Next Article in Journal
Microbiological Ecological Surveillance of Zoonotic Pathogens from Hamadryas Baboons in Southwestern Saudi Arabia
Next Article in Special Issue
Synthetic Microbial Communities Enhance Pepper Growth and Root Morphology by Regulating Rhizosphere Microbial Communities
Previous Article in Journal
Biotic Interaction Underpins the Assembly Processes of the Bacterial Community Across the Sediment–Water Interface in a Subalpine Lake
Previous Article in Special Issue
Metagenomic Analysis Reveals the Effects of Different Land Use Types on Functional Soil Phosphorus Cycling: A Case Study of the Yellow River Alluvial Plain
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Microorganisms
Volume 12
Issue 12
10.3390/microorganisms12122419
microorganisms-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Effects of Increasing the Nitrogen–Phosphorus Ratio on the Structure and Function of the Soil Microbial Community in the Yellow River Delta

by
Jinzhao Ma
1,
Zehao Zhang
1,2,
Jingkuan Sun
1,3,*,
Tian Li
1,
Zhanyong Fu
1,
Rui Hu
1 and
Yao Zhang
1
1
Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Shandong University of Aeronautics, Binzhou 256603, China
2
Institute of Restoration Ecology, China University of Mining and Technology-Beijing, Beijing 100083, China
3
National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying 257347, China
*
Author to whom correspondence should be addressed.
Microorganisms 2024, 12(12), 2419; https://doi.org/10.3390/microorganisms12122419
Submission received: 22 October 2024 / Revised: 21 November 2024 / Accepted: 22 November 2024 / Published: 25 November 2024
(This article belongs to the Special Issue Soil Microbial Carbon/Nitrogen/Phosphorus Cycling)
Browse Figures
Versions Notes

Abstract

Nitrogen (N) deposition from human activities leads to an imbalance in the N and phosphorus (P) ratios of natural ecosystems, which has a series of negative impacts on ecosystems. In this study, we used 16s rRNA sequencing technology to investigate the effect of the N-P supply ratio on the bulk soil (BS) and rhizosphere soil (RS) bacterial community of halophytes in coastal wetlands through manipulated field experiments. The response of soil bacterial communities to changing N and P ratios was influenced by plants. The N:P ratio increased the α-diversity of the RS bacterial community and changed the structure of the BS bacterial community. P addition may increase the threshold, causing decreased α-diversity of the bacterial community. The co-occurrence network of the RS community is more complex, but it is more fragile than that of BS. The co-occurrence network in BS has more modules and fewer network hubs. The increased N:P ratio can increase chemoheterotrophy and denitrification processes in the RS bacterial community, while the N:P ratio can decrease the N-fixing processes and increase the nitration processes. The response of the BS and the RS bacterial community to the N:P ratio differed, as influenced by soil organic carbon (SOC) content in terms of diversity, community composition, mutualistic networks, and functional composition. This study demonstrates that the effect of the N:P ratio on soil bacterial community is different for plant roots and emphasizes the role of plant roots in shaping soil bacterial community during environmental change.

