Complete genome sequence of biocontrol strain Paenibacillus peoriae HJ-2 and further analysis of its biocontrol mechanism

Abstract

Background
Paris polyphylla is a herb widely used in traditional Chinese medicine to treat various diseases. Stem rot diseases seriously affected the yield of P. polyphylla in subtropical areas of China. Therefore, cost-effective, chemical-free, eco-friendly strategies to control stem rot on P. polyphylla are valuable and urgently needed.

Results
In this paper, we reported the biocontrol efficiency of Paenibacillus peoriae HJ-2 and its complete genome sequence. Strain HJ-2 could serve as a potential biocontrol agent against stem rot on P. polyphylla in the greenhouse and field . The genome of HJ-2 consists of a single 6,001,192 bp chromosome with an average GC content of 45% and 5,237 predicted protein coding genes, 39 rRNAs and 108 tRNAs. The phylogenetic tree indicated that HJ-2 is most closely related to P. peoriae IBSD35. Functional analysis of genome revealed numerous genes/gene clusters involved in plant colonization, biofilm formation, plant growth promotion, antibiotic and resistance inducers synthesis. Moreover, metabolic pathways that potentially contribute to biocontrol mechanisms were identified .

Conclusions
This study revealed that P. peoriae HJ-2 could serve as a potential BCA against stem rot on P. polyphylla . Based on genome analysis, the genome of HJ-2 contains more than 70 genes and 12 putative gene clusters related to secondary metabolites, which have previously been described as being involved in chemotaxis motility, biofilm formation, growth promotion, antifungal activity and resistance inducers biosynthesis. Compared with other strains, variation in the genes/gene clusters may lead to different antimicrobial spectra and biocontrol efficacies.

Full text

Jiangetal. BMC Genomics (2022) 23:161
https://doi.org/10.1186/s12864-022-08330-0
RESEARCH
Complete genome sequence ofbiocontrol
strain Paenibacillus peoriae HJ-2 andfurther
analysis ofits biocontrol mechanism
Aiming Jiang1,2, Chengwu Zou1, Xiang Xu3, Zunwei Ke2, Jiangan Hou1, Guihe Jiang1, Chunli Fan1,
Jianhua Gong2 and Jiguang Wei1*
Abstract
Background: Paris polyphylla is a herb widely used in traditional Chinese medicine to treat various diseases. Stem rot
diseases seriously affected the yield of P. polyphylla in subtropical areas of China. Therefore, cost-effective, chemical-
free, eco-friendly strategies to control stem rot on P. polyphylla are valuable and urgently needed.
Results: In this paper, we reported the biocontrol efficiency of Paenibacillus peoriae HJ-2 and its complete genome
sequence. Strain HJ-2 could serve as a potential biocontrol agent against stem rot on P. polyphylla in the greenhouse
and field. The genome of HJ-2 consists of a single 6,001,192 bp chromosome with an average GC content of 45% and
5,237 predicted protein coding genes, 39 rRNAs and 108 tRNAs. The phylogenetic tree indicated that HJ-2 is most
closely related to P. peoriae IBSD35. Functional analysis of genome revealed numerous genes/gene clusters involved in
plant colonization, biofilm formation, plant growth promotion, antibiotic and resistance inducers synthesis. Moreover,
metabolic pathways that potentially contribute to biocontrol mechanisms were identified.
Conclusions: This study revealed that P. peoriae HJ-2 could serve as a potential BCA against stem rot on P. polyphylla.
Based on genome analysis, the genome of HJ-2 contains more than 70 genes and 12 putative gene clusters related
to secondary metabolites, which have previously been described as being involved in chemotaxis motility, biofilm
formation, growth promotion, antifungal activity and resistance inducers biosynthesis. Compared with other strains,
variation in the genes/gene clusters may lead to different antimicrobial spectra and biocontrol efficacies.
Keywords: Paenibacillus peoriae, Paris polyphylla, Stem rot, Genome analysis, Biocontrol mechanism
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Background
Paris polyphylla var. chinensis (Franch.) Hara.is a herb
widely used in traditional Chinese medicine (TCM) to
treat various diseases (e.g., hemostasis, abscess, snake
bite, abnormal uterine bleeding, tumors and analgesia)
[1–4]. Large scale application of Paris in TCM helps eco-
nomic value of herb increase in a dramatic way in China
and other Asian countries. Yet, with the rapidly rising in
demand, wild individuals of these plants have been over-
exploited for the last several decades. Many Paris (e.g.,
Paris polyphylla, Paris fargesii and Paris mairei) have
been listed as endangered species in China from Interna-
tional Union for Conservation of Nature (IUCN). Artifi-
cial cultivation is an effective means to meet the growing
demand for Chinese herbal medicine. e cultivated
area of P. polyphylla in Yunnan had exceeded 1333 hm2
at the end of 2014. However, severity soilborne diseases
(e.g., Stem rot, Anthracnose and Gray mold) seriously
affected the yield of P. polyphylla [5–8]. Stem rot on P.
polyphylla, caused by two species of Fusarium, Fusarium
Open Access
*Correspondence: jiguangwei@gxu.edu.cn
1 College of Agriculture, Guangxi University, Nanning 530004, China
Full list of author information is available at the end of the article
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Jiangetal. BMC Genomics (2022) 23:161
concentricum and Fusarium oxysporum is prevalent in
subtropical areas of China where plants grow under rain-
fed conditions [7, 8]. Plants with stem rot disease devel-
oped stem cracking, shriveling, yellowing, stunting, and
finally wilting, and symptoms of plant death may even-
tually appear within a few weeks [9, 10]. Stem rot on P.
polyphylla ultimately limited the growth of roots as pri-
mary medicinal parts and amount of seeds. e eco-
nomic control approaches of stem rot on P. polyphylla are
challenging due to the long-term survival of mycelia in
soil, weather conditions and the evolution of new races.
Current management options for this disease are mainly
dependent on the use of chemical management measures
[11]. Extensive applications of commercially fungicides
contribute to resistance in fungal pathogens. Moreover,
chemical pesticides and fungicides are forbidden to use
in the planting process of Chinese herb in light of health
issues. erefore, cost-effective, chemical-free, eco-
friendly strategies to control stem rot on P. polyphylla are
valuable and urgently needed.
