Article
https://doi.org/10.1038/s41467-024-53169-6
Conservation agriculture improves soil
health and sustains crop yields after long-
term warming
Jialing Teng
1,7
, Ruixing Hou
2,7
, Jennifer A. J. Dungait
3,4
, Guiyao Zhou
5
,
Yakov Kuzyakov
6
, Jingbo Zhang
1
, Jing Tian
1
, Zhenling Cui
,
Fusuo Zhang
1
& Manuel Delgado-Baquerizo
Climate warming threatens global food security by exacerbating pressures on
degraded soils under intensive crop production. Conservation agriculture is
promoted as a sustainable solution that improves soil health and sustains crop
yields in a changing climate, but these bene
fi
ts may be affected by long-term
warming. Here, we investigate the effects of conservation agriculture com-
pared to conventional agriculture on 17 soil properties, microbial diversity and
crop yields, during eight-years
’
experimental warming. An overall positive
effect of warming on soil health over time under conservation agriculture is
characterized by linear increases in soil organic carbon and microbial biomass
carbon. Warming-triggered shifts in microbial biomass carbon and fungal
diversity (saprogen richness) are directly linked to a 9.3% increase in wheat
yields over eight years, but only under conservation agriculture. Overall,
conservation agriculture results in an average 21% increase in soil health and
supports similar levels of crop production after long-term warming compared
to conventional agriculture. Our work provides insights into the potential
bene
fi
ts of conservation agriculture for long-term sustainable food production
because improved soil health improves resilience to the effects of climate
warming.
Global food security is challenged by climate warming and growth of
the human population
. Soil degradation associated with intensive
agriculture has reduced the availability of land for food production
.
The far-reaching consequences of climate warming combined with the
urgent demand to increase food production require climate-resilient
land management options to simultaneously increase productivity and
promote adaptations to climate change and its mitigation
,
. A sus-
tainable management strategy described as
‘
conservation agriculture
’
is widely promoted as a nature-based solution to maintain food pro-
duction and simultaneously promote soil health
,
–
. Soil health is a
holistic concept that integrates the biological, physical and chemical
aspects of soil, demonstrating the continued capacity of soil as a vital
Received: 18 September 2023
Accepted: 3 October 2024
Check for updates
1
State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green
Development, China Agricultural University, 100193 Beijing, PR China.
2
Key Laboratory of Ecosystem Network Observation and Modeling, Institute of
Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences (CAS), 100101 Beijing, PR China.
3
Geography, College of Life and
Environmental Sciences, University of Exeter, Rennes Drive, Exeter EX4 4RJ, UK.
4
Carbon Management Centre, SRUC-Scotland
’
s Rural College, Edinburgh
EH9 3JG, UK.
5
Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), Consejo
Superior de Investigaciones Cientí
fi
cas (CSIC), 41012 Sevilla, Spain.
6
Department of Soil Science of Temperate Ecosystems, University of Göttingen, 37077
Göttingen, Germany.
7
These authors contributed equally: Jialing Teng, Ruixing Hou.
e-mail:
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| (2024) 15:8785
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4
5
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4
5
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7
8
living ecosystem
,
. Conservation agriculture encompasses reduced or
zero/no tillage, permanent soil cover, and diverse crop rotations, and
is applicable in many different farming contexts
,
. A wide range of
environmental bene
fi
ts associated with its implementation, including
improved soil health related to increased soil organic carbon (SOC)
stocks and soil biodiversity
,
, has led to adoption of conservation
agriculture across 12.5% of arable land in one-third of countries
worldwide
. However, a paucity of systematic and quantitative
assessments of long-term climate warming effects on the potential of
conservation agriculture to support soil health and crop production
creates uncertainty in its ef
fi
cacy under different future climate
projections
. Long-term
fi
eld experiments speci
fi
cally comparing
conservation agriculture with conventional management under
warming conditions are particularly rare
,
–
, but are urgently needed
to explore the interactive effects of management and warming on crop
yield and soil health
.
Predicting the effectiveness of conservation agriculture as the
climate warms is challenging because of the complex interactive
effects of warming and soil management on crop yields and individual
soil properties
. In general, climate warming profoundly affects
agricultural activities in many ways, ranging from yield reductions to
loss of SOC and ecosystem functions
,
. Reductions in crop yields in
response to rising temperature are widely reported
–
, especially at
low latitudes
, mainly due to drought, disturbed crop growth cycles,
and increased pathogen pressures
,
. SOC is a
‘
master
’
soil health
indicator that supports multiple soil functions including nutrient and
water cycling and retention, soil structure formation, and ecosystem
productivity
. Climate warming is anticipated to elevate global SOC
losses by accelerating microbial decomposition
–
. In addition, rising
temperatures may enhance microbial nitrogen mineralization and lead
to nitrogen loss from terrestrial ecosystems
. In contrast, crop residue
retention in conservation agriculture promotes SOC accrual directly
by increasing plant biomass inputs, which also alleviates water and
nutrient limitation for crops by improving soil health, and indirectly by
accelerating microbial turnover and necromass accrual through
organic matter supply
. The soil conditions created by conservation
agriculture can counteract the negative effects of climate change on
food production in some regions
. The complex interactive effects
of warming and soil management create many uncertainties in pre-
diction aggravated by the limitations of process-based crop simulation
models to estimate the effects of climate change on agroecosystem
functions. This is exacerbated by the urgent requirement for empirical
data from long-term
fi
eld warming experiments to improve models
that forecast future farming conditions
; to date, short-term
fi
eld-
warming studies have largely focused on natural ecosystems
.
Soil microbiome are major contributors to sustainable agriculture
because they drive key processes in agroecosystems prerequisite to
optimizing soil health and crop productivity
. Conservation agri-
culture generally promotes the size, diversity, activity and bene
fi
cial
functions of soil microorganisms that contribute to soil health,
including SOC accrual in available and stable pools, and crop
productivity
. In particular, reduced tillage supports the develop-
ment of hyphal networks and a more diverse and abundant soil fungal
biomass, which contributes to multiple soil ecosystem functions
including improved substrate and water supply
. However, the
effects of climate warming on the observed bene
fi
ts of conservation
agriculture for the soil microbiome are dif
fi
cult to anticipate. Intenser
environmental
fi
ltering in warmed forest and grassland soils can create
negative effects on fungal and bacterial diversity
. Stronger nutrient
acquisition by roots induced by warming may lead to reductions in
mycorrhizal
dependence
and
arbuscular
mycorrhizal
fungal
diversity
. Potential increases of soil-borne plant pathogens under
warming conditions are of especial concern in crop production
systems
, though the increase in soil health that supports healthy
crop growth may help counteract disease threats
. Overall, great
uncertainty remains about the response of soil microbiome to inter-
actions between warming and crop management practices, and the
effects on soil health and crop yields.
