Science of the Total Environment 885 (2023) 163896

Contents lists available at ScienceDirect

Science of the Total Environment

journal homepage: www.elsevier.com/locate/scitotenv

Microbiological mechanism for “production while remediating” in Cd-

contaminated paddy fields: A field experiment
Jiguang Gu a, Fang Guo a, Lihong Lin d, Jiexiang Zhang e, Weimin Sun b, Riaz Muhammad d, Haojie Liang d,
⁎
Dengle Duan f, Xingying Deng d, Zheng Lin d, Yifan Wang g, Yuming Zhong d, Zhimin Xu b,c,d,
a
Department of Ecology, Jinan University, Guangzhou 510632, China
b
Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences,
Guangzhou 510650, China
c
Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300350, China
d
College of Resources and Environment, Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
e
GRG Metrology& Test Group Co., Ltd., Guangzhou 510656, China
f
Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
g
Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan

H I G H L I G H T S G R A P H I C A L A B S T R A C T

• Security utilization measures (SUMs)

reshaped the rhizosphere microbial
community.
• SUMs improved degree of DOM aromatiza-
tion participating in soil Cd coordination.
• Taxa related to growth promotion and soil
fertility improvement massively colonized.
• Grain Cd decrease partially relied on co-
precipitation caused by S\\N coupled cycle.

A R T I C L E I N F O A B S T R A C T

Editor: Filip M.G.Tack Security utilization measures (SUMs) for “production while remediating” in moderate and mild Cd-polluted paddy
fields had been widely used. To investigate how SUMs drove rhizosphere soil microbial communities and reduced
Keywords: soil Cd bioavailability, a field experiment was conducted using soil biochemical analysis and 16S rRNA high-
Paddy fields
throughput sequencing. Results showed that SUMs improved rice yield by increasing the number of effective panicles
Security utilization measures
and filled grains, while also inhibiting soil acidification and enhancing disease resistance by improving soil enzyme
DOM
Rhizobacteria community
activities. SUMs also reduced the accumulation of harmful Cd in rice grains and transformed it into Fe\\Mn oxidized
Cd immobilization Cd, organic-bound Cd, and residual Cd in rhizosphere soil. This was partly due to the higher degree of soil DOM aro-
matization, which helped complex the Cd with DOM. Additionally, the study also found that microbial activity was the
primary source of soil DOM, and that SUMs increased the diversity of soil microbes and recruited many beneficial mi-
crobes (Arthrobacter, Candidatus_Solibacter, Bryobacter, Bradyrhizobium, and Flavisolibacter) associated with organic
matter decomposition, plant growth promotion, and pathogen inhibition. Besides, special taxa (Bradyyrhizobium and
Thermodesulfovibrio) involved in sulfate/sulfur ion generation and nitrate/nitrite reduction pathway were observably
enriched, which effectively reduced the soil Cd bioavailability through adsorption and co-precipitation. Therefore,

⁎ Corresponding author at: Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China.
E-mail address: xuzhimin@zhku.edu.cn (Z. Xu).