Biocontrol has been considered a viable alternative
method due to the advantages of environmental friend-
liness, safety and the lack of the induction of pesticide
resistance [12]. e microorganisms, most of which are
Bacillus, Pseudomonas and Paenibacillus spp., have been
successfully applied for suppressing soil-borne patho-
gens [13–16]. Researches on the biocontrol of stem rot
are still in progress and revealing new strategies. Plant
growth-promoting rhizobacteria (PGPR) produces phy-
tohormones such as cytokinins, gibberellins, indole-
3-acetic acid (IAA), and protects plants against pathogens
through antibiotic biosynthesis. Meanwhile, PGPR exhib-
its the abilities of nitrogen fixation, phosphate solubiliza-
tion, siderophore production [17, 18]. In addition to these
effects, many PGPRs increase plant resistance to patho-
gen via the elicitation of induced systemic resistance
(ISR), which is triggered by a range of secondary metabo-
lites referred to as ‘elicitors’ [19, 20]. Different signaling
pathways, such as the jasmonic acid (JA) and ethylene
(ET) pathways, are activated to induce plant resistance
[21–23]. Although a large number of microbe species
that could serve as biocontrolagents(BCAs) to manage
plant pathogens have been discovered, researches on the
biocontrol of stem rot on Paris are scarce.
In this study, we identified an efficient biocontrol
strain, Paenibacillus peoriae HJ-2, which was isolated
from the rhizosphere of P. polyphylla. e results of
greenhouse and field experiments indicated thatP. peo-
riae HJ-2 could serve as a potential BCA against stem rot
on P. polyphylla. Whole-genome sequencing of PGPRs
facilitates studies of gene mutation and molecular evo-
lution mechanisms. Chen (2007) revealed the resistance
mechanisms of Bacillus amyloliquefaciens FZB42 toward
phytopathogen via producing antifungal components by
genome analysis [24]. According to gene function anno-
tation, signaling pathways of volatile compounds emit-
ted from B. amyloliquefaciens FZB42 were described in
detail. Andrés-Barrao (2017) analyzed Enterobacter sp.
SA187 genome and revealed its plant growth promotion
mechanisms for Arabidopsis thaliana under salt stress
[25]. e genome of Paenibacillus polymyxa HY96-2
was sequenced, and the variation in secondary metabo-
lites genes or gene clusters could result in different anti-
microbial activities and biocontrol efficacies between
HY96-2 and other p. polymyxa strains [26]. Further-
more, although P. peoriae is a potential BCA, there are
few studies about biocontrol mechanism of P. peoriae
using genome analysis or other molecular methods so far.
Moreover, the differences in the biocontrol mechanisms
could be revealed on the basis of comparison of genes/
gene clusters. To understand the molecular mechanism
involved in plant–microbe interactions, we provide
a high quality genome assembly and annotation of P.
peoriaeHJ-2.
us, the aims of this study were to (1) identify the
antagonistic activity of P. peoriae HJ-2 against Fusarium
spp. in vivo, (2) evaluate plant growth promotion and
biocontrol efficiency of P. peoriae HJ-2 in the green-
house and field, and (3) compare the genes/gene clusters
involved in biofilm formation, antibiotic and resistance
inducers synthesis with other P. peoriae strains.
Results
Genomic characterisation ofstrain HJ‑2
e complete genome of HJ-2 consists of a single circular
chromosome of 6,001,192bp with an average GC con-
tent of 45% (Fig.1). Genomic DNA sequencing generated
180,325 reads and contained 1,291,048,950bp, and the
sequencing coverage reached 215 × . In total, 5439 genes
were identified, including 5237 coding sequences genes
(CDSs), 39 rRNA and 108 tRNA genes. e general fea-
tures are shown in Table1. Ten putative GIs were found
inHJ-2using the GI prediction methods, and the size of
GIs ranged from 9.8 to 35kb. CRISPRs contain multiple
short and repeated sequences, and the length of which
is generally 21 to 47bp. Nine CRISPRs were involved in
HJ-2, and length of repeated sequences ranged from 9 to
18bp.
According to GO annotation, a total of 2562 genes
were classified into 27 functional groups, and the genes
involved in biological process were most abundantly
(Suppl. Fig. 1). Among biological process group, the
number of genes related to the metabolic process was
highest, with 35.5% respectively. On the basis of COG
database, a total of 3608 genes were assigned to 24
COG categories (Fig. 2). Carbohydrate transport and
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Jiangetal. BMC Genomics (2022) 23:161
metabolism category represented the largest group
(492 genes, 9.37% of all CDSs), followed by transcrip-
tion, whereas only a small number genes were assigned
to extracellular structures category. According to KEGG
annotation, 2423 genes (46.27% of all CDSs) were
assigned to 35 KEGG pathways, and the largest num-
ber of identified genes were classified into metabolism
pathways. Among these pathways, the most represented
pathways included carbohydrate metabolism(289 genes,
5.52% of all CDSs), followed by amino acid metabolism
and energy metabolism pathways (Suppl. Fig.2).
Identication ofstrain HJ‑2
HJ-2 was isolated from the rhizosphere of P.polyphylla,
and cultured at 30°C in Luria–Bertani broth. e 16S
rDNA gene amplified from the genomic DNA of HJ-2
(approximately 1.4kb) was sequenced (GenBank acces-
sion no. MK911741), and the BLAST search revealed
that the sequence shared99.72% identity to Paenibacillus
spp.(e.g., Paenibacillus peoriae HS311, Paenibacillus pol-
myxa ATCC15970 and Paenibacillus polmyxa YC0573).
Fig. 1 Genome map of P. peoriae HJ-2. The bacterial chromosome is 6.0 Mb in size. The distribution of the circle from the outside indicates the
genome size, forward CDS, reverse CDS, repeat sequence, tRNA(black), rRNA(blue), GC ratio(red and green indicate regions where the GC ratio is
higher than average and lower than average, respectively), and CG skew positive (red) and negative (green)
Table 1 General features of the genome of P. peoriae HJ-2
Feature Value
Genome size (bp) 6,001,192
GC content (%) 45
Gene density 906.5genes/Mb
Genomic Islands 10
CDS 5237
Genes assigned to COG 3608(66.33%)
Genes assigned to KEGG 2423(46.27%)
rRNA 39
tRNA 108
CRISPR 9
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Jiangetal. BMC Genomics (2022) 23:161
Average nucleotide identity (ANI) is one of the
most powerful approaches for evolutionary distance
assessment between bacterial species based on digital
whole genome comparison. Based on ANI values, the
genome sequence of HJ-2 displayed highest similar-
ity with the species of P. peoriae with the ANI values
over 96%, whereas the ANI values between HJ-2 and
other strains were lower, and ranged between 64 and
90% (Suppl. Fig.3). By applying whole-genome analy-
sis, the phylogenetic tree construction based on the
single-copy genesfrom the 79 Paenibacillus genomes
available in the Genbank database demonstrated that
HJ-2 appeared to belong to P. peoriae, with the closest
relative to P. peoriaeIBSD35 (Fig.3). We also performed
a pangenome analysis to compare HJ-2 with other nine
strains (P. peoriae HS311, IBSD35, FSLR7-0321, ZF390;
P. polymyxa SQR21, SC2, HY96-2, DSM365, A18).
As shown in Fig.4, 3,481 orthologous protein coding
genes are conserved and constitute the core genome.