Our study aims to assess warming effects on: (i) soil health and
crop yields under conservation agriculture (permanent crop residue
cover and no tillage) versus conventional agriculture (crop residue
removal and annual tillage); and (ii) the contribution of the soil
microbiome to supporting soil health and crop yields. We hypothesize
that, under warming conditions, (i) conservation agriculture improves
crop productivity by increasing carbon inputs aboveground (crop
residues) and belowground (crop roots) that stimulates microbial
growth, promoting soil health characterized by carbon accrual; (ii)
improvements in crop yield and soil health relies on changes in the soil
microbiome; (iii) the bene
fi
ts of conservation agriculture are cumula-
tive over time. To test these hypotheses, we conduct an eight-year-
long
fi
eld experiment to investigate the effects of soil management
systems (conservation agriculture versus conventional agriculture)
and warming levels (warming versus ambient) on crop yields and soil
health, and additionally the in
fl
uence of the soil microbiome, on the
North China Plain. Our experiment is conducted using a typical crop
rotation system (winter wheat (
Triticum aestivum
L.)-summer maize
(
Zea mays
L.)). Two levels of warming are imposed using infrared
heaters:
‘
ambient
’
and
‘
+2 °C
’
according to soil warming predicted by
IPCC greenhouse gas scenarios rates for northern China
. We simul-
taneously assess 17 soil health indicators, microbial diversity and crop
yields to demonstrate the combined effects of warming and manage-
ment. We
fi
nd that long-term warming increases soil health indicators
and crop productivity, but only under conservation agriculture. The
bene
fi
cial effects of conservation agriculture on microbial biomass
carbon and SOC increase through time under long-term warming.
Improved soil health and shifts in soil fungal diversity are related to the
positive warming effects on crop yields over time under conservation
agriculture. Our work demonstrates the potential for climate resilient
farming through the implementation of conservation agriculture to
improve soil health and sustain crop yields in a warming climate.
Results
Similar wheat yields in conservation agriculture and conven-
tional agriculture under warming
Experimental warming was imposed using infrared heaters to plots
used for wheat and maize cultivation adopting conservation agri-
culture or conventional agriculture (Fig.
a). Over the eight-year study
period, soil temperature and moisture were recorded continuously by
in-situ sensors. As expected, experimental warming increased soil
temperature but decreased soil moisture under both conservation and
conventional agriculture (
P
< 0.05; Fig.
b, c; Supplementary Table 1).
The warming effects were modi
fi
ed by soil management, and soils
under conservation agriculture were cooler (14.0 °C vs. 14.7 °C) and
wetter (17.1% vs. 15.9%) than under conventional agriculture (
P
< 0.001;
Fig.
b, c; Supplementary Table 1).
Winter wheat yields were strongly affected by warming (
P
< 0.001;
Supplementary Table 1), but there was no difference between the two
management types (Fig.
d). Conservation agriculture maintained
similar wheat yields to conventional agriculture both under ambient
and warming conditions (Fig.
d). Across the eight-year study, warming
increased wheat yields by 9.3% and 11.2% under conservation and
conventional agriculture, respectively, when compared with the no
warming treatments (
P
< 0.001; Fig.
d; Supplementary Table 1). We
further assessed the warming effect on wheat yields over eight years
using Cohen
’
s
d
index (Fig.
e). Warming-induced positive effects on
wheat yields strengthened with time under conservation agriculture
(
P
< 0.05), but not under conventional agriculture (Fig.
e). In contrast,
the maize yields were only affected by soil management (
P
< 0.001;
Supplementary Table 1), but not in
fl
uenced by warming (Supplemen-
tary Fig. 1). Conservation agriculture supported larger maize yields
Article
https://doi.org/10.1038/s41467-024-53169-6
| (2024) 15:8785
2
than conventional agriculture under both ambient and warming con-
ditions (
P
< 0.001; Supplementary Fig. 1; Supplementary Table 1).
Conservation agriculture improved soil health under warming
Seventeen soil properties, including physical, chemical, and biological
attributes, were analyzed in 2020 using samples from two soil depths
(0
–
5 cm and 5
–
15 cm depth) to evaluate the cumulative effects of long-
term warming on soil health. Principal Component Analysis (PCA) was
used to select representative indicators of soil health (Fig.
a; Sup-
plementary Fig. 2). The
fi
rst two principal components accounted for
75.2% (PC1 = 57.9% and PC2 = 17.3%) and 59.8% (PC1 = 35.8% and PC2 =
24.0%) of the cumulative percent variability in soil health at 0
–
5 cm
and 5
–
15 cm depth, respectively (Fig.
a; Supplementary Fig. 4a). The
soil health score (Cornell Soil Health Assessment Scoring) was affected
by management, warming, and their interaction (
P
< 0.05; Supple-
mentary Table 2). The response of soil health to warming varied
depending on soil management (
P
< 0.05; Supplementary Table 2).
Warming increased the soil health score by 6.3% and 8.1% at 0
–
5 cm
and 5
–
15 cm soil depth under conservation agriculture, but only
increased soil health score by 5.2% at 5
–
15 cm depth under conven-
tional agriculture (
P
< 0.01; Fig.
b; Supplementary Fig. 4b; Supple-
mentary Table 2). The soil health score under conservation agriculture
was 21.5% and 7.1% greater than conventional agriculture at 0
–
5 cm and
5
–
15 cm depth in ambient conditions, respectively (Fig.
b; Supple-
mentary Fig. 4). Warming ampli
fi
ed the advantages of conservation
agriculture in terms of soil health, and resulted in a 31.4% and 10.1%
greater soil health score than conventional agriculture at 0
–
5 cm and
5
–
15 cm depth, respectively (Fig.
b; Supplementary Fig. 4b).