http://dx.doi.org/10.1016/j.scitotenv.2023.163896
Received 20 March 2023; Received in revised form 25 April 2023; Accepted 28 April 2023
Available online 4 May 2023
0048-9697/© 2023 Elsevier B.V. All rights reserved.
J. Gu et al.
SUMs not only changed the soil physicochemical properties (e.g., pH), but also drove rhizosphere microbes to partic-
ipate in the chemical species transformation of soil Cd, thus reducing Cd accumulation in rice grains.
1. Introduction
Cadmium (Cd) pollution in paddy fields is a global environmental issue
due to human activities, such as industrial activities and the excessively use
of phosphate fertilizers containing Cd (Ngo et al., 2021; Zou et al., 2021).
The affected area is not negligible, with an estimated 150 million hectares
of paddy fields worldwide being contaminated with toxic metal Cd (Zoli
et al., 2021). According to a 2019 report by the Food and Agriculture Orga-
nization (FAO) of the United Nations, the average Cd contents in rice sam-
ples of many countries was found to be above the recommended maximum
limit of 0.1 mg/kg set by the Codex Alimentarius Commission (CAC), such
as 0.15 mg/kg in China and 0.11 mg/kg in Bangladesh (Zhao et al., 2022b).
Soil Cd accumulates highly in rice, a staple food for millions of people
worldwide (particularly in Asia), which can cause severe health problems,
including renal dysfunction, osteoporosis, and cancer (Reyes-Hinojosa
et al., 2019). Therefore, the management and remediation of Cd-
contaminated paddy fields have become urgent priorities for protecting
public health and ensuring food security.
Over the years, several remediation technologies have been developed
for Cd-contaminated paddy fields, including physical methods (soil wash-
ing and electrokinetic remediation), bioremediation (phytoremediation
and microbial transformation), and chemical fixation/stabilization (Liu
et al., 2020a), but they have their own limitations. For instance, soil wash-
ing can be expensive, cause soil degradation, and generate large amounts of
toxic waste due to the use of chemicals to extract Cd from soil, while the use
of phytoremediation can be limited by factors such as slow growth rates,
low biomass production, and soil types (Gluhar et al., 2020; Shen et al.,
2022). Chemical amendments involve adding materials such as lime, phos-
phate, compost, or biochar to the soil to reduce Cd bioavailability, while are
often costly and may require repeated applications to maintain their effec-
tiveness (Kumpiene et al., 2019). Most importantly, these contaminated
paddy fields cannot be abandoned and fallowed for lengthy remediation
projects. Therefore, in the case of effectively protecting the edible safety
of rice, it is more necessary to develop the sustainable security utilization
pattern of “production while remediation”.
Security utilization measures (SUMs) in Cd-contaminated paddy fields
is a strategy of cultivating rice while simultaneously restoring the soil's
health and reducing the levels of Cd contamination (Fässler et al., 2010).
This approach involves a combination of agronomic practices, such as the
application of soil amelioration, low-Cd accumulating rice cultivars, leaf
cadmium inhibitors, and field water management (Chen et al., 2022). The
mechanisms of the strategy can be summarized as follows: i) to reduce
the Cd bioavailability by increasing organic content, water-holding capac-
ity (soil redox potential and element cycling), and pH in the soil (Xu
et al., 2021b); ii) to improve the crop productivity while reducing the Cd
uptake by selecting and cultivating these low-Cd cultivars (Wang et al.,
2021b); iii) to prevent Cd from being taken up by rice via element antago-
nism (Wang et al., 2022). Despite the benefits of the “production while
remediation” pattern, there are still some unclear aspects of the mecha-
nisms, especially regarding the roles in soil amelioration and Cd immobili-
zation of rhizosphere microbial communities. It is well known that plant
genotypes or soil environments can select for specific microbial communi-
ties, and these selective pressures are particularly strong in the rhizosphere
(Korenblum et al., 2020). Domestication of a favorable rhizosphere micro-
bial community by altering the rhizosphere environment may provide new
opportunities to improve plant performance, with benefits for crop produc-
tion and resistance to heavy metal toxicity (de Vries et al., 2020; Yue et al.,
2023). Several studies have shown that rhizosphere microbes play a crucial
role in the biogeochemical cycling of Cd in paddy fields (Bandara et al.,
2022; Xu et al., 2022b), such as increased Fe/Mn plaque formation
2
Science of the Total Environment 885 (2023) 163896
promotes the deposition of metals to the root surface, thereby limiting the
uptake and transfer of Cd/As in rice tissues (Li and Zhou, 2020; Qian
et al., 2022). Therefore, the SUMs may drive rhizosphere microbial commu-
nity succession and then play potential roles in reducing soil Cd uptake by
rice. More research is needed to better understand the evolution tendency
and roles of soil microbes in this security utilization pattern and to optimize
its effectiveness.
At present, the SUMs of “production while remediation” aimed at
Cd-polluted paddy fields, has been applied in the actual remediation
projects, especially in areas with medium and mild Cd pollution (Chen
et al., 2022; Huang et al., 2019). In this study, a paddy field exhibiting
mild Cd pollution (0.77 mg/kg dry soil) that exceeds the national stan-
dard limit of 0.3 mg/kg in China was selected as the research subject,
and the assembly characteristics of rhizosphere microbial communities
after “security utilization” measures application and its roles in soil
amelioration and Cd pollution remediation were studied through phys-
ical and chemical analysis, microbial 16S rRNA high-throughput
sequencing, and statistical model analysis.
2. Materials and methods
2.1. Experimental field
The experimental field is situated in Sanrao Town (N 23.99°/E
116.82°), Chaozhou City, Guangdong Province, China, and covers an
area of approximately 17.33 hm2. The field's location is illustrated in
Fig. S1a. The physical and chemical properties of the paddy soil are as
follows: pH 4.28, total nitrogen 1.23 g/kg, total phosphorus
0.72 g/kg, total organic carbon 74.62 g/kg, and cation exchange capac-
ity 24.24 cmol/kg. The total Cd concentration (0.77 mg kg −1 dry soil)
in soil exceeded the limit (0.30 mg kg −1, pH < 5.55) set by the Soil
Environmental Quality Risk Control Standard for Soil Contamination
of Agricultural Land (GB 15618—2018, China). Levels of other heavy
metals did not exceed the standard (Table S1).
2.2. Safe cropping patterns for production while remediating
In this study, considering the current situation of pollution level, rice
varieties, and farming practices, comprehensive prevention and control
measures were implemented, including soil amelioration, agronomic regu-
lation, and leaf Cd absorption barrier, to ensure the security utilization of
polluted paddy fields in the experimental area. These technical measures
were widely employed in farmland remediation projects (Chen et al.,
2022; Hussain et al., 2021). Specifically, before planting, a mixture of
750 kg of soil conditioner (CaO ≥ 20.0 %, SiO2 ≥ 10.0 %, organic
matter≥12.0 %, and pH = 10) and 750 kg of organic fertilizer (organic
matter≥40.0 % and CFU ≥ 0.20 million/g) were applied per hectare of
topsoil (0-20 cm). Two weeks later, rice seedlings were planted. Addition-
ally, 1.52 L of leaf Cd absorption barrier agent was sprayed once per hectare
during the young panicle differentiation stage and heading stage of rice, re-
spectively. It should be noted that the heavy metal content of these inputs
should comply with relevant standards (GB15618–2018, GB18877–2009,
and GB5084–2021), and foliar application should only be performed
under windless conditions or relatively high humidity with low evapora-
tion (Ullah et al., 2021). Following the rice heading, the field was kept
flooded for 28 days. Once the rice was fully mature, the field was then
drained and kept dry for approximately 7 days before harvesting (Wen
et al., 2021). The paddy fields with the above series of remediation mea-
sures were regarded as the remediation groups (SUMs), while the farmland
without such measures was regarded as the CK groups.
J. Gu et al.
2.3. Sample collection and chemical analysis
To ensure sample representativeness, multi-point collection was con-
ducted using the chessboard layout method. Specifically, within a
20 m × 20 m range, soil samples from at least 5 sites were evenly mixed
to create 1 sampling point, resulting in a total of four sampling points
(Tan, 1995). Prior to collection, soil in contact with the metal sampler
was removed using bamboo chips. After collection, samples were packaged
in individual sample bag. Rice samples were collected in collaboration with
the soil samples, and their growth indices, such as plant height and bio-
mass, were recorded. Two to three rice plants were collected from each
site, and samples from five sites were mixed into one. The collected rhizo-
sphere soil was used to determine pH at a ratio of 1:5 (water: soil) (Xu
et al., 2021b), while dried soil samples were analyzed for the chemical spe-
ciation of Cd using the Tessier sequential extraction method (Sut-Lohmann
et al., 2022). Fresh soil was used to analyze the activities of urease, catalase,
acid phosphatase, and sucrase by the phenol‑sodium hypochlorite colori-
metric method, permanganate titration, phenyl disodium phosphate color-
imetric method, and 3, 5-dinitrosalicylic acid colorimetric method (Jiang
et al., 2022; Nurzhan et al., 2022). In addition, dried rice samples including
roots, shoots, and grains were digested with 70 % concentrated nitric acid,
and their Cd contents in plant and soil samples were determined by graph-
ite furnace atomic absorption spectrometry (AA-6800; Shimadzu) (Xu et al.,
2021c). The rhizosphere soil solution was scanned using a fluorescence
spectrometer (FP-6500; JASCO) with an emission wavelength (Em) set to
250–550 nm (in 5 nm increments) and an excitation wavelength (Ex) set
to 200–485 nm (in 5 nm increments). To eliminate the inner filter effect,
the DOM (dissolved organic matter) concentration was diluted to approxi-
mately 10 mg/L (Liu et al., 2021).
2.4. Soil DNA extraction and high-throughput sequencing
The soil samples for microbial analysis should be collected from the area
attached to the surface of rice roots, and the sampling method used, which in-
volved mixing soil samples taken from 5 sites evenly, was consistent with the
aforementioned requirement. Following the method outlined by Shanghai
Majorbio Bio-Pharm Technology Co., Ltd., the root tissue, along with 1 mm
of soil attached to its surface, was placed in a sterile bottle filled with 50 ml
of sterile PBS, and the adhered soil was subsequently eluted (Edwards
et al., 2015). Afterward, 1 ml of the mixed solution was drawn into a pipette
and placed into a 2 ml centrifuge tube, then centrifuged at 10,000g for 30 s to
obtain concentrated soil sediment for DNA extraction by Sigma GenEluteTM
DNA Isolation Kit (Sigma-Aldrich, USA). The V3-V4 regions of the bacterial
16S rRNA genes were amplified through the ABI GeneAmp® 9700 PCR in-
strument in 20 μl reaction system including TransStar fastpfu DNA polymer-
ase and a pair of primers 338F (5′- ACTCCTACGGGAGGCAGCAG-3′) and
806R (5′-GGACTACHVGGGTWTCTA AT-3′). Purified amplicons were pooled
in equimolar and paired end sequenced (2 × 300) on an Illumina MiSeq plat-
form (Illumina, San Diego, USA) (Li et al., 2021a).
2.5. Data analysis and visualization
The statistical analysis used the independent sample Student's t-test and
one-way ANOVA test (SPSS 19.0, Chicago, USA), with statistically signifi-
cant results indicated by an asterisk (*) for p-values <0.05 and extremely
significant results indicated by two asterisks (**) for p-values <0.01. Taxo-
nomic analysis of OTUs representative sequences was performed using the
RDP classifier Bayesian algorithm at a similarity level of 97 %. >400 OTUs
were obtained for each sample. The maximum sequencing depth of each
sample was 1 × 105 reads. Alpha diversity was characterized by Shannon
index and Simpson index. Beta diversity was evaluated by calculating the
Bray-Curtis distances. Two independent samples of Wilcoxon test were per-
formed using the “wilcox.test” package. The species composition of the
community was visualized in a heat map of the data presented in a two-
dimensional matrix or table, which was generated using the “vegan” pack-
age (Sun et al., 2022). The distribution of dominant species in different
3
Science of the Total Environment 885 (2023) 163896
samples was visualized using the Circos sample-to-species diagram, which
was drawn using the “circlize” package (Li et al., 2022b). The co-
occurrence network was visualized using the interactive platform
Cytoscape version 3.7.2, with a group attribute layout of phylum or genus
(Xu et al., 2023), and using r > 0.7 and p < 0.05 as the thresholds for
Spearman correlations between species. The OTUs were selected to con-
struct the evolutionary tree using the approximate maximum-likelihood
(Likelihood Phylogeny Trees) method, and the evolutionary tree was
drawn using the “ggtreeExtra” package. The functional metagenome of
Clusters of Orthologs Groups (COGs) was predicted using the PICRUST
analysis (Xu et al., 2022b).
3. Results and discussion
3.1. Rice growth promotion and soil quality improvement under security utilization
pattern
In this study, the safe utilization measures (SUMs; Remediation) included
three stages (Fig. 1a and S1b). Firstly, a soil conditioner was applied to ad-
dress soil acidification and nutrient deficiencies during plowing (Li et al.,
2019). Secondly, organic fertilizer was applied before transplanting to in-
crease soil microorganisms, improve soil aggregation, and increase soil or-
ganic matter content (Hamid et al., 2020). Thirdly, a leaf Cd absorption
barrier agent was sprayed during the young panicle differentiation stage
and heading stage to hinder the absorption and transportation of Cd from
shoots to grains (Yang et al., 2022). Finally, water management was imple-
mented before harvest to reduce soil redox potential and Cd bioavailability
(Xu et al., 2021a). After the SUMs implementation (Remediation), significant
increases were observed in plant height, effective panicle per 6 plants (Pro-
ductive ear), grain yield per 6 plants (Grain yield), and filled grains per pan-
icle of rice (NFGP), which were 1.06, 1.15, 1.16, and 1.32 times higher than
those of the control group (CK) (Fig. 1b, p < 0.05). However, there was no
significant difference among them observed in weight per 1000 grains
(Grain weight) (Fig. 1b). These results indicated that the SUMs implementa-
tion significantly enhanced the growth and yield of rice, primarily by aug-
menting the number of effective panicles and filled grains. The number of
grains per panicle and the growth of young panicle were found to be closely
associated with the pre-existing spikelet count, which, in turn, was directly
impacted by the mineral elements and C/N metabolism (Gan et al., 2022;
Huang et al., 2021). These results highlighted the critical roles of nutrient
balance in regulating floret differentiation and panicle development and
pointed to the advantages for the used soil conditioner and organic fertilizer
implementation to mitigate soil nutrient deficiencies.
In this study, the SUMs implementation resulted in a noteworthy increase
in the rhizosphere soil pH, from 5.0 to 6.06 (Fig. 1e). Moreover, soil enzyme
activities displayed a marked rise, with urease, catalase, and sucrase activities
experiencing increments of 40.92 %, 26.49 %, and 26.49 %, respectively
(Fig. 1f). The results indicated that the SUMs implementation enhanced the ac-
tivities of the multienzyme system in the soil, thus promoting enzymatic reac-
tions and improving the soil's microecological environment (Lin et al., 2022).
For instance, urease catalyzed the hydrolysis of amide peptide bonds in urea, a
nitrogen-containing organic compound presented in soil, resulting in the pro-
duction of ammonia, which was a key source of plant nitrogen nutrition
(Zuccarini et al., 2023). Moreover, catalase could decompose hydrogen perox-
ide generated during the respiratory process of all organisms in the soil,
thereby reducing its harmful effects on plants (Zhang et al., 2022). Further-
more, sucrase suppressed soil acidity and aided plants in resisting infections
caused by pathogens (Liu et al., 2020b). These findings highlighted the poten-
tial of SUMs implementation to enhance soil fertility and disease resistance,
thereby contributing to sustainable agricultural practices.
3.2. Cd accumulation in rice and its chemical immobilization mechanism in soil
under security utilization pattern
The Cd accumulation in rice served as a critical indicator to evaluate the
safe utilization of Cd-polluted fields. This study reported a significant
J. Gu et al. Science of the Total Environment 885 (2023) 163896

