameter of 15 ± 5 cm) were dug at a predicted using FAPROTAX (Louca et al., 2016; Nguyen et
distance of about 70 cm from the trees, and the fertilizer was al., 2016).
spread into the holes, then holes were covered with the Statistical analysis: SPSS version 24.0 was used to conduct
excavated soil. statistical analysis. Continuous variables such as bacterial α-
Soil samples were collected from each group after six months. diversity are expressed as mean ± standard deviation (SD)
Two points were taken about 75 cm from each tree, 30 cm unless otherwise noted. A paired Student’s t-test was used
above the fertilizer application point, and the top 5 cm of soil when comparisons between the two groups followed a normal
was removed with a sterilized spade. The undecomposed litter distribution. The non-parametric Kruskal-Wallis sum-rank
layer on the soil surface was removed, and a sterilized shovel test was used for non-normally distributed data. All of the
was used to remove 5 cm of soil on the surface. Samples of statistical tests were two-tailed, and p < 0.05 was defined as
10–15 g were obtained from the uncovered soil, put into a the margin of significance.
sterile plastic bag, and combined. The collected samples were
marked, placed in an ice box, and brought back to the RESULTS
laboratory, where they were mashed, passed through a 2 mm
sieve, and distributed into 2 mL EP tubes. Processed samples OTU analysis of soil bacterial community: A total of
were then snap-frozen in liquid nitrogen and stored in a 959,372 pairs of sequences were obtained by high-throughput
refrigerator at −80°C. Three parallel samples were taken from sequencing. A total of 943,391 valid sequences were
each combined batch for DNA extraction. generated after double-end sequence quality control and
DNA extraction, PCR amplification, and sequencing: The splicing. At least 78,346 valid sequences were generated for
TGuide S96 magnetic bead method soil/fecal DNA kit from each sample, with an average of 78,616 valid sequences and
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Soil bacterial diversity and community structure
an average sequence length of 416/417/418 bp. A total of asymptotic (Figure 3), indicating that the majority of useful
2174 OTUs were obtained by clustering the sequences at a genetic material present in the samples was isolated.
similarity level of 97.0%. The number of OTUs in different
processes is ranked as Group 3 > Group 4 > Group 2 >
Group 1.
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Sun, Wu, Lin, Wang, Zhu, Chen, Jia, Wang & Shen
Table 1. Changes in bacterial diversity index of soil samples with different treatments.
Samples Shannon Simpson ACE Chao1
Group 1 8.972±0.1528a 0.993±0.0016a 1820.34±16.88b 1869.65±17.03b
Group 2 9.346±0.0092a 0.995±0.0001a 1942.48±9.828a 1973.22±10.15a
Group 3 9.047±0.1494a 0.994±0.0009a 1934.57±30.60a 1952.34±31.15ab
Group 4 9.370±0.0241a 0.996±0.0002a 1967.10±7.828a 1984.88±6.412a
there is a significant distance between Group 4 and Group 1, level in this experiment, the analysis was carried out at the
indicating that soil bacterial content was significantly taxonomic level to further analyze the differences between
influenced by the treatment. Permutation multivariate bacterial community components. The relative abundances of
analysis of variance (PERMANOVA, p = 0.001) further Solibacteraceae Subgroup 3, Gemmatimonadaceae,
indicated that there were significant differences in soil Acidobacteriales, SC-I-84, Xanthobacteraceae,
microbial content after different treatments. Chthoniobacteraceae, and the WD2101 soil group in Groups
2 and 3 all increased in comparison to the control group
(Group 1). The relative abundance of Sphingomonadaceae,
Acidobacteriaceae Subgroup 1, and Rhodobacteraceae
decreased; the proportions of Acidobacteriales, SC-I-84,
Xanthobacteraceae, uncultured_bacterium_c_Subgroup_6,
Chthoniobacteraceae, Chitinophagaceae, and the WD2101
soil group of Group 4 were larger, while the rest of the
sampled populations declined.