In addition, the number of gene families unique to
strain ZF390 was 791, which was the highest among all
of the analyzed strains. e annotation revealed that
these specific genes encoded a large number of tran-
scriptional regulators, helicase domain proteins, hypo-
thetical proteins, aminotransferases, transposases, drug
resistance transporters, chloramphenicol resistance
proteins, etc. Nucleic acid co-linearity results showed
that strain HJ-2 has high co-linearity with P. peoriae
HS311 (Suppl. Fig.4).
Biocontrol potential ofstrain HJ‑2
As shown in Fig.5A,the strain HJ-2 presented antago-
nistic activity against five Fusarium spp. in vitro. HJ-2
exerted maximum antifungal activity against F. tricinc-
tum and F. concentricum. e antifungal activity of HJ-2
against F. solani and F. graminearum s.str. were low-
est (Suppl. Table2). In addition, HJ-2 could inhibit the
spores germination ofF. concentricum(Fig.5B). Based on
the above results, we infer thatHJ-2 has the potential to
suppress stem rot on P. polyphylla. To verify this hypoth-
esis, we conducted greenhouse and field experiments,
and the results indicated that HJ-2 could significantly
controlstem rot on P. polyphylla in both the greenhouse
and the field. e symptoms of stem rot on P. polyphylla
in theHJ-2 treatment were significantly weaker in com-
pared with the control treatment (Fig.5C and D). e
incidence rate of stem rot on P. polyphylla with theHJ-2
treatment was 35.3% in greenhouse and 11% in the field,
which was significantly lower than that (89.2%, 52%) with
the control treatment (Table2).
In addition, the plant growth promotion capability of
HJ-2 was evaluated in the greenhouse and field experi-
ments. As shown in Table 2, the growth parameters
(the length, fresh and dry weight of stem and root) of P.
Fig. 2 Distribution of genes across COG functional categories in the chromosome of P. peoriae HJ-2
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Jiangetal. BMC Genomics (2022) 23:161
Fig. 3 Phylogenetic tree for P. peoriae HJ-2 and the genus Paenibacillus based on homologous genes. Coloured blocks represent gene clusters for
biosynthesis of fusaricidin, tridecaptin, polymyxin, pelgipeptin and surfactin detected in genus Paenibacillus, whilst white space represents gene
clusters absence. Number in the branches represent bootstrap values. Scale bar represents sequence divergence
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Jiangetal. BMC Genomics (2022) 23:161
polyphylla with the HJ-2 treatment were significantly
higher than those of the control treatment. In the field
experiment, HJ-2 exhibited a significant effect on plant
growth-promoting in compared with the control treat-
ment (Suppl. Fig. 5). e results of IAA production,
nitrogen fixation, and phosphate solubilization assays
indicated that the strain HJ-2 possessed most common
PGP characteristics (Suppl. Fig.6).
Colonization andbiolm formation ofstrain HJ‑2
As shown in Fig. 6A, arrangements of flagella in HJ-2
is peritrichous, and multiple flagella arise from along
the cell body. On the basis of previous researches, core
genes involved in the assembly of flagellum, such as flg-
BCDEGKL, fliAEGHJLMPRSW, flhABFG, motA and
motB were detected in genome of HJ-2 (Suppl. Table3)
[27]. Flagellin containing N-terminally conserved flg22
was also found in the P. peoriae HJ-2 (Fig.6B). As shown
in Fig.7, bacterial cells attaching on the surface of roots
could be observed after 16 days of inoculation. e
number (3.16 ± 0.15 × 107 CFU/g) of strain HJ-2 sta-
bly colonizing in the rhizosphere of Paris was superior
to those in the other HJ-2-inoculated plants (pepper:
2.93 ± 0.2 × 103 CFU/g; tomato: 6.3 ± 0.28 × 103 CFU/g;
tobacco: 2.5 ± 0.5 × 104 CFU/g, respectively) after
inoculation for fifty days. During the colonization pro-
cess, the population of the strain declined dramatically
during the next eight days after inoculation, and then
began to increase until finally stable colonization.
e core genes involved in biofilm formation path-
ways were selected from KEGG database for comparison
between the strain HJ-2, ZF390 and HS311 using BLAST.
As shown in Table3, key genes involved in biofilm forma-
tion were found in genome of HJ-2, ZF390 and HS311,
and the sequence identity exceeded 97%. e sequence
identity between HJ-2 and HS311 exhibited higher than
that between strain HJ-2 and ZF390.
Genes /gene clusters forantibiotic synthesis andinduction
ofplant resistance
On the basis of antiSMASH database, twelve clusters
related to secondary metabolite synthesis were identi-
fied in HJ-2. Among these gene clusters, three clusters
were specific and existed only in HJ-2, while nine clus-
ters existed in more than one strain (Suppl. Table 4).
Six clusters involved in antifungal and antibacterial
peptides (fusaricidin; polymyxin, tridecaptin, pelgipep-
tin, paenilan and paeninodin) biosynthesis were found
in genome of strain HJ-2 (Table4). However, no gene
clusters encoding the biosynthesis of pelgipeptin or
Fig. 4 Flower plot representing the total (outermost layer), unique (second layer) (strain specific), and core proteins (center of the plot) in P. peoriae
and other five P. polymyxa strains
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Fig. 5 Strain HJ-2 could serve as a potential biocontrol agent against stem rot on P. polyphylla (A), antagonistic activity of strain HJ-2 against plant
pathogens in vitro (B), effect of HJ-2 on spore germinations of F concentricum (C), biological control effect of HJ-2 against stem rot on P. polyphylla in
the greenhouse (D), biological control effect of HJ-2 against stem rot on P. polyphylla in the field
Table 2 Evaluation of P. peoriae HJ-2 on biocontrol efficacy and the plant growth parameters of P. polyphylla in greenhouse and field
experiments
The data are means ± SDs. The dierent lowercase letters in the same column indicate signicant dierent at the P < 0.05 level, using LSD test
Parameter P. polyphylla
Greenhouse experiment Field experiment
Control Treatment Control Treatment
Disease incidence (%) 89.2 ± 0.3a 35.3 ± 0.4c 52.0 ± 0.2b 11.0 ± 0.15d
Control efficacy (%) 53.9 ± 1.3 41.0 ± 0.6
Stem Length(cm) 5.6 ± 0.2c 8.8 ± 0.3b 7.6 ± 0.4bc 11.2 ± 0.6a
Fresh weight(g) 12.3 ± 0.7c 15.8 ± 0.4bc 18.3 ± 0.5b 25.3 ± 0.7a
Dry weight(g) 2.1 ± 0.1c 2.7 ± 0.2c 4.3 ± 0.1b 7.1 ± 0.3a
Root Length(cm) 1.5 ± 0.1c 2.1 ± 0.2b 2.3 ± 0.2b 3.5 ± 0.3a
Fresh weight(g) 4.5 ± 0.2c 6.7 ± 0.3bc 7.3 ± 0.2b 9.2 ± 0.4a
Dry weight(g) 0.6 ± 0.1c 1.2 ± 0.1b 1.6 ± 0.2ab 2.7 ± 0.2a
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Jiangetal. BMC Genomics (2022) 23:161
paenilan were detected in HS311, and the gene clusters
encoding the biosynthesis of polymyxin or pelgipeptin
were not detected in ZF390. According to the compari-
son of gene clusters involved in biosynthesis of fusarici-
din and tridecaptin, the result shown that the two gene
clusters sequences in strains HS311 and ZF390 exhib-
ited very high similarities with those in strain HJ-2,
with the similarity of 99.3%, 93.2% and 98.4%, 95.5%,
respectively.