Fig. 1. Safe utilization patterns for “production while remediating” (a); Plant height, effective panicle per 6 plants (Productive ear), grain yield per 6 plants (Grain yield),
weight per 1000 grains (Grain weight), and filled grains per panicle of rice (NFGP) of rice (b); The Cd content in roots, shoots, and grains of rice (fresh weight) (c); The
contents of exchangeable Cd, carbonate-bound Cd, Fe-Me oxidized Cd, organic-bound Cd, and residual Cd in rhizosphere soil (d); Rhizosphere soil pH (e); Rhizosphere
soil enzyme activities (f); Correlation analysis (g); Schematic of the mechanisms of safe utilization patterns (h). CK: Normal planting pattern, Remediation: Safe utilization
patterns. Asterisks (*, **, and ***) were significant at the levels of 0.05, 0.01, and 0.001, respectively.

decrease in the Cd content of rice root, shoot, and grain (fresh weight) by
33.68 %, 24.56 %, and 59.09 %, respectively, following the SUMs imple-
mentation compared to the CK (Fig. 1c; p < 0.05). Notably, SUMs imple-
mentation reduced the Cd content in grain (fresh weight) from
0.22 mg/kg to 0.09 mg/kg, well below the maximum level of contaminants
in foods set by the China Food Safety National Standard (0.2 mg/kg; GB
2762–2012) (Fig. 1c). This indicated that SUMs implementation achieved
the goal of production while remediating and ensured grain security.
Many studies confirmed that Cd accumulation in grain was closely related
to the chemical speciation of Cd in rhizosphere soil, especially the
exchangeable Cd and carbonate-bound Cd which had obvious positive
contributions (Li et al., 2021b; Wang et al., 2019). After SUMs implementa-
tion, a significant reduction was observed in contents of exchangeable and
carbonate-bound Cd in the rhizosphere soil, by 34.62 % and 27.42 %,
respectively (Fig. 1d; p < 0.05). Concurrently, there was a significant
trend of transformation towards Fe\\Mn oxide-bound Cd, organic-bound
Cd, and residual Cd, as evidenced by a noteworthy increase in the content
of these three chemical species of Cd, by 53.78 %, 66.22 %, and 74.71 %,
respectively (Fig. 1d; p < 0.05). The exchangeable Cd could easily be
taken up by the rice roots, while the carbonate-bound Cd was adsorbed
onto the soil particles and released as the pH decreases, making it more
bioavailable for rice uptake (Xu et al., 2021b). The key determinants of
chemical speciation of Cd in the uptake and translocation of Cd from soil
to rice grain were further confirmed by the significant negative correlation
between grain Cd and rhizosphere soil pH, and the significant positive
correlation between grain Cd and exchangeable Cd/carbonate-bound Cd
(Fig. 1g; p < 0.05).
Dissolved organic matter (DOM) comprised a significant number of
functional groups capable of adsorbing and forming complexes with soil
Cd (Liu et al., 2021). In this study, the fluorescence spectral characteristics