The relative abundance of bacterial content in each group was
calculated and compared using LefSe analysis. Bacteria with
an LDA score greater than 3.5 were analyzed, and it was
found that there were significant differences between all
treatment groups. Bacterial phylum, class, order, family,
genus, and species branch were analyzed (Figure 5). There
were a total of 57 species with significant differences in
different treatment groups, of which Group 3 had the highest
number, including 1 class Acidobacteriia, 2 orders
Solibacterales, Betaproteobacteriales, SC-I-84,
Flavobacteriaceae (Xanthobacteraceae) and 4 other families,
Figure 4. Principal coordinate analysis (PCoA) and Candidatus and other 5 genera, and 5 unnamed species.
permutation multivariate analysis of variance Group 4 had the second highest total, with 16 characteristic
(PERMANOVA) of soil samples with different groups: Alphaproteobacteria (Alphaproteobacteria) 1 class,
treatments. Flavobacteriales (Flavobacteriales), Elsterales and 4 other
orders, Flavobacteriaceae (Flavobacteriaceae),
Soil bacterial community: For soil bacterial phyla at the Nitrosomonadaceae (Nitrosomonadaceae) and 4 other
taxonomic level, it can be seen that the bacterial species families, Flavobacterium (Flavobacterium), 4 other genera,
contained in all samples were comparable, but there were and 3 unnamed species). Group 2 was next, with 13
differences in species distribution. The 10 phyla with the characteristic populations (namely, 1 phylum Patescibacteria,
highest average abundance in all treatments were 1 class Thermoleophilia, 2 orders Micropepsales and
Proteobacteria, Acidobacteria, Actinobacteria, Gaiellales, 2 families including Micropepsaceae, 4 genera
Planctomycetes, Gemmatimonadetes, Verrucomicrobia, including Gemmatimonas, and 3 unnamed species). Group 1
Bacteroidetes, Chloroflexi, Firmicutes, and WPS-2. (the control) had the fewest characteristic populations, 11 in
Compared with the control group (Group 1), the proportion of total: Actinobacteria (Actinobacteria) 1 phylum,
Verrucomicrobia in Groups 2, 3, and 4 was significantly Actinobacteria (Actinobacteria) 1 class, Xanthomonadales
increased, and the relative abundances reached 6.34%, 4.30%, (Xanthomonas spp.) order, Sphingomonadales
and 6.23%, respectively, becoming the dominant phylum in (Sphingomonadales), Frankiales, Micrococcales
all three groups. In addition, the proportion of Planctomycetes (Micrococcus) 4 orders, Rhodanobacteraceae,
in Group 2 and the proportions of Acidobacteria and Sphingomonadaceae (Sphingomonadaceae),
Gemmatimonadetes in Group 3 were significantly increased. Xanthomonadaceae (Xanthomonadaceae) 3 families,
Due to the low reliability of species annotation at the genus Rhodanobacter 1 genus, and 1 unnamed species.
4
Soil bacterial diversity and community structure
(a)
(b)
(c)
5
Sun, Wu, Lin, Wang, Zhu, Chen, Jia, Wang & Shen
bacteria was the highest in Group 3 (5.09%) and the lowest in even in conjunction with organic fertilizer improvements.
Group 1 (2.78%). The relative abundance of fermenting There were no significant differences in Shannon and
bacteria in Group 2 and Group 4 was significantly higher than Simpson indices among the four treatment groups, indicating
that in Group 1 and Group 3. The relative abundance of that rapeseed cake cannot produce a long-term increase in
nitrogen-fixing bacteria had little difference between groups, bacterial diversity in soil. (It is possible that some short-term
with the highest in Group 4 (3.11%) and the lowest in Group increase in bacterial diversity did occur but had normalized
2 (2.25%). The relative abundance of predatory or between treatment application and sampling.) The results of
exoparasitic bacteria in Group 4 was significantly higher than PCoA and PERMANOVA showed that microbial inoculants
that in Group 2 but did not show a significant trend across all had little effect on soil bacterial community structure. When
groups. Nitrifying bacteria had the lowest relative abundance potassium fulvic acid and rapeseed cake were used together,
in Group 2 (1.15%). The relative abundances of other groups the richness and diversity of bacterial communities were
were greater than 2%; these “other” bacterial species did not lower than those in the treatment group using only rapeseed
have a role clearly defined by FAPROTAX. cake, and the β-diversity analysis also showed that there were
significant differences between the two. Therefore, in this
experiment, potassium fulvic acid mixed with rapeseed cake
fertilizer did not show a significant improvement over
rapeseed cake used alone.