Based on numerous reported examples of elicitor, the
genes coding for resistance inducers were selected for
comparison between the strainHJ-2, ZF390 and HS311
using BLAST. As shown in Table5, the genes coding for
several elicitors, such as 2, 3-butanediol, acetoin, pepti-
doglycan and EF-Tu were all detected in HJ-2, ZF390
and HS311, meanwhile flgL was detected in the HJ-2 and
HS311except for the strain ZF390. e sequence identity
between HJ-2 and HS311 exhibited higher than those
between strain HJ-2 and ZF390.
Discussion
Bacillus peoriae was originally recognized as a new spe-
cies of gas-producingBacillus polymyxaon the basis of
DNA relatedness, multilocus enzyme electrophoresis
analysis, and other phenotypic characteristics. It was later
reclassified as Paenibacillus peoriae with an emended
description of the species. Phylogenetic reconstruction
based on the single-copy genes from the nomenclatural
type strains of currently recognized Paenibacillus species
has clearly demonstrated that the species P. peoriae is
closely related to P.polymyxa, and gene clusters involved
in antifungal and antibacterial peptides (fusaricidin; poly-
myxin, tridecaptin, paenilan and paeninodin) biosynthe-
sis have been found encoded in the genomes of P. peoriae
and P.polymyxa. Pair-wise ANI values for the HJ-2 and
five P.polymyxa strains ranged between 89.8 and 89.9%.
Meanwhile, pair-wise ANI values for HJ-2 and four P.
peoriae strains ranged between 96.5 and 97.3%, which
were considerably higher than the above percentage
Fig. 6 A Transmission electron microscopy section of HJ-2 (B), Conservation of flg22 motif. The N-terminal of FliC proteins of HJ-2 shown a highly
conserved motif shared with Paenibacilus flg22
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Jiangetal. BMC Genomics (2022) 23:161
range. Under the assumption that ANI values of 95–96%
indicate bacterial species boundaries, these results are
congruent with the phylogenetic tree.
Due to the advantages of plant growth promotion and
broad-spectrum antimicrobial activity, the species P. p eo-
riae is a potential BCA used as biofertilizer. However,
limitednumber of comprehensive studies have revealed
the biocontrol mechanism of P. peoriae to date. With the
aim of providing some insight into biocontrol mecha-
nisms in molecular level,the genome of P. peoriae HJ-2
was completely sequenced. In contrast to other species
of P. peoriae, the genome of HJ-2 is smaller than that of
HS311 (6,219,810bp) and ZF390 (6,383,990bp), and was
found to share 3510 orthologous genes with IBSD35. is
number is slightly larger than those (HJ-2 vs HS311, 3421;
HJ-2 vs ZF390, 3436; HJ-2 vs FSL R7-0321, 3497) shared
between HJ-2 and other three P.peoriae strains, reflect-
ing the closer phylogenetic relationship of P.peoriae HJ-2
and P.peoriae IBSD35. Based on the results of genome
assembly and annotation report, numerous coding genes
for rRNAs were found in P. peoriae strains. e genome-
encoded divergent rRNAs regulate gene expression at
the ribosome level in bacteria.With the characteristic of
possessing numerous rRNAs, soil microorganisms have
capacities to rapidly cope with ceaseless nutritional com-
positions changes [35, 36]. GIs are composed of inte-
grated foreign DNA fragments, which are frequently
associated with pathogenesis, metabolism and antibiotic
Fig. 7 Colonization of P. peoriae HJ-2 on the seeding roots (A), Green fluorescence protein (GFP)-tagged P. peoriae HJ-2 mainly colonized the P.
polyphylla roots (B), the content of effectively colonized bacteria on the roots of four plants. Bars = 100 µm
Table 3 Comparison of core genes involved in biofilm formation in strain HJ-2, HS311 and ZF390
Gene name Location Product Identity(%)
ZF390 HS311
kinB 2,363,269 2,364,546 sensor kinase 97.03 97.73
spoOF 3,760,041 3,760,352 stage 0 sporulation protein F 98.72 99.04
spoOA 1,218,318 1,219,121 stage 0 sporulation protein A 97.76 98.88
degU 3,007,565 3,008,287 response regulator 98.2 99.45
degS 3,008,292 3,008,813 sensor histidine kinase 99.81 100.00
AbrB 3,635,054 3,635,596 transcriptional regulator 99.26 99.82
spoOB 2,363,269 2,364,546 sporulation sensor kinase 97.03 97.73
rapZ 3,796,330 3,797,229 RNase adapter protein 98.22 99.56
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Jiangetal. BMC Genomics (2022) 23:161
resistance [37]. GIs are important players in genome
plasticity, thus supporting their rapid adaptation. Bac-
teria have multiple immune functions to remove exoge-
nous virus genes by CRISPRs [38, 39]. e result suggests
that the strain HJ-2 successfully resisted bacteriophages
invasion. No plasmid has been identified when assem-
bling the P.peoriae HJ-2 genome sequence data.
Effective colonization is a prerequisite for PGPRs to
implement their biocontrol function. Colonization of
PGPRs are influenced by various factors, such as root
exudates and environmental factors. Plant could recruit
beneficial rhizobacteria via secreting metabolite, and
the major inducible root-secreted metabolite selectively
activated chemotactic mobility of rhizobacteria [40].