4
J. Gu et al.
Fig. 2. Three-dimensional fluorescence spectroscopy characteristic of DOM in rhizosphere soil from Remediation and CK.
of DOM in rhizosphere soil showed significant differences between the CK
and Remediation, especially in the spectral ranges of Em/Ex = 300–350
and 380–420/250–290 and 280–320, the positions and intensities of
fluorescence peaks were different (Fig. 2a and b). The fluorescence index
(FI) before and after SUMs implementation was 1.97 and 2.12, respectively
(TableS2), which were both >1.9, indicating that the source of DOM was
mainly the endogenous input produced by soil microbial activities (Xue
et al., 2022). Furthermore, the biological index (BIX) decreased signifi-
cantly from 0.92 to 0.63 after the SUMs implementation (TableS2), indicat-
ing low levels of DOM degradation, likely due to the influence of human
input, such as the use of soil conditioners (Chen et al., 2019). Most impor-
tantly, after SUMs implementation, low-molecular substances such as
protein-like substances in DOM decreased, while high-molecular humus in-
creased significantly (Fig. 2a and b). Rich high-molecular components in
DOM could form complexes with soil Cd2+ through their carboxyl groups
and phenolic hydroxyl groups, thereby reducing the Cd bioavailability
and migration (Li and Gong, 2021). The SUMs implementation led to an in-
crease in the aromaticity and hydrophobicity of soil DOM, as indicated by
the rise in SUA254 from 23.46 to 33.02 (TableS2). This change was brought
about by the decomposition of input-rich organic fertilizer by microorgan-
isms and the subsequent increase in soil pH, which positively influenced the
characteristics of DOM. The higher the degree of aromatization of DOM, the
stronger its affinity for Cd, and the greater the stability of the DOM\\Cd2+
complex with increasing soil pH values (Meng et al., 2023). The role of soil
DOM in predicting Cd bioavailability was found to be decisive (Li et al.,
2022a). This study identified microbial activity as the primary source of
soil DOM, with the intensity of organic matter decomposition by rhizo-
sphere microbes having a significant effect on the structure and compo-
nents of DOM in soil (Zhao et al., 2022a). Therefore, the microbial
activities were also found to be a key factor influencing the complexation
of DOM with Cd. Generally, as shown in the Fig. 1h, the mechanisms of
SUMs mainly included the Cd absorption inhibition in leaves caused by
5
Science of the Total Environment 885 (2023) 163896
element antagonistic (Yang et al., 2022), the reaction OH— + Cd2+ ⇋
CdOH+ promoted by soil pH increase, the reaction S2— + Cd2+ ⇋ CdS pro-
moted by flooding management (Zhang et al., 2023), and the passivation of
Cd coupled with element circulation by soil microbes.
3.3. Assembly and structural feature of microbial community under security uti-
lization pattern
In the rhizosphere, implementing a series of SUMs might result in vari-
ous single or compound effects that regulated the structure of the microbial
community, ultimately influencing soil health and rice growth (Xu et al.,
2022b). The NMDS analysis based on weighted Unifrac distances indicated
that, among all 8 sampling sites, the samples from SUMs sampling sites and
CK sampling sites were divided into two distinct areas (Fig. 3a; p < 0.05).
This suggested that SUMs implementation significantly drove the remodel-
ing of the rhizosphere soil microbial community. The cluster and ANOSIM
analysis, using similarity distance, revealed significant differences in micro-
bial species composition between the sampling sites in the CK groups and
those in the SUMs groups (R = 0.9792; p = 0.0282) (Fig. 3b and c). The
Shannon index and Simpson index both showed significant increases and
decreases after the SUMs implementation, indicating that SUMs implemen-
tation improved microbial diversity in the rhizosphere soil (Fig. 3d and e).
The Circos diagram (the top 12 taxa with high relative abundance) at the
phylum level shown obvious differences in composition and proportion of
dominant species between the CK and SUMs samples (Fig. 3f). After
SUMs implementation, the relative abundances of dominant microbiota
Actinobacteriota and Firmicutes increased significantly, from 14.21 % to
33.12 % and from 7.27 % to 12.32 %, respectively (Fig. 3f). In contrast,
the relative abundances of Proteobacteria and Acidobacteriota decreased
from 23.76 % to 14.37 % and from 14.89 % to 7.34 %, respectively
(Fig. 3f). Similar results could also be observed for microbial community
composition at the genus level (Fig. 3g). These findings suggested that
J. Gu et al.
Fig. 3. NMDS plots based on Bray-Curtis distance (a); Hierarchical clustering dendrogram (b); ANOSIM analysis (c); Shannon diversity index (d) and Simpson diversity index
(e); Circos plot of top 12 bacterial composition at the phylum level (f); The bar plot of bacterial composition at the genus level (g); CK: Normal planting pattern, Remediation:
Safe utilization patterns.
SUMs implementation accelerated the enrichment of beneficial bacteria in
the rhizosphere, which were involved in the decomposition and mineraliza-
tion of organic matter in soil, while inhibiting the harmful bacteria repro-
duction that contributed to soil acidification and pathogen outbreaks
(Xiao et al., 2022; Xu et al., 2022b).
Pairwise comparisons of communities across treatments shown by heat
trees in this study confirmed that SUMs implementation drove the specific-
ity of rhizosphere microbial community (Fig. 4a and b). Two figures
provided a visual representation of microbial communities, showing domi-
nance of Actinobacteria, Proteobacteria, Firmicutes, Chloroflexi, and
Acidobacteriota (Fig. 4a and b). However, heat trees highlighted variations
in enrichment levels for each taxon within the community, revealing a
more complex microbial community after SUMs implementation
(Fig. 4a). In summary, these results indicated that SUMs implementation
had a significant impact on the rhizosphere environment, resulting in a
6
Science of the Total Environment 885 (2023) 163896
distinct microbial community. The implications of these changes on plant
growth and Cd immobilization would be further discussed in the following
sections.
3.4. Preferential colonization of special taxa associated with growth promotion
and rhizosphere soil cd immobilization under security utilization pattern
Pie chart analysis indicated that microbial taxa differences between CK
and SUMs samples at the phylum level were primarily belonged to
Actinobacteriota (26.50 %), Proteobacteria (17.78 %), Chloroflexi (14.54 %),
Firmicutes (11.25 %), and Acidobacteriota (10.89 %) (Fig. S2). Furthermore,
the Wilcoxon rank-sum analysis shown that the relative abundances of
Actinobacteriota, Nitrospirota, and Methylomirabilota in the rhizosphere soil
after SUMs implementation were significantly higher than CK group, while
those of Proteobacteria, Acidobacteriota, and Patescibacteria were significantly
J. Gu et al. Science of the Total Environment 885 (2023) 163896

Fig. 4. Heat trees showing the overall difference of community structure in soil samples of CK (a) and Remediation (b). In the heat trees, size and color of nodes and edges are
correlated with the relative abundance of bacteria in each community.