Fig. 1 | Effects of warming and management on soil microclimate and crop
yields. a
Experimental settings for treatments.
b
,
c
Effects of warming and man-
agement on soil temperature and moisture over eight years was estimated by linear
mixed model with sampling time as random factors. Statistical signi
fi
cance is based
on Wald type II
χ
² tests (
n
= 8 independent soil samples per treatment). All reported
P
values result from two-sided statistical tests. Boxplots display the mean (hor-
izontal line), the 25th and 75th percentiles (colored box), the minimum and max-
imum (whiskers).
d
Average winter wheat yields. Boxplots display the mean
(horizontal line), the 25th and 75th percentiles (colored box), the minimum and
maximum (whiskers). The winter wheat yield data were analyzed based on eight
sampling years (
n
= 24 independent soil samples per treatment). Statistical analysis
was performed using a linear mixed model with sampling time as random factors.
Statistical signi
fi
cance is based on Wald type II
χ
² tests. All reported
P
values result
from two-sided statistical tests. Asterisks indicate signi
fi
cant differences in the
warming effect of the individual management system as compared with their
matched ambient condition.
e
Shift in the effect size of warming on crop yields over
time for conservation and conventional agriculture, respectively. A linear regres-
sion model with two-sided test was used for the statistical analysis, and adjusted
R-squared was used. Relationships are denoted with solid lines and
fi
t statistics (R
2
and
P
values) for each management practice. The solid line represents the sig-
ni
fi
cant linear regression (
P
< 0.05), and the gray shading indicates the 95% con-
fi
dence intervals. All reported
P
values result from two-sided statistical tests where
*
P
< 0.05, **
P
< 0.01, and ***
P
< 0.001. Conserv-Amb, conservation agriculture
without warming; Conserv-Warm, conservation agriculture with warming; Conven-
Amb, conventional agriculture without warming; Conven-Warm, conventional
agriculture with warming. Source data are provided as a Source Data
fi
le.
Article
https://doi.org/10.1038/s41467-024-53169-6
| (2024) 15:8785
3
We also calculated the warming effects on individual soil indica-
tors that contributed to the soil health score between paired warmed
and ambient plots under the two management systems (Fig.
c
–
g;
Supplementary Fig. 3; Supplementary Fig. 4c
–
g; Supplementary
Table 2). Warming enhanced mean weight diameter (MWD) and the
proportion of soil aggregates larger than 0.25 mm (R
0.25
) under con-
servation agriculture but not conventional agriculture, indicating
better water in
fi
ltration, storage and supply (Fig.
c; Supplementary
Figs. 3
–
5). Warming also promoted nutrient cycling, storage and sup-
ply under conservation agriculture, characterized by increased DOC,
SOC, TN, AK, and NO
3
−
-N concentration under warming (Fig.
c; Sup-
plementary Figs. 3
–
5). Conservation agriculture increased MBC and
MBN and suggested greater microbial activity under warming (Fig.
Supplementary Figs. 3
–
5). We calculated the weighting values of indi-
vidual soil properties and recognized DOC, MBC, SOC, and TN as the
key contributors to the soil health score (Supplementary Fig. 3).
Increased DOC, MBC, SOC, and TN were stimulated by warming and
collectively improved the soil health of conservation agriculture
(Fig.
c
–
g; Supplementary Fig. 3; Supplementary Fig. 4c
–
g). We further
assessed the warming effect on DOC, MBC, SOC, and TN over eight
years (Fig.
–
k; Supplementary Fig. 4d
–
k). Across the eight-year
study, the average soil DOC was increased by warming under both
conservation and conventional agriculture (
P
< 0.05; Fig.
d-g; Sup-
plementary Fig. 4d-g; Supplementary Table 1), but changes in MBC and
SOC in response to warming varied depending on soil management at
0
–
5 cm depth (
P
< 0.05; Fig.
d, f; Supplementary Fig. 4d, f; Supple-
mentary Table 1). Warming increased MBC and SOC under conserva-
tion agriculture but not under conventional agriculture (
P
< 0.05;
Fig.
e, f; Supplementary Table 1). Moreover, the positive effects of
warming on MBC and SOC strengthened with time under conservation
agriculture (
P
< 0.05; Fig.
h
–
k), indicating a cumulative bene
fi
t of
conservation agriculture over time for these soil carbon pools.
Fig. 2 | Effects of warming and management on soil attributes and soil health
score at 0-5 cm soil depth. a
Two dimensions of Principal Component Analysis
(PCA) for eigenvalues of the seventeen soil attributes, including MWD, R
0.25
, SM,
BD, pH, DOC, SOC, NH
4
+
-N, NO
3
-
-N, DON, TN, AP, TP, AK, TK, MBC, and MBN. All
parameters were analyzed based on soil sampling in 2020 (
n
= 4 independent soil
samples per treatment).
b
Effects of warming and management on soil health score.
Data are presented with mean values ± s.e.m. Statistical analysis was performed
using two-way ANOVA analysis. Soil health score was evaluated based on soil
sampling in 2020 (
n
= 4 independent soil samples per treatment).
c
Estimates of the
warming effects on soil attributes depending on management. The effect size was
estimated by Cohen
’
d
. Data are presented with mean values ± s.e.m. Statistical
analysis was performed using two-way ANOVA analysis (
n
= 4 independent soil
samples per treatment).
d
–
g
Average of key soil attributes over eight years deter-
mined using a linear mixed model. Statistical signi
fi
cance is based on Wald type II
χ
²
tests (
n
= 24 independent soil samples per treatment). Boxplots display the mean
(horizontal line), the 25th and 75th percentiles (colored box), the minimum and
maximum (whiskers).
h
–
k
Temporal changes of warming effects on key soil
properties over time depending on management. The effect size was estimated by
Cohen
’
d
. The solid line represents the signi
fi
cant linear regression (
P
< 0.05), and
the gray shading indicates the 95% con
fi
dence interval (i.e., error bands represent
slopes ± 95% con
fi
dence intervals). All reported
P
values result from two-sided
statistical tests where *
P
< 0.05, **
P
< 0.01, and ***
P
< 0.001. Conserv-Amb, con-
servation agriculture without warming; Conserv-Warm, conservation agriculture
with warming; Conven-Amb, conventional agriculture without warming; Conven-
Warm, conventional agriculture with warming. MWD, mean weight diameter; R
0.25
,
aggregate content with particle size larger than 0.25 mm; SM soil moisture, BD bulk
density, DOC dissolved organic carbon, SOC soil organic carbon, NH
4
+
-N ammo-
nium, NO
3
−
N nitrate, DON dissolved organic nitrogen, TN total nitrogen, AP avail-
able phosphorus, TP total phosphorus, AK available potassium, TK total potassium,
MBC microbial biomass carbon, MBN microbial biomass nitrogen. Source data are
provided as a Source Data
fi
le.