Rhizobacteria finally reach the surface of plant roots by
flagella-driven motion. However, a few PGPRs coloniza-
tion is not limited to a specific region in the plant (such as
rhizosphere), and they can be transported to other tissues
using transmission systems (e.g. bacterial endophytes). In
the process of colonization, bacterial endophytes often
produces many enzymes, such as endoglucanases and
endopolygalacturonidases [41]. To examine the ability of
HJ-2 to colonize plant roots, we labeled the strain with
GFP. In the present study, HJ-2-gfp cells were found to
be attached to the surface of Paris roots. We also found
that the bacterial cells could colonize on pepper, tomato
and tobacco roots, but lesser than that on Paris roots. As
a signal to attract or repel microbes, the root exudates
serve as a carbon source for soil microorganisms. ere-
fore, we surmise that the root exudates of Paris contain
one or more signaling molecules that directly bind to
receptor domains. Such direct binding enables a highly
sensitive response over a wide dynamic range of back-
ground ligand concentrations. e formation of biofilm is
a dynamic process involving an attachment stage, accu-
mulation stage, maturation stage and dispersal stage. e
cells residing in the biofilm are encased within a self-pro-
duced exopolymeric matrix that commonly comprises
lipids, proteins (frequently exhibiting amyloid-like prop-
erties), eDNA and exopolysaccharides [42]. is matrix
fulfills a variety of functions for the community, from
providing structural rigidity and protection from the
external environment to controlling gene regulation and
nutrient adsorption [43]. Previous studies have revealed
Table 4 Comparison of gene clusters involved in antibiotic biosynthesis in strain HJ-2, HS311 and ZF390
Antibiotic name Activity Location Identity (%)
HJ‑2 HS311 ZF390 HS311 ZF390
Fusaricidin Broad antimicrobial activity against Fusarium sp., also suppresses
G+ bacteria [28]3,650,067 -3,719,981 63,180
- 131,651 62,571
- 131,051 99.3 98.4
Tridecaptin Suppresses G− bacteria [29] 89,772- 182,664 2,578,853
-2,671,371 2,419,321
-2,511,835 93.2 95.5
Polymyxin Broad antimicrobial activity, especially against G−bacteria [30] 2,710,256
-2,790,093 5,116,022
- 5,197,037 95.1
Pelgipeptin Broad antimicrobial activity against G + and G− bacteria [31];
PelgipeptinA and PelgipeptinB against Fusarium graminearum
and Rhizoctonia solani [32]
485,090
- 558,941 - - - -
Paenilan Suppresses G+ bacteria [33] 5,331,079
- 5,358,085 - 1,620,879
- 1,647,885 - 96.2
Paeninodin Broad antimicrobial activity against G + and G− bacteria [34] 5,011,316
- 5,035,438 1,439,160
- 1,463,275 1,301,862
- 1,325,980 97.2 96.3
Table 5 Comparison of genes involved in synthesis of resistance inducers in strain HJ-2, HS311 and ZF390
Resistance inducers Plant
resistance
type
Gene name Location Product Identity(%)
ZF390 HS311
2,3-Butanediol ISR alsS 5,251,050 5,251,535 Acetolactate synthase 98.77 98.97
alsD 5,947,927 5,948,673 Acetolactate decarboxylase 98.80 98.80
bdh 1,893,383 1,893,679 2,3-butanediol dehydrogenase 96.26 97.98
Acetoin ISR alsD 5,947,927 5,948,673 Acetolactate decarboxylase 98.80 98.80
Peptidoglycan PTI dacA 3,710,123 3,710,332 carboxypeptidase 94.39 95.81
Flagellin PTI flgL 2,996,323 2,996,535 Flagellin - 92.45
EF-Tu PTI tuf 2,113,547 2,113,711 elongation factor Tu 96.96 98.71
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Page 11 of 17
Jiangetal. BMC Genomics (2022) 23:161
the signaling pathway for biofilm formation in B.subtilis,
the signals are sensed through histidine kinases(KinA-
KinD) that phosphorylate Spo0F, Spo0F∼Ptransfers the
phosphate to Spo0A, and Spo0A∼P leads to SinI accu-
mulation and matrix gene expression [44]. Among this
signaling pathway, Spo0A is a key transcription regula-
tory factor that controls the expression of genes involved
in biofilm formation and sporulation [45]. Meanwhile,
biofilm formation is negative regulated by Rap family
of phosphatases, which lower the Spo0A∼P level in the
cell, and prevent sporulation [46]. To date, the signaling
pathway of biofilm formation has not been reported in
P. peoriae. In this study, core genes involved in biofilm
formation were detected in genome of HJ-2, ZF390 and
HS311, with high sequence identity. erefore, the sign-
aling pathway for biofilm formation in P. peoriae probably
possess high similarity with those reported in B.subtilis.
PGPRs have attracted considerable attention owing
to their demonstrated ability to solubilize mineral
phosphates, fix nitrogen, synthesize phytohormones
and degrade lignocellulose and increase plant toler-
ance to abiotic stress by reducing host ethylene levels
through 1-aminocyclopropane -1-carboxylate (ACC)
deaminase activity [47]. In this study, greenhouse and
field experiments have confirmed that selected strain
HJ-2 could improve the growth of physical parameters
in P. polyphylla. IAA plays a vital role in plant growth
and development as a regulator of numerous biologi-
cal processes. e capacity for IAA production of HJ-2
was proved in vitro by using LC/MS method. Accord-
ing to the KEGG database analysis, genes encoding key
enzymes in the IAA biosynthesis were found in strain
HJ-2 (Suppl. Table 5). Another strategy that PGPRs use
to enhance plant growth is nitrogen fixation. P. peoriae
HJ-2 established nitrogen-fixing potential through the
ARA method. As reported in N2-fixing strains within
the genus Paenibacillus, nitrogen fixation is carried out
by molybdenum-dependent nitrogenases, which are
encoded by a conserved nif gene cluster (comprised by
nine genes: nifB, nifH, nifD, nifK, nifE, nifN, nifX, hesA,
and nifV) [48]. According to the KEGG database analysis,
six of these genes were also detected in genome of HJ-2
(Suppl. Table5). At present, the excessive use of nitrogen
fertilizer leads to environment pollution. e detrimental
effect may be lessened by using the nitrogen-fixing rhizo-
bacteria, and P. peoriae HJ-2 could be utilized as bioferti-
lization in agriculture.
e genus Paenibacillus is known for its potential
to produce a series of bioactive compounds, including
non-ribosomally synthesized lipopeptides (LPs), pol-
yketides and ribosomally synthesized peptides [49]. LPs
(e.g. polymyxins, pelgipeptin, surfactins, and fusarici-
dins) have been reported as strong antibacterial agents
mostly active against phytopathogens [50, 51]. Fusari-
cidins displayed excellent antifungal activities against
many plant pathogenic fungi, especially Fusarium spp,
invitro [52]. e antifungal mechanism of fusaricidin
is through permeabilization and disruption of the cell
membraneis. e production of fusaricidins by P. poly-
myxa is encoded on the NRPS gene cluster called fus
with eight genes(fusA-fusH) [53]. In addition to P. poly-
myxa, we also found the fus cluster existed in species of
P. peoriae, and the majority of these gene clusters are
conserved in all P. peoriae strains. Polymyxins and tri-
decaptin have been described in species of P. polymyxa
for possessing strong antimicrobial activity against
Gram-negative bacteria. On the basis of antiSMASH
database, the majority of these gene clusters were also
detected in genomes of P. peoriae strains except for
ZF390. Pelgipeptins were first discovered as second-
ary metabolites in Paenibacillus elgii, and the variants
A and B display antifungal activity against several soil
borne pathogens, including Fusarium graminearum
and Rhizoctonia solani. e gene cluster encoding pel-
gipeptin biosynthesis was merely detected in genomes
of P. peoriae strainsHJ-2, and was not typical in other
P. peoriae strains. e diversifications of antibiotic
gene clusters in P. peoriae presumably explain the dif-
ferences of their target profiles and efficiency against
phytopathogens.