7
J. Gu et al. Science of the Total Environment 885 (2023) 163896

lower than CK group (Fig. S3; p < 0.05). At the genus level, SUMs implemen-
tation resulted in significant rhizosphere enrichments of Arthrobacter
(21.69 %), Bacillus (7.35 %), norank_f__norank_o__Vicinamibacterales (1.48 %),
and norank_f__norank_o__Gaiellales (1.15 %), which belonged to the dominant
species (Fig. 3g and S4). Arthrobacter was known for its ability to strongly de-
grade soil organic matters, including atrazine and antibiotics, while Bacillus
and norank_f__norank_o__Vicinamibacterales exhibited specific fertilizer effects
and promoted plant growth by secreting iron carriers and indoleacetic acid,
as well as participating in carbon‑nitrogen transformation (Lin et al., 2019;
Yin et al., 2022). Additionally, these microbes could produce alkaline poly-
amines, raising soil pH (Cheng et al., 2022). The Norank_f__norank_o__Gaiellales
was a microbe that thrived in the pH range of 6.5–7.5 (Lin et al., 2019). The
relative abundances of norank_f__Xanthobacteraceae and norank_f__norank_
o__Acidobacteriales decreased by 82.30 % and 51.76 % respectively (Fig. 3g
and S4), which also signified an improvement in soil health and reduced acid-
ification (Xu et al., 2022a). In addition to the bacteria mentioned above with
relatively high abundance, SUMs implementation also resulted in the enrich-
ment of some bacteria that played essential roles in plant growth, material
transformation, and harmful substances degradation (Fig. S5). For instance,
Candidatus_Solibacter, Bryobacter, and Bradyrhizobium could decompose
organic matters and promote the soil carbon cycle and nitrogen fixation (de
Faria et al., 2021), and Massilia produced dimethyl disulfide, which effectively

Fig. 5. Procrustes analysis on microbial community based on Bray−Curtis dissimilarity metrics (a); RDA analysis based on the chemical species of soil Cd and microbial
community (b); Correlations of the networked community structures (Bray–Curtis distance) with total soil Cd, soil enzyme activities, and rhizosphere soil pH (c);
Correlations of the networked community structures (Bray–Curtis distance) with chemical species of soil Cd (d); Edge width corresponds to the Mantel's r value, and the
edge color denotes the statistical significance based on 9999 permutations. Pairwise correlations of these variables are shown with a color gradient denoting Pearson's
correlation coefficient.