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https://doi.org/10.1038/s41467-024-53169-6
| (2024) 15:8785
4
Effects of warming and management on microbial diversity and
community composition
Soil fungal and bacterial diversity and community composition were
determined across eight years (Fig.
; Supplementary Fig. 6; Supple-
mentary Tables 2
–
3). Our results based on NMDS ordinations and
nested PERMANOVA analysis indicated that soil fungal and bacterial
communities at 0-5 cm depth were affected by management
(R
2
= 0.089
–
0.103,
P
< 0.001), warming (R
2
= 0.014
–
0.017,
P
< 0.01),
and their interaction (R
2
= 0.009
–
0.010,
P
< 0.05) (Fig.
a; Supple-
mentary Table 3). The microbial diversity over eight years, as esti-
mated by richness, was further assessed through linear mixed
modelling (Supplementary Table 1). The soil bacterial richness was not
affected by management, warming, and their interaction (Supple-
mentary Table 1). The total soil fungal richness was in
fl
uenced by
interactions between warming and management (
P
< 0.05; Fig.
Supplementary Table 1), indicating differential responses of the soil
fungal community to warming under conservation and conventional
agriculture. Warming decreased fungal richness by 4.1% compared to
the no-warming treatment under conservation agriculture (
P
< 0.05),
but not under conventional agriculture (Fig.
c). Speci
fi
cally, the
richness of fungal functional guilds was in
fl
uenced by management,
but not warming (Fig.
c; Supplementary Table 1). Conservation agri-
culture supported the greater richness of AMF (
P
< 0.001; Supple-
mentary Table 1) and lesser richness of saprogens and pathogens
(
P
< 0.05; Supplementary Table 1) at 0
–
5 cm soil depth (Fig.
c).
Warming decreased the richness of saprogens under conservation
agriculture only (
P
< 0.05; Supplementary Table 1) (Fig.
c).
Soil fungal and bacterial communities in the 5
–
15 cm soil depth
were affected by management (R
2
= 0.061
–
0.072,
P
< 0.001), warming
(R
2
= 0.024,
P
< 0.01), and their interaction (R
2
= 0.023,
P
< 0.05) (Sup-
plementary Fig. 6b; Supplementary Table 3). Bacterial richness was
only affected by management and was greater under conventional
agriculture (
P
< 0.01; Supplementary Fig. 6c; Supplementary Table 1).
Total fungal richness was not affected by management, but richness of
AMF and saprogen varied between management systems (Supple-
mentary Fig. 6b; Supplementary Table 1). Conservation agriculture
supported more AMF (
P
< 0.001; Supplementary Table 1) and less
saprogens (
P
< 0.05; Supplementary Fig. 6c; Supplementary Table 1).
Warming decreased total fungal richness (
P
< 0.01) and decreased
saprogens (
P
< 0.001) and pathogens (
P
< 0.01) under conventional
agriculture (Supplementary Fig. 6c; Supplementary Table 1).
Soil health and the microbiome contributed to wheat yields
under conservation agriculture with warming
We selected the best soil properties to predict crop yield using linear
mixed models (Fig.
; Supplementary Figs. 7
–
8). The MBC and rich-
ness of saprogens at 0
–
5 cm soil depth, and fungal community
composition at 5
–
15 cm soil depth, were most closely linked to wheat
yields under conservation agriculture (Fig.
a, b; Supplementary
Fig. 7). There were corresponding strong positive correlations
Fig. 3 | Effects of warming and management on microbial diversity and com-
munity composition at 0-5 cm soil depth. a
,
b
Nonmetric multidimensional
scaling (NMDS) ordination of soil fungal and bacterial communities based on the
Bray-Curtis dissimilarity. Statistical analysis was performed using nested permu-
tational multivariate analysis of variance (nested PERMANOVA) analysis.
c
Effects of
warming and management on microbial richness of soil total fungi, fungal guild,
and bacteria. Boxplots display the mean (horizontal line), the 25th and 75th per-
centiles (colored box), the minimum and maximum (whiskers). Data were analyzed
based on eight sampling years (
n
= 24 independent soil samples per treatment).
Statistical analysis was performed using linear mixed model with sampling time as
random factors. Statistical signi
fi
cance is based on Wald type II
χ
² tests. All reported
P
values result from two-sided statistical tests where *
P
< 0.05, **
P
< 0.01, and
***
P
< 0.001. Conserv-Amb, conservation agriculture without warming; Conserv-
Warm, conservation agriculture with warming; Conven-Amb, conventional agri-
culture without warming; Conven-Warm, conventional agriculture with warming.
Source data are provided as a Source Data
fi
le.
Article
https://doi.org/10.1038/s41467-024-53169-6
| (2024) 15:8785
5
between wheat yields and MBC, but negative correlations with
saprogen richness (Fig.
b). Soil MBC stimulated by warming,
reductions in saprogen richness and variations of the fungal com-
munity contributed most to wheat yields under conservation agri-
culture (Fig.
b; Supplementary Fig. 7). In addition, the richness of
soil bacteria and pathogens also affected wheat yields under con-
servation agriculture (Fig.
a; Supplementary Fig. 7). In contrast, the
soil microclimate (temperature and moisture) and DOC were most
relevant to wheat yield under conventional agriculture (Fig.
a, c;
Supplementary Fig. 7). Summer maize yields were also affected by
soil properties, but the measured soil variables did not lead to
changes in maize yields under warming (Supplementary Fig. 8). In
conclusion, crop yields under conservation agriculture were more
in
fl
uenced by the soil microbiome (including MBC, fungal richness,
and fungal community composition) than under conventional
agriculture.
The key indicators of soil health were also affected by soil
microbial richness and community composition (Fig.
d, e; Supple-
mentary Fig. 9), especially under conservation agriculture. Soil MBC
and SOC were more relevant to soil fungal richness or community
composition compared with bacteria under conservation agriculture
(Fig.
d, e; Supplementary Fig. 9). The intense relationship between
soil
fungi
and carbon emphasized the
microbially-mediated
mechanisms that underlie soil carbon accrual observed under con-
servation agriculture.