In addition to producing a spectrum of antimicrobial
peptides, P. peoriae HJ-2 produces antibacterial proteins,
most of which are cell wall-degrading enzymes synthe-
tized by ribosomes, such as β-1,3-glucanase and chitinase.
β-1,3-glucanase can hydrolyze the cell wall of most
plant-pathogenic fungi, thus inhibiting the growth of the
hyphae. e β-1,3-glucan metabolism enzymes mainly
include three important enzymes: endo-β-1,3-glucanase,
exo-β-1,3-glucanase and β-1,3-glycosyltransferase [54].
According to the Carbohydrate-Active enZYmes Data-
base, a series of endo-β-1,3-glucanases are produced by
P. peoriae HS311. Based on the analysis of the KEGG
database, genes encoding endoglucanase were also found
in P. peoriae HJ-2 (Suppl. Table6). β-1,3-glucanase pro-
duced by Gliocladium catenulatum inhibited Fusarium
spp. growth, conidia germination and degraded the cell
walls of the pathogen [55]. e inhibition of the spore
germination and hyphal growth of pathogenic fungi by
fusaricidin or β-1,3-glucanase or both is not well under-
stood. Based on the current data and previous studies,
the activities of β-1,3-glucanase are repressed by glucose
and reduced under an acidic pH.
ISR can be triggered by PGPRs or fungi and lead to
resistance priming against subsequent exposure to
biotic and abiotic stresses. Several compounds secreted
by PGPRs have been identified as bacterial elicitors
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Page 12 of 17
Jiangetal. BMC Genomics (2022) 23:161
responsible for ISR, such as 2, 3-butanediol, acetoin and
surfactin [56]. e genes coding for several elicitors were
detected in genome of HJ-2, ZF390 and HS311, with high
sequence identity. Bacterial flagellin or EF-Tu is a general
conserved elicitor that results in intracellular signaling
in defense responses known as pathogen or microbe-
triggered immunity (PTI/MTI) [57]. Flagellin contain-
ing N-terminally conserved flg22 was also found in P.
peoriae HJ-2 (Fig.6B). Previous studies have shown that
the plant growth-promoting rhizobacteria could elicited
reactive oxygen species (ROS) burst in plant leaves and
roots, and PGPR tolerated higher oxidative stress than
plant pathogen via two-component regulatory system
ResDE. According to this mechanism, PGPR can success-
fully colonize in both root and leaf of plants [58]. To infer,
P. peoriae HJ-2 could trigger ISR and accelerate defenses
against plant pathogen.
Conclusions
In summary, the results of this study indicate that P. peo-
riae HJ-2 could serve as a potential BCA against stem rot
on P. polyphylla. e genome of HJ-2 consists of a single
6,001,192bp chromosome with an average GC content of
45% and 5,237 predicted protein coding genes, 39 rRNAs
and 108 tRNAs. e phylogenetic tree indicated that HJ-2
is most closely related to P. peoriae IBSD35. Based on
genome analysis, the genome of HJ-2 contains more than
70 genes and 12 putative gene clusters related to second-
ary metabolites, which have previously been described as
being involved in chemotaxis motility, biofilm formation,
growth promotion, antifungal activity and resistance
inducers biosynthesis. e underlying biocontrol mecha-
nisms can be inferred as follows: (1) Plant recruits PGPR
tocolonize in the rhizosphere via secreting metabolite;
(2) Biofilm formation and antibiotics biosynthesis pro-
tect plant against pathogen infection; (3) PGPR greatly
revitalize plant growth through nitrogen fixing, phyto-
hormones biosynthesis and phosphate solubilization; and
(4) ISR can be triggered by PGPR and lead to resistance
priming against biotic and abiotic stresses, etc. is study
may provide a scientific basis for the further optimiza-
tion of biofertilizers based on P. peoriae HJ-2 in terms of
field application. e knowledge obtained can be further
translated into comprehensive strategies for establish-
ing sustainable agricultural practices by using biocontrol
agents to suppress plant pathogens.
Materials andmethods
Isolation ofrhizosphere bacteria
Soil samples (50g) were collected from Parispolyphylla
roots in a herb plantation of Saiwudang, Shiyan, Hubei
Province, China (32°27′58″N; 110°40′45″E). Bacteria was
isolated with the dilution plating method. Subsamples
(5g) were diluted with 50mL of sterile distilled water,
thoroughly dispersed by shaking (150 r/min) for 30min
at 28°C, and further diluted 103–107−fold. A 100 μL of
the diluted samples was spread onto Luria–Bertani (LB)
agar plates and maintained at 25°C for 24h. After incu-
bation, the bacterial colonies were picked and repeatedly
restreaked onto agar plates until their purity was con-
firmed for 16S rRNA gene analysis. e isolated strains
were maintained at -80 °C in LB media with glycerol
(30%, v/v) for long-term storage.
In vitro antagonism test
To evaluate the biocontrol potential ofP. peoriae HJ-2,
we performed a co-cultivation assay on PDA mediumin
vitro. Five Fusarium spp. including F. oxysporum, F.
graminearum sensu stricto, F. solani var. coeruleum
(Sacc.) Booth., F. concentricum and F. tricinctum were
used as pathogenic fungus. F. oxysporum and F. concentri-
cum which had been reported causing stem rot on P. poly-
phylla in China were isolated in our lab from infected P.
polyphylla. e 6mm plugs from the edge of pathogenic
fungus were inoculated in the center of PDA medium
(90mm in diameter), and then the HJ-2 was inoculated
on both sides of the culture dish by using sterile paper
disks (8mm in diameter), filter paper with sterile water
was used as the control. After incubated for 7 days at
25°C, the colony diameters were measured and recorded.
Effect of P. peoriae HJ-2 on F. Concentricum spore ger-
mination assays were performed as described by Jiang
[59]. e top surface of P. peoriae HJ-2 cultured in LB
broth was sliced and removed. Subsequently, the sub-
layer was transferred to a 1.5mLcentrifugetube(sterile).
e centrifugetube was inoculated with 10 μL conidium
suspension of F. concentricum (1 × 105conidia/mL), and
incubated for 24h at 25°C. e germination of conidia
was observed using Phenix BMC500 microscope (Phenix
China, Inc.). e experiment was conducted three times
with two replicates per treatment.