8
J. Gu et al.
controlled soil pathogenic fungi and nematodes (Dahal et al., 2021). More-
over, Flavisolibacter was a rhizobacteria that could promote root development
(Zhou et al., 2022). The correlation analysis further confirmed that a signifi-
cant positive correlation between soil pH levels and soil enzyme activities,
and the dominant soil microflora (Arthrobacter, Candidatus_Solibacter,
Bryobacter, and Bradyrhizobium) (Fig. 5b; p < 0.05). Overall, SUMs implemen-
tation significantly increased the abundance of these bacteria in the rhizo-
sphere soil, improving the paddy field's micro-ecological environment,
promoting rice growth, and reducing Cd accumulation toxicity.
Procrustes tests revealed no obvious association between CK and Reme-
diation (SUMs) (M = 0.3169; p = 0.1667) (Fig. 5a), indicating that SUMs
implementation drove the remodeling of rhizosphere soil microbial com-
munity. Based on RDA analysis, the first and second sorting axes effectively
explained the correlation between the soil microbial community structure
and the chemical species of Cd with a cumulative variable of 79.44 %
(Fig. 5b). Specifically, the contents of exchangeable and carbonate-bound
Cd were significantly linked to changes in soil microbial communities in
the CK group, and the SUMs implementation had a positive impact on the
contents of Fe\\Mn oxide-bound Cd, organic-bound Cd, and residual Cd
due to the soil microbial community's influence (Fig. 5b). Based on correla-
tion analysis, the chemical species of Cd with poor migration ability, includ-
ing Fe\\Mn oxide-bound Cd, organic-bound Cd, and residual Cd, showed a
positive correlation with the relative abundances of Bradyyrhizobium,
Thermodesulfovibrio, Candidatus Solibacter, and Bacillus in soil (Fig. 5d;
p < 0.05). Co-occurrence network analysis revealed that the key species
in the network were primarily from Actinobacteriota (21.53 %),
Proteobacteria (19.44 %), Acidobacteriota (16.67 %), Chloroflexi (11.81 %),
and Firmicutes (9.03 %) (Fig. 6). Among them, the chemical species of Cd
Fig. 6. Network co-occurrence analysis showing the correlations among the soil enzyme activities, rhizosphere soil pH, chemical species of soil Cd, and the abundant
microbial populations (top 100 most abundant OTUs). The same color in a module represents close association within a region. The sizes of the nodes (OTUs) are
proportional to the number of connections. Only nodes (OTUs) that were significantly correlated with each other (Spearman's > |0.70| and p < 0.05) were connected (edges).
9
Science of the Total Environment 885 (2023) 163896
with low mobility were significantly and positively correlated with Gaiella
(OTU 1900), Acidothermus (OTU 3671), Arthrobacter (OTU 485),
Terrabacter (OTU 1880), Burkholderiales (OTU 1918), Bacillus (OTU
2811), and Candidatus _ Solibater (OTU 3313 and OTU 3565) (Fig. 6;
p < 0.05). Bradyyrhizobium had been found to encode the soxA/B/X/Z
gene of thiosulfate oxidation pathway, which facilitated the oxidation of re-
duced sulfur into sulfate (SO2−
4 ), leading to the passivation of soil Cd (Xie
et al., 2022). Thermodesulfovibrio could utilize sulfate, oxidized sulfides, or
sulfur as electron acceptors, reducing these substances to S2− and ulti-
mately forming CdS (Rambabu et al., 2020). Candidatus Solibacter and Bacil-
lus could drive the corrosion of iron, and the generated iron oxide had a
large specific surface area and strong chemical activity (Zhang et al.,
2020), which could adsorb Cd2+ ions and affected bioavailability of Cd in
soil. Phenotypic analysis revealed that the SUMs implementation resulted
in a significant increase in microbial biofilm, a reduction of potential path-
ogenic bacteria, and weakened stress tolerance (Fig. 7a). This suggested
that some soil Cd might be complexed by organic functional groups on
the surface of biofilm, which reduced their mobility and biological toxicity
(Shan et al., 2019). Functional analysis of microbial communities also
showed that SUMs implementation down-regulated the dissimilatory arse-
nate reduction pathway responsible for reducing adsorbed As (V) to As (III),
while up-regulating the nitrate ammonification pathway that catabolized
nitrate to ammonium, as well as the nitrate/nitrite reduction pathway
(Fig. 7b). These results indicate that SUMs implementation altered the
structure of rhizosphere flora and the iron‑nitrogen cycle, ultimately affect-
ing the Cd bioavailability through adsorption and co-precipitation (Wang
et al., 2021a). Namely, SUMs implementation drove the assembly of micro-
bial communities in the rhizosphere soil, thereby influencing the
J. Gu et al.
Fig. 7. Wilcoxon rank-sum test on phenotype of microbial community (a; p < 0.05); Functional analysis of microbial community (b).
functioning of the microbial community. This, in turn, affected the cycling
pathways of soil elements, such as nitrogen, phosphate, and sulfate anabo-
lism pathways (Xie et al., 2022), and indirectly or directly altered the chem-
ical speciation of soil Cd.
4. Conclusions
In this study, SUMs implementation significantly improved rice yield
and soil quality, while reducing Cd levels in rice grain below national safety
standards. SUMs implementation increased soil pH and DOM aromatiza-
tion, promoting the conversion of exchangeable and carbonate-bound Cd
to other insoluble chemical speciation. Importantly, SUMs implementation
reshaped the rhizosphere soil microbial community, recruiting lots of
special microbes (e.g., Arthrobacter, Candidatus_Solibacter, Bryobacter,
Bradyrhizobiu, and Thermodesulfovibrio) associated with plant growth
promotion, pathogen inhibition, organic matter degradation, and element
cycling. Furthermore, the degradation intensity of organic matter by
10
Science of the Total Environment 885 (2023) 163896
rhizosphere soil microbes affected the structure and composition of DOM,
which in turn directly and indirectly affected the chemical speciation of
soil Cd. Besides, SUMs implementation influenced rice growth and Cd accu-
mulation in grain by regulating the rhizosphere microbial community in-
volved in the coupled cycle of elements (e.g., sulfur‑nitrogen coupling).
This study provided insight into the mechanisms by which rhizosphere mi-
crobes acted as a barrier against soil Cd under SUMs implementation.
CRediT authorship contribution statement
Zhimin Xu designed the experiment and was responsible for admin-
istration and reviewing of project. Jiguang Gu, Fang Guo, and Yuming
Zhong were responsible for editing and reviewing of the original draft.
Jiexiang Zhang, Weimin Sun, Riaz Muhammad, and Dengle Duan gave
guidance during the experiment. Haojie Liang, Lihong Lin, Xingying
Deng, Zheng Lin, and Yifan Wang measured relevant indicators in this
study.
J. Gu et al.
Data availability
Data will be made available on request.
Declaration of competing interest
The authors declare that they have no known competing financial inter-
ests or personal relationships that could have appeared to influence the
work reported in this paper.
Acknowledgements
This work was funded by the National Natural Science Foundation of
China (42007375), the Natural Science Foundation of Guangdong Province
(2023A1515012532), the Science and Technology Planning Project of
Guangdong Province (2020B1212060048), the Key Laboratory of Pollution
Processes and Environmental Criteria (Nankai University), Ministry of Edu-
cation (2021b06), the Foundation for Young Innovative Talents in Higher
Education of Guangdong (2021KQNCX154), and the Innovation and Entre-
preneurship Training Program for College Students of Zhongkai University
of Agriculture and Engineering (S202211347104 and x202211347386).