Discussion
This study provides rare empirical evidence for the advantages of
conservation agriculture to improve soil health and sustain crop yields
in a warming world and emphasizes the potential of conservation
agriculture in long-term food security. The bene
fi
ts of conservation
agriculture for multiple soil functions have been reported
, but the
interactive effects of management practices and climate warming on
the maintenance of soil health and crop productivity have not been
tested before in arable land in situ. Both crop yields and key indicators
of soil health (e.g., SOC and MBC) strengthened over time in response
to warming, but only under conservation agriculture. These bene
fi
cial
responses were tightly linked to soil fungal richness and community
composition. In summary, we provide evidence that conservation
agriculture can support greater soil health without compromising crop
yields under long-term warming compared to conventional agriculture
and reveal a key role of the soil microbiome.
The improvement of soil health to deliver resilient
‘
climate-smart
’
farming systems is recognized as a fundamental strategy that is vital to
mitigate and adapt to the adverse effects of climate warming to
maintain global food security
,
. We found that conservation
Fig. 4 | Effects of abiotic and biotic factors on winter wheat yield and key
indicators of soil health of 0-5 cm soil depth. a
Individual effect of the model
predictors to winter wheat yield under conservation and conventional agriculture,
respectively. Red, green and orange colors represent microclimate, soil, and
microbial factors, respectively.
b
,
c
Correlations between wheat yield and key
predictors under conservation and conventional agriculture. Solid line in each
panel shows signi
fi
cant model
fi
t using linear mixed-effect regression (
P
< 0.05),
and the shading around the
fi
tted line represents the 95% con
fi
dence intervals (i.e.,
error bands represent slopes ± 95% con
fi
dence intervals).
d
,
e
Correlations between
soil microclimate and microbial diversity and key indicators of soil health at 0
–
5 cm
soil depth under conservation and conventional agriculture. The color denotes the
correlation coef
fi
cient determined by the linear mixed-effects model. Statistical
signi
fi
cance is based on Wald type II
χ
² tests. ST soil temperature, SM soil moisture,
DOC dissolved organic carbon, MBC microbial biomass carbon, SOC soil organic
carbon, TN total nitrogen. Bacteria, Fungi, AMF, Saprogen, and Pathogen indicated
richness of microbial group. F_PC1, F_PC2, B_PC1, and B_PC2 indicated fungal and
bacterial community composition, respectively. All reported
P
values result from
two-sided statistical tests where *
P
< 0.05, **
P
< 0.01, and ***
P
< 0.001. Source data
are provided as a Source Data
fi
le.
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https://doi.org/10.1038/s41467-024-53169-6
| (2024) 15:8785
6
agriculture improved a suite of soil properties involved in key soil
functions (water in
fi
ltration and storage, carbon and nutrient cycling,
and microbial activity) after eight years of warming (Figs.
). Soil C is
considered a principal indicator of soil health and agronomic sus-
tainability due to its impact on physical, chemical and biological
properties
,
,
. Warming can promote plant carbon inputs (includes
root biomass, exudation, and crop resides) to soil, thereby increasing
substrates for the soil microbial community
,
. In our study, con-
servation agriculture increased all soil C pools (DOC, MBC, and SOC)
compared to conventional agriculture (Fig.
). Moreover, we observed
positive warming effects on SOC and MBC under conservation agri-
culture that increased linearly with experimental duration (Fig.
i, j),
indicating a long-term advantage of conservation agriculture in sup-
porting microbial activity and contributing to soil carbon accrual
,
Reduced soil disturbance under conservation agriculture promotes
soil aggregate formation and stability indicated by MWD and R
0.25
(Fig.
c). Soil aggregate stability is considered a useful indicator of soil
structure that supports multiple soil functions including water trans-
port and storage and the provision of stable microbial habitats con-
ducive to the preferential accumulation of microbial biomass and
necromass formation and further SOC accrual
. The increased soil
aggregate stability can enhance water conservation and microbial
variables, that directly facilitate nutrient cycling and soil carbon
storage
. The tighter correlations between soil fungal richness and
community composition, rather than bacteria (Fig.
), suggested soil
fungi may be the major contributor to SOC formation and
accumulation under conservation agriculture. Collectively, conserva-
tion agriculture is a sustainable management and performs better in
adapting climate warming than conventional agriculture in Northern
China Plain. Previous studies found that conservation agriculture
accumulates soil C at the surface rather than the whole soil pro
fi
or even changed distribution of C in the soil pro
fi
le instead of
increasing the total SOC
. Yet our long-term monitoring only focu-
ses on C accumulation at surface soil (0
–
15 cm) and may overestimate
bene
fi
ts in C sequestration over the whole soil pro
fi
le. The changes of
SOC in the deeper soil pro
fi
les need to be pay more attention in the
future research.
Globally, crop yields under conservation agriculture are estimated
to be 2.5% less than those of conventional agriculture
, but we did not
observe reductions in wheat or maize under conservation agriculture
in either ambient or warming conditions (Fig.
; Supplementary Fig. 1).
Previous studies in the tropics have reported warming decreased crop
yields
,
. We found warming increased wheat yields by 9.3% and 11.2%
under conservation and conventional agriculture (Fig.
a), respec-
tively, on temperate semi-arid climate of the North China Plain. Here,
warming extends the growing season allowing earlier planting and
later harvests, and can reduce cold injury and frost damage in
seedlings
, which directly improves crop growth and productivity
In accordance with predictions that crop yields would be enhanced by
warming in middle-to-high latitude regions
,
, we observed a positive
relationship between wheat yields and soil temperature under con-
ventional agriculture (Fig.
a). By comparison, increased wheat yields
under conservation agriculture and warming were most strongly
associated with improved soil microbial quality indicated by microbial
biomass carbon (MBC). Positive correlations between crop pro-
ductivity and MBC are reported
because the microbial biomass is
not only a labile carbon pool but also a nutrient reservoir
. The soil
microenvironment (soil and temperature) was also relatively impor-
tant for wheat yields under conservation agriculture with warming
(Fig.
a, b) because no tillage and residue retention moderate soil
temperature and retain soil moisture (Fig.