Biocontrol experiments ingreenhouse andeld
To evaluate plant growth promotion and biocontrol
effect of P. peoriae HJ-2, greenhouse and field experi-
ments were carried out in this study. For the greenhouse
experiment, the seeds of P. polyphylla were sown into
autoclaved soil with one seedling per pot and then cul-
tivated in a greenhouse at 20/25°C (night/day) with 70%
humidity and 14-h photoperiod. e seedling was treated
with 10mL of bacterial suspension of HJ-2 at OD600 of
0.8 by sprinkling the root in combination with spraying
the leaf when the seedling grew to six leaves, and ster-
ile water served as a control. Ten days later, the seed-
ling in each treatment was inoculated with 10mL spore
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Page 13 of 17
Jiangetal. BMC Genomics (2022) 23:161
suspensions of F. concentricum (1 × 105 conidia/mL). e
length, fresh weight, dry weight of roots and stems, and
the incidence rate of disease were recorded and photo-
graphed after inoculation for twenty-five days. All experi-
ments were conducted three times with twenty seedlings
per treatment.
Moreover, the field experiments were conducted in a
herb plantation of Saiwudang, Shiyan, Hubei Province,
China (32°27′58″N; 110°40′45″E), and the experiments
did not involve endangered or protected species. Two
treatments were established, and water was used as a
mock control. A 20mL of bacterial suspension of HJ-2
at OD600 of 0.8 was poured onto the roots, and sprayed
on both sides of the leaves when the seedlings grew to six
leaves. Fifty days later, the effects on plant growth pro-
motion and the incidence rate of disease were recorded
and photographed. All experiments were conducted
three times with fifty seedlings per treatment.
Indole 3 acetic acid (IAA) production, nitrogen xation,
andphosphate solubilization assays
e production of IAA was measured using LC/MS
method previously described [60], with some modifi-
cations. A 20 μL of bacterial suspension at OD600 of 0.5
(106—107CFU/mL) was added to 20mL of liquid Landy
medium (20 g/L glucose, 5 g/L glutamic acid, 1 g/L
KH2PO4, 0.5 g/L MgSO4·7H2O, 0.5 g/L KCl, 5 mg/L
MnSO4, 0.16 mg/L CuSO4, 0.15 mg/L FeSO4, 2 mg/L
L-pheny- lalanine, 1 g/L yeast powder). e medium
was maintained at 28°C for 72h by shaking (160 r/min),
and the culture was centrifuged at 4°C with 8000rpm
for 2min. en, a 100mL of filtrate was collected with
a 0.22μm microporous membrane, and extracted with
ethyl acetate for three times. e organic solvents were
collected and dissolved with methanol after vacuum
drying for LC–MS analysis. An Agilent 1100 Series LC/
MS system and an Agilent Zorbax Exteng-C18 chro-
matographic column (2.1mm × 150 mm, 3.5μM) were
used. IAA (Sigma) were prepared by methanol dissolu-
tion, and each standard sample had a concentration of
5 × 10−7g/L.
Nitrogen fixation ability of HJ-2 was tested using the
acetylene reduction assay (ARA), as described by Bod-
dey [61]. A 20 μL bacterial suspension at OD600 of 0.5
was inoculated to 4 ml of semi-solid (0.18% agar–agar)
NFb media. After incubation for 72h at 28°C in the dark,
10% (v/v) of the air phase was replaced with acetylene.
e amount of C2H4 was measured using a gas chroma-
tograph (Agilent 7890A) after incubation for 1 h with
acetylene. e protein concentration of bacteria was col-
lected and determined by using protein extraction kit
(TaKaRa, DaLian, China).
e ability of phosphate solubilization was tested as
previously described [62]. A 5 μL bacterial suspension
at OD600 of 0.5 was inoculated to NBRIP medium (0.5%
Ca3(PO4)2, 1% glucose, 0.01% (NH4)2SO4, 0.5% MgCl2,
0.02% KCl, 0.025% MgSO4·7H2O, 1.5% agar). After incu-
bation for ten days at 28°C, the growth of bacterial was
recorded. e experiments were conducted three times.
Colonization assays withthestrain HJ‑2 onseedling roots
e GFP-labelled P. peoriae HJ-2 was constructed with
the pHT01EGFP plasmid, which carried the gfp and CmR
genes. e competent cells of HJ-2 and transformation
were obtained as described previously [63]. e seeds of
four plants (P. polyphylla, pepper, tomato and tobacco)
were surface-sterilized by soaking in 20% sodium
hypochlorite solution for 20min and cultured in flower-
pot with autoclaved soil. When the roots of seeding were
approximately 2cm (cm) in length, a 10mL of bacterial
suspension at OD600 of 0.8 was inoculated onto the roots.
For GFP observation, root surfaces were rinsed with ster-
ile water and stained with 10μg ml−1 propidium iodide
(PI) for 15min. Excitation and emission wavelengths for
detecting the GFP- tagged HJ-2 were 488 and 510nm,
respectively. Excitation and emission wavelengths for
detecting the PI- stained root were 535 and 617 nm,
respectively. e colonization of the strain HJ-2 on seed-
ling roots was observed using NikonDS-Ri2 microscope
(Nikon Japan, Inc.).
Bacteria counting was performed by using the plate
counting method with LB medium containing Chloram-
phenicol (Cm, 5μg mL−1) as described previously [64].
e roots of four plants were harvested after inoculation
for 5 d, 8 d, 16 d, 22 d, 25 d, 30 d, 35 d, 40 d, 45 d and 50
d, and washed twice with phosphate buffer (1M, pH 7.0).
en, the effectively colonized bacteria was remove from
roots to sterile water. Last, the CFU count was recorded
after 48h of incubation at 28°C, and the sterile water
was applied as control. All bioassays and experiments
were conducted three times with twenty seedlings per
treatment.
DNA extraction, PCR amplication, 16S rRNA gene analysis
Genomic DNA was extracted with a DNA Mini Bacteria
Kit (Invitrogen, Shanghai) following the manufacturer’s
instructions. e 16SF-(AGA GTT TGA TCC TGG CTC
AG) and 16SR-(GGT TAC CT- TGT TAC GACTT) uni-
versal primers were used for PCR amplification [65]. e
16S rRNA gene was sequenced by Life Technologies Inc.
(Shanghai, China) and manually aligned with reference
sequences retrieved from the GenBank database follow-
ing BLAST searches for fast identification.