Appendix A. Supplementary data
Supplementary data to this article can be found online at https://doi.
org/10.1016/j.scitotenv.2023.163896.
References
Bandara, T., Krohn, C., Jin, J., Chathurika, J., Franks, A., Xu, J., et al., 2022. The effects of bio-
char aging on rhizosphere microbial communities in cadmium-contaminated acid soil.
Chemosphere 303, 135153.
Chen, M., Li, C., Zeng, C., Zhang, F., Raymond, P.A., Hur, J., 2019. Immobilization of relic an-
thropogenic dissolved organic matter from alpine rivers in the himalayan-tibetan plateau
in winter. Water Res. 160, 97–106.
Chen, W., Kang, Z., Yang, Y., Li, Y., Qiu, R., Qin, J., et al., 2022. Interplanting of rice cultivars
with high and low cd accumulation can achieve the goal of “repairing while producing”
in cd-contaminated soil. Sci. Total Environ. 851, 158229.
Cheng, Z., Shi, J., He, Y., Wu, L., Xu, J., 2022. Assembly of root-associated bacterial commu-
nity in cadmium contaminated soil following five-year consecutive application of soil
amendments: evidences for improved soil health. J. Hazard. Mater. 426, 128095.
Dahal, R.H., Chaudhary, D.K., Kim, J., 2021. Genome insight and description of antibiotic pro-
ducing Massilia antibiotica sp. nov., isolated from oil-contaminated soil. Sci. Rep. 11,
1–11.
de Faria, M.R., Costa, L.S.A.S., Chiaramonte, J.B., Bettiol, W., Mendes, R., 2021. The rhizo-
sphere microbiome: functions, dynamics, and role in plant protection. Tropical Plant
Pathol. 46, 13–25.
de Vries, F.T., Griffiths, R.I., Knight, C.G., Nicolitch, O., Williams, A., 2020. Harnessing rhizo-
sphere microbiomes for drought-resilient crop production. Science 368, 270–274.
Edwards, J., Johnson, C., Santos-Medellín, C., Lurie, E., Podishetty, N.K., Bhatnagar, S., et al.,
2015. Structure, variation, and assembly of the root-associated microbiomes of rice. Pro-
ceedings of the National Academy of Science 112, E911–E920.
Fässler, E., Robinson, B.H., Gupta, S.K., Schulin, R., 2010. Uptake and allocation of plant
nutrients and cd in maize, sunflower and tobacco growing on contaminated soil and
the effect of soil conditioners under field conditions. Nutr. Cycl. Agroecosyst. 87,
339–352.
Gan, Q., Song, F., Zhang, C., Han, Z., Teng, B., Lin, C., et al., 2022. Ca2+ deficiency triggers
panicle degeneration in rice mediated by Ca2+/H+ exchanger OsCAX1a. Plant, Cell &
Environment 46, 1610–1628.
Gluhar, S., Kaurin, A., Lestan, D., 2020. Soil washing with biodegradable chelating agents and
EDTA: technological feasibility, remediation efficiency and environmental sustainability.
Chemosphere 257, 127226.
Hamid, Y., Tang, L., Hussain, B., Usman, M., Lin, Q., Rashid, M.S., et al., 2020. Organic soil
additives for the remediation of cadmium contaminated soils and their impact on the
soil-plant system: a review. Sci. Total Environ. 707, 136121.
Huang, Y., Wang, L., Wang, W., Li, T., He, Z., Yang, X., 2019. Current status of agricul-
tural soil pollution by heavy metals in China: a meta-analysis. Sci. Total Environ.
651, 3034–3042.
Huang, L., Hua, K., Xu, R., Zeng, D., Wang, R., Dong, G., et al., 2021. The LARGE2-APO1/
APO2 regulatory module controls panicle size and grain number in rice. Plant Cell 33,
1212–1228.
Hussain, B., Umer, M.J., Li, J., Ma, Y., Abbas, Y., Ashraf, M.N., et al., 2021. Strategies for re-
ducing cadmium accumulation in rice grains. J. Clean. Prod. 286, 125557.
Jiang, Y., Yi, X.-T., Liu, M.-Y., Liu, B.-b., Zhou, H., Zeng, P., et al., 2022. Dynamic responses of
soil enzymes at key growth stages in rice after the in situ remediation of paddy soil con-
taminated with cadmium and arsenic. Sci. Total Environ. 830, 154633.
11
Science of the Total Environment 885 (2023) 163896
Korenblum, E., Dong, Y., Szymanski, J., Panda, S., Jozwiak, A., Massalha, H., et al., 2020. Rhi-
zosphere microbiome mediates systemic root metabolite exudation by root-to-root signal-
ing. Proceedings of the National Academy of Sciences 117, 3874–3883.
Kumpiene, J., Antelo, J., Brännvall, E., Carabante, I., Ek, K., Komárek, M., et al., 2019. In
situ chemical stabilization of trace element-contaminated soil–field demonstrations
and barriers to transition from laboratory to the field–a review. Appl. Geochem. 100,
335–351.
Li, Y., Gong, X., 2021. Effects of dissolved organic matter on the bioavailability of heavy
metals during microbial dissimilatory iron reduction: a review. Rev. Environ. Contam.
Toxicol. 257, 69–92.
Li, T., Zhou, Q., 2020. The key role of geobacter in regulating emissions and biogeochemical
cycling of soil-derived greenhouse gases. Environ. Pollut. 266, 115135.
Li, G.D., Conyers, M.K., Helyar, K.R., Lisle, C.J., Poile, G.J., Cullis, B.R., 2019. Long-term sur-
face application of lime ameliorates subsurface soil acidity in the mixed farming zone of
South-Eastern Australia. Geoderma 338, 236–246.
Li, Y., Zhang, M., Xu, R., Lin, H., Sun, X., Xu, F., et al., 2021a. Arsenic and antimony co-
contamination influences on soil microbial community composition and functions: rele-
vance to arsenic resistance and carbon, nitrogen, and sulfur cycling. Environ. Int. 153,
106522.
Li, Z., Liang, Y., Hu, H., Shaheen, S.M., Zhong, H., Tack, F.M., et al., 2021b. Speciation,
transportation, and pathways of cadmium in soil-rice systems: a review on the envi-
ronmental implications and remediation approaches for food safety. Environ. Int.
156, 106749.
Li, Q., Wang, Y., Li, Y., Li, L., Tang, M., Hu, W., et al., 2022a. Speciation of heavy metals in
soils and their immobilization at micro-scale interfaces among diverse soil components.
Sci. Total Environ. 153862.
Li, Y., Yang, R., Guo, L., Gao, W., Su, P., Xu, Z., et al., 2022b. The composition, biotic network,
and assembly of plastisphere protistan taxonomic and functional communities in plastic-
mulching croplands. J. Hazard. Mater. 430, 128390.
Lin, Y., Ye, G., Kuzyakov, Y., Liu, D., Fan, J., Ding, W., 2019. Long-term manure application
increases soil organic matter and aggregation, and alters microbial community structure
and keystone taxa. Soil Biol. Biochem. 134, 187–196.
Lin, J., Ma, K., Chen, H., Chen, Z., Xing, B., 2022. Influence of different types of nanomaterials
on soil enzyme activity: a global meta-analysis. Nano Today 42, 101345.
Liu, Y., Tie, B., Peng, O., Luo, H., Li, D., Liu, S., et al., 2020a. Inoculation of cd-contaminated
paddy soil with biochar-supported microbial cell composite: a novel approach to reduc-
ing cadmium accumulation in rice grains. Chemosphere 247, 125850.
Liu, Y.-M., Cao, W.-Q., Chen, X.-X., Yu, B.-G., Lang, M., Chen, X.-P., et al., 2020b. The re-
sponses of soil enzyme activities, microbial biomass and microbial community structure
to nine years of varied zinc application rates. Sci. Total Environ. 737, 140245.
Liu, N., Lou, X., Li, X., Shuai, Z., Liu, H., Jiang, Z., et al., 2021. Rhizosphere dissolved organic
matter and iron plaque modified by organic amendments and its relations to cadmium
bioavailability and accumulation in rice. Sci. Total Environ. 792, 148216.
Meng, F., Huang, Q., Cai, Y., Xiao, L., Wang, T., Li, X., et al., 2023. A comparative assessment
of humic acid and biochar altering cadmium and arsenic fractions in a paddy soil. J. Soils
Sediments 23, 845–855.
Ngo, H.T.T., Watchalayann, P., Nguyen, D.B., Doan, H.N., Liang, L., 2021. Environmental
health risk assessment of heavy metal exposure among children living in an informal e-
waste processing village in Viet Nam. Sci. Total Environ. 763, 142982.
Nurzhan, A., Tian, H., Nuralykyzy, B., He, W., 2022. Soil enzyme activities and enzyme activ-
ity indices in long-term arsenic-contaminated soils. Euras. Soil Sci. 55, 1425–1435.