). Importantly, we also
observed that the warming-induced positive effects on wheat yield
strengthened with time (Fig.
b). Warming had no effect on maize
yields regardless of management type (Supplementary Fig. 1); the
maize growing season is in summer (June
–
September) and C4 phy-
siology is adapted to warmer temperatures and drier conditions
. The
results for wheat emphasize the vital role of soil health in reducing the
sensitivity of production of this key cereal crop to long-term changes
in climate and reducing climate-driven yield variability
. In con-
sideration of undifferentiated wheat yield and higher maize yield
compared to conventional agriculture both under ambient and
warming conditions, we assumed that conservation agriculture per-
formed better in productivity in a warmer world.
Soil microbiota are prominent actors in SOC accrual, decom-
position and nutrient cycling
, and consequently strongly in
fl
uence
agroecosystem services
,
, so it imperative to assess their response to
long-term warming in situ. Reduced soil biodiversity is reported in
some natural ecosystems under warming, mainly due to environ-
mental
fi
ltration by temperature and soil moisture reduction
,
We observed a reduction of total fungal richness, but not of bacteria, in
soil from the 0
–
5 cm depth under conservation agriculture (Fig.
Supplementary Fig. 6), corresponding to previous studies showing
greater sensitivity of fungi to warming compared to bacteria
. The
decrease of fungal richness was predominantly a consequence of a
decrease in saprogen richness under conservation agriculture with
warming (Fig.
; Supplementary Fig. 6). Less saprogen richness may be
linked to slower rates of organic matter decomposition
that con-
tributes to SOC accrual in conservation agriculture under warming
(Fig.
), that supports yield increase through the net effect on soil
health (Fig.
a, b). Soil AMF can enhance plant nutrient uptake and
reduce plant stress
, and were more diverse under conservation
Fig. 5 | Conceptual model illustrating shifts of soil health, microbial diversity,
and crop yield under conservation agriculture response to warming.
Experi-
mental warming triggered shifts in soil fungal richness and community composi-
tion and resulted in an improved soil health under conservation agriculture,
including increased water in
fi
ltration and storage, carbon and nutrient cycling, and
microbial activity. The improvement in soil health and shifts in soil fungal diversity
contributed to higher crop yields under conservation agriculture. The up or down
arrows showed increased or decreased soil health indicators response to warming
under conservation agriculture. The linear trends indicated warming effects on
crop yields and soil health indicators over time under conservation agriculture.
MWD, mean weight diameter; R
0.25
, aggregate content with particle size larger than
0.25 mm; DOC dissolved organic carbon, SOC soil organic carbon, NO
3
−
nitrate, AK
available potassium, MBC microbial biomass carbon, MBN microbial biomass
nitrogen. The soil microbiome drawing elements were produced using
fi
gdraw.com.
Article
https://doi.org/10.1038/s41467-024-53169-6
| (2024) 15:8785
7
agriculture with warming (Supplementary Table 1). Soil-borne plant
pathogens were less diverse under conservation agriculture with
warming, providing further advantages for crop production and dis-
ease management
,
,
. Overall, the direct and indirect effects of
conservation agriculture on the fungal community and plant patho-
gens were related to enhanced crops yield and soil health.
In summary, this study provides empirical evidence for the
potential bene
fi
ts of conservation agriculture for long-term sustain-
able food production because improved soil health improves resi-
lience to the effects of climate warming through its effects on physical,
chemical and biological soil properties. However, we recognize that
local climatic conditions are an important driver of soil health and crop
yield
and careful regional assessments are needed when considering
the potential consequences of adopting conservation agriculture
We propose that our
fi
ndings may be generalized to other regions
where water does not limit productivity (e.g., irrigated regions). As
illustrated in Fig.
, the combination of conservation agriculture and
experimental warming for eight years on the temperate semi-arid cli-
mate of the North China Plain stimulated an increase in soil health
indicators indicating improved water in
fi
ltration and storage (soil
aggregate stability), carbon and nutrient cycling, and microbial activ-
ity. The improvement in soil health and shifts in soil fungal diversity
(less saprogen richness, increased AMF and less plant pathogens)
supported similar crop yields to conventional agriculture. These
fi
ndings emphasize the potential cumulative bene
fi
ts of conservation
agriculture with time and strengthen the evidence for conservation
agriculture as
‘
climate-smart
’
management tool to adapt to climate
warming and ensure good security by improving soil health.
Methods
Study sites
This study is based on a long-term climate change
fi
eld trial located at
North China Plain at Yucheng Comprehensive Experiment Station of
Chinese Academy of Science (36° 50
’
N, 116° 34
’
E, elevation is 20 m).
The study region has a temperate semi-arid climate with an annual
mean temperature of 13.6 °C, and annual mean precipitation of
575 mm with 70% occurring between June and September. The soil
type of this site is Calcaric Fluvisol (FAO-UNESCO system) with typical
soil texture 12% sand, 66% silt, 22% clay, and a mean pH of 7.1. The
experiment was conducted at a crop rotation system (winter wheat
(
Triticum aestivum
L.)-summer maize (
Zea mays
L.)) since 2010.
Experimental design and soil sampling
The system included four treatments: conventional agriculture with
and without warming (Conven-Warm and Conven-Amb), conservation
agriculture with and without warming (Conserv-Warm and Conserv-
Amb). A randomized complete block design randomized with four
replicates was employed. The warmed soils (+2 °C) were continuously
heated (since February, 2010) using an MSR-2420 infrared heater
(Kalglo Electronics Inc, Bethlehem, PA, USA) suspended approximately
3 m above the ground to achieve a surface soil warming of 2 °C, which
is predicted by IPCC greenhouse gas scenarios rates for northern
China
. The control plots (i.e., without warming) were treated with a
‘
dummy
’
infrared heater to simulate the shading effects of the heaters.
There was a 5 m border between adjacent blocks and at least 10 m
between the plots to avoid heating the control plots by the infrared
radiators.