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Page 14 of 17
Jiangetal. BMC Genomics (2022) 23:161
Whole‑genome sequencing andannotation
DNA was extracted from cells harvested from LB broth
culture medium of HJ-2 with a Genomic DNA extrac-
tion kit (TaKaRa, DaLian, China). e whole genome was
sequenced using the PacBio Sequel platform. Reads were
assembled using HGAP (version 2.3.0, SMRT Analysis)
[66]. e assembly data for the complete genome have
been deposited in GenBank with the accession number
PRJNA580302. Coding DNA sequence (CDS) predic-
tion was performed using Glimmer 3.02 [67]. A circular
map of the genome was obtained using Circos version
0.64 [68]. Genomic islands (Gis) were predicted using the
IslandPath- DIOMB GI prediction method [69]. tRNAs
and rRNAs were predicted using tRNAscan-Sev1.3.1
and Barrnap 0.7 software4, respectively [70]. Clustered
regularly interspaced short palindromic repeat sequences
(CRISPRs) were identified using MinCED [71]. Func-
tional annotation was based on BLASTP searches
(BLAST 2.2.28 +) against the NCBI nonredundant (NR)
database and gene database, the STRING database, and
the Gene Ontology (GO) database. Based on the string
database, BLASTP comparisons were used to perform
Clusters of Orthologous Groups of proteins (COG) anno-
tation, according to which protein functions could be
classified [72]. e BLAST algorithm was used to com-
pare the predicted genes with the KEGG database, and
the corresponding genes involved in specific biological
pathways were identified according to the KEGG Orthol-
ogy (KO) numbers obtained from the alignment[73]. GO
was annotated with Blast2GO [74].
Genome comparison
103 genome sequences of Paenibacillus spp. were
obtained from GenBank. e accession numbers of the
strains used for the analysis are provided in Supple-
mentary TableS1. Phylogenetic Tree was conducted by
using the Phylogenetic Tree Building Service available
at the Patric website (https:// www. patri cbrc. org), with
codon tree method and 1000 genes selected for analy-
sis as option [75]. ANI values were computed by using
OrthoANI Tool version 0.93.1. Heatmap of the ANI
matrix was computed using Morpheus (https:// softw are.
broad insti tute. org/ morph eus) with Hierarchical clus-
tering applied using euclidian distance matric and com-
plete linkage clustering method. Pangenome analysis was
conducted for P. peoriae HJ-2 and other nine strains by
using OrthoMCL software [76]. Nucleic acid co-linearity
was assessed for P. peoriae HJ-2 and P. peoriae HS311
by using MUMmer 3.0 software [77]. e gene clusters
for secondary metabolites (containing antibiotics) in
P. peoriae HJ-2 were annotated using the antiSMASH
database version 4.0.2, and the other antibiotics were
selected based on previous studies [78]. BLAST was used
to compare the identities of the genes or gene clusters
between HJ-2 and other strains.
Transmission electron microscopy (TEM) section ofHJ‑2
A single colony from the LB agar plate was inoculated
into 20 mL of liquid medium. After incubation, the
medium was maintained at 30°C for 12h by shaking (160
r/min). A bacterial suspension at OD600 of 0.5 was gath-
ered and washed with phosphate-buffered saline (PBS)
(pH = 7.2). en, the strain was negatively stained with
2% phosphotungstic acid (Sigma). Finally, the stained
bacteria was deposited on a carbon-coated grid, followed
by observation under a HT-7700 transmission electron
microscope (HT-7700, HitachiHigh-Tech Corporation,
Tokyo, Japan).
Statistical analysis
All datas were analysed by using analysis of variancein-
SPSS24.0 (IBMSPSS Inc.,United States). Significant
differences between means were compared by using
the LSD test (Fisher’s protected least significant differ-
ences test) at P = 0.05. A P value < 0.05 was considered
significant.
Abbreviations
TCM: Traditional Chinese medicine; PGPR: Plant growth-promoting rhizobacte-
ria; JA: Jasmonic acid; ET: Ethylene; BCA: Biocontrol agent; IAA: Indole 3 acetic
acid; GI: Genomic Island; GO: Gene ontology; COG: Clusters of Orthologous
Groups; KEGG: Kyoto Encyclopedia of Genes and Genomes; ISR: Induced
systemic resistance; TEM: Transmission Electron Microscopy.
Supplementary Information
The online version contains supplementary material available at https:// doi.
org/ 10. 1186/ s12864- 022- 08330-0.
Additional le1: Table1. Genome sequences used for analysis in
this study. Table2. The antifungal activity of HJ-2 against Fusarium
spp. Table3. Chemotaxis and assembly of flagella. Table4. Secondary
metabolite clusters identified in this study by using antiSMASH database.
Table5. IAA biosynthesis and nitrogen fixation. Table6. The genes cord-
ing for endoglucanase in the P. peoriae HJ-2.
Additional le2: Figure1. GO annotation. Figure2. Kyoto Encyclopedia
of Genes and Genomes (KEGG) Pathway annotation. Figure3. ANI values
matrix heatmap. Figure4. Nucleic acid co-linearity of strain HJ-2 with P.
peoriae HS311. Figure5. The growth-promoting effect of P. peoriae HJ-2
on P. polyphylla. Figure6. IAA production, nitrogen fixation, and phos-
phate solubilization of HJ-2.
Acknowledgements
We would like to thank Mr. Gaolei Cai at Shiyan Academy of Agricultural
Science for kindly sharing P. polyphylla seeds; We thank Instrumental Analysis
Center of Frasergen for technical assistance.
Authors’ contributions
AJ and ZK conceived the experiments; AJ and ZK performed the experiments;
XX, JH, GJ and CF collected data; AJ and JG conducted analyses; AJ wrote the
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Page 15 of 17
Jiangetal. BMC Genomics (2022) 23:161
manuscript; CZ and JW revised the manuscript. All authors read and approved
the final manuscript.
Funding
The research was supported by the National Science and Technology Devel-
opment Project of China (Project No. 2018ZYYD002) and Guangxi innovations
union of agriculture science and technology, Grant/Award Number: 202011.
Availability of data and materials
The data reported in this paper have been deposited in the NCBI Sequence
Read Archive (SRA) database (https:// www. ncbi. nlm. nih. gov/ subs/ sra) under
accession no. PRJNA580302.
Declarations
Ethics approval and consent to participate
The research was performed in accordance with the Regulations of the Peo-
ple’s Republic of China on Wild Plant Protection. We confirm that all methods
were performed in accordance with the relevant guidelines and regulations.
Consent for publication
Not applicable.
Competing interests
The authors declare that they have no competing interests.
Author details
1 College of Agriculture, Guangxi University, Nanning 530004, China. 2 College
of Chemistry and Environmental Engineering, Hanjiang Normal University,
Shiyan 442000, China. 3 Institute of Basic Medical Sciences, Hubei University
of Medicine, Shiyan 442000, China.
Received: 25 June 2021 Accepted: 19 January 2022
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