Qian, X., Lü, Q., He, X., Wang, Y., Li, H., Xiao, Q., et al., 2022. Pseudomonas sp. TCd-1 signif-
icantly alters the rhizosphere bacterial community of rice in Cd contaminated paddy
field. Chemosphere 290, 133257.
Rambabu, K., Banat, F., Pham, Q.M., Ho, S.-H., Ren, N.-Q., Show, P.L., 2020. Biological reme-
diation of acid mine drainage: review of past trends and current outlook. Environ. Sci.
Ecotechnol. 2, 100024.
Reyes-Hinojosa, D., Lozada-Pérez, C., Cuevas, Y.Z., López-Reyes, A., Martínez-Nava, G.,
Fernández-Torres, J., et al., 2019. Toxicity of cadmium in musculoskeletal diseases. Envi-
ron. Toxicol. Pharmacol. 72, 103219.
Shan, S., Guo, Z., Lei, P., Wang, Y., Li, Y., Cheng, W., et al., 2019. Simultaneous mitigation of
tissue cadmium and lead accumulation in rice via sulfate-reducing bacterium. Ecotoxicol.
Environ. Saf. 169, 292–300.
Shen, X., Dai, M., Yang, J., Sun, L., Tan, X., Peng, C., et al., 2022. A critical review on the
phytoremediation of heavy metals from environment: performance and challenges.
Chemosphere 291, 132979.
Sun, X., Kong, T., Li, F., Häggblom, M.M., Kolton, M., Lan, L., et al., 2022. Desulfurivibrio spp.
mediate sulfur-oxidation coupled to Sb (V) reduction, a novel biogeochemical process.
ISME J. 16, 1547–1556.
Sut-Lohmann, M., Ramezany, S., Kästner, F., Raab, T., Heinrich, M., Grimm, M., 2022. Using
modified tessier sequential extraction to specify potentially toxic metals at a former sew-
age farm. J. Environ. Manag. 304, 114229.
Tan, K.H., 1995. Soil Sampling, Preparation, and Analysis. CRC Press.
Ullah, A., Tahir, A., Rashid, H.U., Danish, S., Hussain, B., et al., ur Rehman, T., 2021. Strate-
gies for reducing Cd concentration in paddy soil for rice safety. Journal of Cleaner Pro-
duction 316, 128116.
Wang, Y.-M., Tang, D.-D., Zhang, X.-H., Uchimiya, M., Yuan, X.-Y., Li, M., et al., 2019. Effects
of soil amendments on cadmium transfer along the lettuce-snail food chain: influence of
chemical speciation. Sci. Total Environ. 649, 801–807.
Wang, C., Huang, Y., Zhang, C., Zhang, Y., Yuan, K., Xue, W., et al., 2021a. Inhibition effects of
long-term calcium-magnesia phosphate fertilizer application on Cd uptake in rice: regula-
tion of the iron-nitrogen coupling cycle driven by the soil microbial community.
J. Hazard. Mater. 416, 125916.
Wang, L., Zhang, Q., Liao, X., Li, X., Zheng, S., Zhao, F., 2021b. Phytoexclusion of heavy
metals using low heavy metal accumulating cultivars: a green technology. J. Hazard.
Mater. 413, 125427.
J. Gu et al.
Wang, J., Yuan, R., Zhang, Y., Si, T., Li, H., Duan, H., et al., 2022. Biochar decreases cd
mobility and rice (Oryza sativa L.) uptake by affecting soil iron and sulfur cycling. Sci.
Total Environ. 836, 155547.
Wen, E., Yang, X., Chen, H., Shaheen, S.M., Sarkar, B., Xu, S., et al., 2021. Iron-modified bio-
char and water management regime-induced changes in plant growth, enzyme activities,
and phytoavailability of arsenic, cadmium and lead in a paddy soil. J. Hazard. Mater.
407, 124344.
Xiao, J., Chen, S.-y., Sun, Y., Yang, S.-d., He, Y., 2022. Differences of rhizospheric and endo-
phytic bacteria are recruited by different watermelon phenotypes relating to rind colors
formation. Sci. Rep. 12, 6360.
Xie, H., Chen, Z., Feng, X., Wang, M., Luo, Y., Wang, Y., et al., 2022. L-theanine exuded from
Camellia sinensis roots regulates element cycling in soil by shaping the rhizosphere
microbiome assembly. Sci. Total Environ. 837, 155801.
Xu, Y., Feng, J., Li, H., 2021a. Water management increased rhizosphere redox potential and
decreased cd uptake in a low-cd rice cultivar but decreased redox potential and increased
Cd uptake in a high-Cd rice cultivar under intercropping. Sci. Total Environ. 751,
141701.
Xu, Z., Lu, Z., Zhang, L., Fan, H., Wang, Y., Li, J., et al., 2021b. Red mud based passivator re-
duced Cd accumulation in edible amaranth by influencing root organic matter metabo-
lism and soil aggregate distribution. Environ. Pollut. 275, 116543.
Xu, Z.-M., Wang, J.-F., Li, W.-L., Wang, Y.-F., He, T., Wang, F.-P., et al., 2021c. Nitrogen fer-
tilizer affects rhizosphere Cd re-mobilization by mediating gene AmALM2 and AmALMT7
expression in edible amaranth roots. J. Hazard. Mater. 418, 126310.
Xu, D., Ling, J., Qiao, F., Xi, P., Zeng, Y., Zhang, J., et al., 2022a. Organic mulch can suppress
litchi downy blight through modification of soil microbial community structure and func-
tional potentials. BMC Microbiol. 22, 1–12.
Xu, Z.-M., Zhang, Y.-X., Wang, L., Liu, C.-G., Sun, W.-M., Wang, Y.-F., et al., 2022b.
Rhizobacteria communities reshaped by red mud based passivators is vital for reducing
soil Cd accumulation in edible amaranth. Sci. Total Environ. 826, 154002.
Xu, Z., Zhang, Y., Xu, Z., Zhong, Y., Wang, L., Liu, C., et al., 2023. Dysregulation of gut health
in zebrafish by differentially charged nanoplastics exposure: an integrated analysis of
histopathology, immunology, and microbial informatics. Environmental Science: Nano
10, 933.
Xue, S., Liu, Z., Fan, J., Xue, R., Guo, Y., Chen, W., et al., 2022. Insights into variations on dis-
solved organic matter of bauxite residue during soil-formation processes following 2-year
column simulation. Environ. Pollut. 292, 118326.
12
Science of the Total Environment 885 (2023) 163896
Yang, Y., Xia, S., Li, J., Zhong, K., Wang, J., Shi, L., et al., 2022. Screening of foliar barrier
agents and reduces the absorption and transport of cd in wheat. Bull. Environ. Contam.
Toxicol. 1–7.
Yin, S., Suo, F., You, X., Chu, D., Yuan, Y., Yu, X., et al., 2022:. Biochar-compost amendment
enhanced sorghum growth and yield by improving soil physicochemical properties and
shifting soil bacterial community in a coastal soil. Frontiers in environmentalScience
2154.
Yue, H., Yue, W., Jiao, S., Kim, H., Lee, Y.-H., Wei, G., et al., 2023. Plant domestication shapes
rhizosphere microbiome assembly and metabolic functions. Microbiome 11, 1–19.
Zhang, X., Bian, F., Zhong, Z., Gai, X., Yang, C., 2020. Deciphering the rhizosphere
microbiome of a bamboo plant in response to different chromium contamination levels.
J. Hazard. Mater. 399, 123107.
Zhang, P., Bing, X., Jiao, L., Xiao, H., Li, B., Sun, H., 2022. Amelioration effects of coastal
saline-alkali soil by ball-milled red phosphorus-loaded biochar. Chem. Eng. J. 431,
133904.
Zhang, S., Ke, C., Jiang, M., Li, Y., Huang, W., Dang, Z., et al., 2023. S (-II) reactivates Cd2+-
stressed shewanella oneidensis via promoting low-molecular-weight thiols synthesis and
activating antioxidant defense. Environ. Pollut. 121516.
Zhao, C., He, X., Dan, X., He, M., Zhao, J., Meng, H., et al., 2022a. Soil dissolved organic mat-
ters mediate bacterial taxa to enhance nitrification rates under wheat cultivation. Sci.
Total Environ. 828, 154418.
Zhao, D., Wang, P., Zhao, F.-J., 2022b. Dietary cadmium exposure, risks to human health and
mitigation strategies. Crit. Rev. Environ. Sci. Technol. 1–25.
Zhou, X., Zhang, X., Ma, C., Wu, F., Jin, X., Dini-Andreote, F., et al., 2022. Biochar amendment
reduces cadmium uptake by stimulating cadmium-resistant PGPR in tomato rhizosphere.
Chemosphere 307, 136138.
Zoli, M., Paleari, L., Confalonieri, R., Bacenetti, J., 2021. Setting-up of different water manage-
ments as mitigation strategy of the environmental impact of paddy rice. Sci. Total Envi-
ron. 799, 149365.
Zou, M., Zhou, S., Zhou, Y., Jia, Z., Guo, T., Wang, J., 2021. Cadmium pollution of soil-rice
ecosystems in rice cultivation dominated regions in China: a review. Environ. Pollut.
280, 116965.
Zuccarini, P., Sardans, J., Asensio, L., Peñuelas, J., 2023. Altered activities of extracellular soil
enzymes by the interacting global environmental changes. Glob. Chang.Biol. 29,
2067–2091.