The size of each plot was 2 m × 2 m. Winter wheat was seeded
between 10 and 15 October and harvested during the
fi
rst 10 days of
June. Then summer maize was seeded 5 days later and harvested
during the
fi
rst 10 days of October. After harvest, in the conventional
agriculture treatment, the residues were removed and the soil was
cultivated with a rotary tiller annually. In the conservation agriculture
treatment, all residues were chopped to approximately 5 cm in length
and retained on the soil surface, and adopted no tillage. The
conventional and conservation agriculture treatments had the same
total
N
application rate, but part of the
N
application was from dif-
ferent sources. The total
N
application for conventional agriculture
and conservation agriculture treatments in winter wheat growing
seasons was 285 kg N ha
−
1
yr
−
1
following optimal application of
fertilization
. For conservation agriculture, the
N
input was
112.5 kg ha
−
1
of mineral fertilizer, 124.5 kg ha
−
1
of urea, and 48 kg ha
−
1
residue N. For conventional agriculture, the N input was 112.5 kg ha
−
1
of
mineral fertilizer, and 172.5 kg ha
−
1
of urea. The total N application for
conventional agriculture and conservation agriculture in summer
maize growing seasons was 207 kg N ha
−
1
yr
−
1
. For conservation agri-
culture, the N input was 175 kg ha
−
1
of urea and 32 kg ha
−
1
residue N. For
conventional agriculture, the
N
input was 207 kg ha
−
1
of urea. All other
management procedures were the same for conventional agriculture
and conservation agriculture.
Three composite soil samples from 0
–
5 and 5
–
15 cm soil depths
were collected for each plot after harvest of winter wheat from 2010 to
2019. Composite samples were collected by hand augur consisting of
fi
ve randomly selected soil cores in each plot, then mixed together to
make a composite sample. All samples were passed through a 2 mm
sieve for subsequent analysis. Soil temperature (ST) and volumetric
soil moisture (SM) at 0
–
15 cm depth was monitored by PT100 ther-
mocouples and FDS100 soil moisture sensors (Unism Technologies
Incorporated, Beijing), respectively.
Assessing crop productivity
Crop yields were determined through harvest of each plot by hand. At
physiological maturity of each crop, 1 m
2
of crop was harvested for
each plot and the sample was threshed using a static machine. Crop
yield was measured after air-drying to a constant value. Plot yield was
recalculated on a dry matter basis and the harvested area was used to
determine yield per unit area (t ha
−
1
).
Assessing soil health
Seventeen soil health indicators were measured as variables to proxy
soil physical, chemical, and biological attributes in 2020 to evaluate
cumulative changes after long-term experimental warming. Soil sam-
ples (0
–
5 cm and 5
–
15 cm depth) were collected after the harvest of
winter wheat to measure soil properties including: aggregate mean
weight diameter (MWD), aggregate content with particle size larger
than 0.25 mm (R
0.25
), soil moisture (SM), bulk density (BD), pH, dis-
solved organic carbon (DOC), soil organic carbon (SOC), NO
3
−
-N, NH
4
+
-
N, dissolved organic nitrogen (DON), total nitrogen (TN), available
phosphorus (AP), total phosphorus (TP), available potassium (AK),
total potassium (TK), microbial biomass carbon (MBC) and microbial
biomass nitrogen (MBN). Soil samples (0
–
5 cm and 5
–
15 cm depth)
were collected after harvest of winter wheat to measure soil properties.
Soil aggregate mean weight diameter (MWD) and content with
particle size larger than 0.25 mm (R
0.25
) was obtained using wet siev-
ing. Soil pH was measured using a 1:2.5 (w/v) soil to 0.01 M CaCl
2
ratio
with a glass electrode. Soil bulk density (BD) was obtained from oven
dry mass relative to the sample volume. The subsamples for SOC and
TN analysis were air-dried at room temperature and determined using
elemental analysis (Vario EL III, Elementar, Germany) and Kjeldahl
digestion
. The concentration of DOC and dissolved nitrogen (DN)
was measured according to Jones and Willett
:
fi
eld-moist soil samples
(equivalent to 15 g oven-dried soil) were extracted with 60 ml of
0.05 mol/L K
2
SO
4
(soil to solution ratio 1:4) for 1 h, and the extract was
passed through a 0.45 mm membrane
fi
lter and analyzed for DOC and
DN using a Multi 3100 N/C TOC analyzer (Analytik, Germany). Soil NH
4
+
and NO
3
−
were determined by extraction with 2 mol L
−
1
KCl. The DON
concentration was calculated as DN minus NH
4
+
-N and NO
3
−
-N content.
Soil TP was measured by colorimetric analysis after digestion with
sulfuric acid and perchloric acid. Soil AP was determined by the Olsen
method. Soil TK and AK were determined by
fl
ame photometer. The
Article
https://doi.org/10.1038/s41467-024-53169-6
| (2024) 15:8785
8
content of MBC and MBN was determined according to method of Wu
et al.
: fresh soil samples were fumigated with chloroform (48 h) and
subsequent extracted with 0.5 M K
2
SO
4
(soil to solution ratio 1:4) and
organic carbon and nitrogen in the extractant were measured using an
elemental analyzer (Vario PYRO Cube, Hanau, Germany).
We used the Cornell Soil Health Assessment (CSHA) scoring
method to calculate soil health scores
. The total data set, including
17 soil indicators (physical attributes: MWD, R
0.25
, SM, BD; chemical
attributes: soil pH, SOC, DOC, TN, DON, NH
4
+
-N, NO
3
−
-N, AP, TP, AK,
TK; biological attributes: MBC and MBN), were normalized as indivi-
dual CSHA scores
. The weighting value of individual soil indicators
was based on PCA of all soil indicators (Supplementary Fig. 2), repre-
senting the sum of the eigenvectors derived from the
fi
rst three prin-
cipal components, which were selected based on Kaiser
’
s cut-off
(eigenvalues > 1). These
fi
rst three principal components cumulatively
accounted for over 70% of variance, capturing most of the variation
among the soil indicators. The overall soil health score (%) was com-
puted as a weighted average of all individual CSHA scores as
follows
:
Soil health score
=
A
1
×
w
1
+
A
2
×
w
2
+
+
A
n
×
w
n
w
1
+
w
2
+
+
w
n
ð
1
Þ
where
A
is the CSHA score for each individual soil indicator, and
w
is
the weighting value of the soil indicators (Supplementary Fig. 2).
Amplicon sequencing and soil biodiversity
To discern whether climate warming and management practices affect
soil bacterial and fungal diversity, soil DNA was extracted from 0.25 g
soil with PowerSoil Isolation kit (MoBio Laboratories, Carlsbad, CA,
USA) following the modi
fi
ed manufacturer
’
s recommendations. DNA
concentrations were quality checked (NanoDrop One; Thermo Fisher
Scienti
fi
c, Waltham, MA) and quanti
fi
ed (PicoGreen assay; Quant-iT
™
PicoGreen® dsDNA Reagent, Life Technologies). Finally, all DNA sam-
ples were stored at
−
80 °C until sequencing analysis.