The bacterial species observed under different fertilization
treatments were similar, with the dominant flora being species
from the Proteobacteria, Acidobacteria, Actinobacteria,
Planctomycetes, and Bacillus phyla, which were similar to the
reported soil microorganisms under fertilization management.
Proteobacteria and Acidobacteria accounted for more than
50% of the total relative abundance in each group.
Proteobacteria are widely present in soil and play an
important role in the decomposition and transformation of
organic matter. Studies have shown that an increase in the
abundance of Proteobacteria can improve nitrogen
transformation rates (Liu et al., 2014; Moulin et al., 2001).
Acidobacteria are mostly acidophilic bacteria, and the
application of nitrogen fertilizer will reduce the relative
abundance of Acidobacteria in soil (Wang et al., 2016). This
Figure 7. Functional annotation of soil bacteria under experiment was performed in acidic soil with low nutrient
different fertilization treatments. content, so the relative abundance of Acidobacteria was, as
expected, high. Among the four treatments, the control group
DISCUSSION had the lowest relative abundance of Acetobacter, possibly as
a result of urea administration.
Bacteria are an important part of soil health, accounting for Chemical fertilizers play an important role in fruit tree
approximately 70–90% of all soil microorganisms. They play cultivation, but the excessive application of fertilizer can
an important role in soil nutrient cycling, with a direct cause environmental pollution (Havens et al., 2009). The
relationship between bacterial content and available soil application of organic fertilizer can greatly improve the
nutrients (Diane et al., 2017). The main components of physical and chemical properties of the soil, reduce the
rapeseed cake are protein, crude fiber and crude fat, which are harmful flora in the soil, speed up the activation of nutrients,
comprehensive in nutrients and can provide microorganisms increase the content of soil nutrients, and keep the supply of
with carbon sources and other substances required for growth, available nutrients in a balanced state (Huang et al., 2010).
and can effectively promote the reproduction of Rhodanobacter is a heavy metal-susceptible flora, and it has
microorganisms (Qiao et al., 2021). This study found that a very significant negative correlation with exchangeable
beneficial soil bacteria content was significantly higher in the organic matter and a significant positive correlation with
groups treated with rapeseed cake fertilizer than in the groups pineapple heart rot and watermelon fusarium wilt, but
treated with compound fertilizer and urea. This result is whether it will affect peach trees has not been reported (Hu et
consistent with the results of studies using rapeseed cake al., 2022; Tian et al.,2018; Guo et al., 2017). The relative
fertilizer on bananas and flue-cured tobacco (Qiao et al., abundance of Rhodanobacter in the control group was
2021; Tian et al., 2017; Wang et al., 2011). Microbial significantly higher than that in the other groups, indicating
inoculation also significantly improved soil bacterial content, that the application of rapeseed cake could reduce its relative
6
Soil bacterial diversity and community structure
abundance in the soil and increase exchangeable organic rapeseed cake fertilizer and potassium fulvic acid increased
matter content in affected soil. the relative abundance of metabolic pathways involved in
Xanthomonas is a gram-negative, disease-causing genus of carbon and nitrogen cycling and facilitated the accumulation
bacteria that can infect more than 400 different plant hosts and of organic matter in the soil.
can cause XAP bacterial spot in peach trees (Timilsina et al., Conflict of Interest: The Authors declare that there is no
2020; Bardsley et al., 2013). In this study, Xanthomonas conflict of interest
species were more abundant in the control group, indicating Authors’ Contribution Statements: PS, XL and JS designed
that rapeseed cake fertilizer could significantly reduce the experiments. JW, YW, CC and JZ performed experiments.
relative abundance of Xanthomonas in Taoyuan and reduce SP, JW, and XL analyzed data and compiled figures.PS, JW
the occurrence of diseases. Flavobacterium, Bacillus, and and JS wrote the manuscript. HJ and XW edited the final
Acidobacter are beneficial soil bacteria that can improve the manuscript. All authors contributed to the article and
physical and chemical properties of soil (Shi et al., 2020; approved the submitted version
Saleem et al., 2019). In each group treated with rapeseed cake
fertilizer, these genera were present in greater quantities. REFERENCES
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Sun, Wu, Lin, Wang, Zhu, Chen, Jia, Wang & Shen