The library construction and sequencing of the 16S rRNA gene and
ITS gene were performed. The universal primer sets, 515 F (5
’
-
GTGCCAGCMGCCGCGC-3
’
)
and
907 R
(5
′
-CCGTCAATTCMTT-
TRAGTTT-3
′
) targeting the V4-V5 hypervariable regions of the bacterial
16S rRNA gene, and gITS7F (5
’
-GTGARTCATCGARTCTTTG-3
’
) and
ITS4R (5
’
-TCCTCCGCTTATTGATATGC-3
’
) for the fungal IT, were used
in this study. After PCR and puri
fi
cation, a DNA library was constructed
and run on an Illumina Hiseq platform at MagiGene Biotechnology Co.,
Ltd. (Guangzhou, China).
The raw sequence data were processed with the USEARCH (ver-
sion 11.0.667)
software for quality
fi
ltering and assembling of pair-
end reads. Strict quality control steps were applied to the sequencing
data. First, assembled contigs without exact match to one of the bar-
codes sets or primers (degenerate bases were not taken into con-
sideration) were discarded. Subsequently, the remaining sequences
were clustered into high accuracy exact amplicon sequence variants
(ASVs) with the UNOISE
. Singletons that found only once across all
samples were removed from subsequent analyses. Taxonomic classi-
fi
cation of each ASV of bacteria and fungi was determined using the
Ribosomal Database Project (RDP) classi
fi
er with a con
fi
dence
threshold of 0.5 against the SILVA
and the UNITE
database,
respectively. ASVs that were not classi
fi
ed into bacteria or fungi were
removed. To normalize samples to the same total read abundance, an
average of 26,000 and 20,000 sequence reads per sample were ran-
domly selected (resampled) for each sample obtained for 16S rRNA
gene and ITS, respectively. Bacterial and fungal richness was calculated
based on the phylogenetic trees and ASV tables using the R package
picante
.
We obtained the relative abundance of potential arbuscular
mycorrhizal mutualists, saprotrophs, and plant pathotrophs from
amplicon sequencing by parsing the soil fungal phylotypes using
FUNGuild database
. Fungi representing <1% of the ASVs were not
considered. Only highly probable and probable guilds were used in
these analyses.
Statistical analyses
Linear mixed models (LMMs) were used to assess the effects of
warming and management practices on soil properties, biodiversity,
and crop yield measured repeatedly across eight years
. In the LMMs,
warming (0 for ambient temperature and 1 for warming) and man-
agement practices (0 for conservation agriculture and 1 for conven-
tional agriculture) were considered as
fi
xed effects, while sampling
time (year) was termed as random intercept effects (y ~ warming ×
management + (1 | year)). Wald Type II
χ
² tests were used to calculate
the
P
values from the LMMs. The
lme4
R package was used to imple-
ment LMMs. Differences between four treatments (Conven-Amb,
Coven-Warm, Conserv-Amb, and Conserv-Warm) were estimated
through pairwise comparison with estimated marginal means. The
emmeans
R package was use to implement pairwise comparison. Two-
way ANOVA was used to evaluate the effects of warming and man-
agement practices on soil parameters and soil health score. To evalu-
ate the effects size of warming on crop yield, soil health and each soil
indicator, we calculated Cohen
’
s
d
from different management prac-
tices by comparing them against the common control without warm-
ing through
effsize
R package. The temporal changes of warming
effects on each soil indicator and crop yield were estimated through a
linear regression.
Non-metric multidimensional scaling (NMDS) based on Bray-
Curtis dissimilarity and nested permutational multivariate analysis of
variance (nested PERMANOVA) was used to illustrate the effects of
warming and management practices on soil microbial community
composition through
vegan
R package. To link the soil microbial
diversity and community composition to soil health and crop yield,
the correlations were tested using the linear mixed-effects model, in
which sampling year were termed as random intercept effects. The
correlation r was represented by the regression coef
fi
cients in the
LMMs, and Wald type II
χ
² tests were used to calculate the
P
values
from the LMMs. Hierarchical partitioning analysis to calculate the
individual contributions of each predictor was conducted with the
glmm.hp
R package to determine the relative importance of each
environmental factor
. All the analyses were performed in
the R 4.3.0.
Reporting summary
Further information on research design is available in the Nature
Portfolio Reporting Summary linked to this article.
Data availability
The DNA sequences of the 16S rRNA gene and ITS amplicons in this
study have been deposited in the National Center for Biotechnology
Information (NCBI) under project accession numbers
Silva database is available at
. UNITE database
is available at
. Source data are provided with
this paper.
Code availability
The analysis code that supports the
fi
ndings of this study is available
on GitHub (
https://github.com/bio-carbon/warming_soil_health
)
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Acknowledgements
This study was supported by the National Natural Science Foundation of
China (grant nos. U23A20158, Z.L.C., and 32071629, J.T.), National Key
R&D Program of China (2023YFD1901500, J.T.), 2115 Talent Development
Program of China Agricultural University and Beijing Advanced Dis-
ciplines, F.S.Z., Z.L.C., J.B.Z., J.T., and the China Postdoctoral Science
Foundation (2022M71339, J.L.T.). We thank the drawing tools provided
by Figdraw.
Author contributions
All authors contributed intellectual input and assistance to this study
and manuscript preparation. T.J., Z.L.C., and M.D.B. designed the origi-
nal concept and experiment strategy. J.L.T. and R.X.H. collected the
data. J.L.T. and J.T. analyzed the data. R.X.H. carried the
fi
eld experi-
ment. J.L.T., J.T., J.A.J.D., G.Y.Z., Y.K., J.B.Z., Z.L.C., F.S.Z., and M.D.B.
drafted the manuscript and all authors involved in critical revisions and
gave
fi
nal approval for publication.
Competing interests
The authors declare no competing interests.
Additional information
Supplementary information
The online version contains
Supplementary Material available at
https://doi.org/10.1038/s41467-024-53169-6
Correspondence
and requests for materials should be addressed to
Jing Tian, Zhenling Cui or Manuel Delgado-Baquerizo.
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