1. Introduction

N and P are the major limiting elements in terrestrial ecosystems and have received widespread attention. Previous studies have suggested that plant growth at high latitudes is usually limited by N, while at low latitudes, it is limited by P [1]. However, atmospheric N deposition continues to increase due to human activities, resulting in a shift from N-limited to P-limited plant growth at high latitudes [2,3]. The N input due to human activities increases more rapidly than the P input [4]. Unparallel N and P inputs may accelerate the bioavailability limitation of P. There are various sources of N, including the burning of fossil fuels, industrial emissions, and the abuse of N-rich fertilizers [5]. The P input has a single source, including mainly the weathering of rocks, which limits the amount of P input [6]. Although human activities have also increased the P content in soil and water, the overall increase in the P input is still too small in comparison with the N input [4]. The effects of the increased N:P ratio imbalance have been observed and reported in soil bacterial community structure and function, as well as in plant community species composition [4,7]. The impact of the continued increase in the N and P imbalance is being magnified. Currently, more and more studies are focusing on the effect of the N:P ratio [8].
Soil bacteria are considered to be important drivers in regulating biogeochemical cycles and the decomposition of plant litter and SOC in terrestrial ecosystems, and they play an important role in maintaining the structure and function of subsurface ecosystems [9]. Studies have shown the effects of N deposition on bacterial communities, and most of these studies found negative effects of N deposition on bacterial communities [10,11]. However, it was also found that N addition had positive effects on the bacterial community due to the fact that N addition increased carbon release from plant roots and alleviated carbon limitation during microbial growth [12]. P addition was found to mitigate the negative effects of N deposition on microbial communities, which is a process indirectly caused by P addition affecting soil carbon cycling and chemistry [13]. In contrast, in N-rich tropical rainforest areas, P addition had insignificant effects on bacterial community diversity but significantly changed the bacterial community composition [14]. However, there are fewer studies examining the effects of the N and P input ratio (due to N and P inputs) on bacterial communities and mostly focus on plant and soil C cycles. The response mechanism of the bacterial community structure and characterization to the imbalanced increase in the soil N:P ratio is still unclear.
In ecosystems where N and P are co-limited, plant productivity is usually determined by the N:P ratio [15]. The low level of the N:P ratio might not cause P limitation in plant growth [16], while at high levels of N input, the soil-available P (AP) content restricted plant growth [16]. Although N addition also induces phosphatase activity and thus increases P availability, the increase is insufficient to balance the increase in P demand [17]. Changes in the N:P ratio of terrestrial ecosystems directly affect plant biomass and indirectly affect consumers and decomposers [15]. For example, changes in nutrients can lead to shrinking root systems and reduced fine root biomass, thereby reducing bacterial community diversity [18]. Plants provide a habitat for soil microbial communities, so there may be consistency between the response of soil microbial communities and the response of plants to the N:P ratio [19]. However, there are differences in the physiology and growth strategies between plants and microorganisms, which may also lead to differences in their response to the N:P ratio [19].
The Yellow River Delta (YRD) is the most extensive and youngest coastal wetland [20]. The N:P ratio in the coastal wetlands of the YRD and Bohai Bay are severely imbalanced due to increased atmospheric N deposition, sewage discharge, and the continuous input of inorganic N and inorganic P pollutants from the Yellow River [8,21]. In YRD, studies of N:P ratios have focused on plant community structure and plant ecological stoichiometry [8,22] and mostly analyzed the relationship between soil C, N, and P contents, as well as their stoichiometric ratios and plant biomass, while the study of analyzing their effects on the soil microbial community from the perspective of the growing unbalanced degree of the N:P ratio has not yet been reported. In addition, previous studies have ignored the effects of plants on bacterial communities. In fact, the effects of N on the soil bacterial communities of different plants differ [23]. Under conditions of increased soil N:P imbalance, are there differences in the degree of variability in the N:P imbalance between RS and BS? Assuming there are, how will that affect the soil bacteria around them? What relationship exists among plant and soil N:P imbalances and microbial communities? To deepen our understanding of the effects of N and P ratios on coastal wetlands, an experiment with different N:P addition ratio gradients was set up in the coastal wetlands of the YRD to study (1) the response of soil bacterial communities to N:P input ratios and (2) the difference between the response of plant RS and BS bacterial communities to the N:P ratio by 16s rRNA sequencing from the perspective of α-diversity, community structure, and functional structure. We predicted that changes in the RS and BS bacterial communities are different when faced with changes in N:P ratios.

2. Materials and Methods

2.1. Description of Study Area

The present study was conducted in the YRD wetlands, Dongying, Shandong, China (E 118°44′2″, N 38°1′18″, Figure 1). The YRD enjoys a warm-temperate monsoon climate, with little climatic variation within its borders. The average annual sunshine hours are 2590–2830 h. The average annual temperature is 11.7–12.8 °C. The average annual precipitation is 530–630 mm, with 70% of the rainfall occurring in summer. The average annual evaporation is 1900–2400 mm. Influenced by its geographic location, the soil is dominated by coastal tidal saline soils. The soil type is mainly salinized tidal soil. The soils are sandy and clayey. More than 50% is salinized to varying degrees, and the degree of salinization is relatively high. Influenced by soil salinity, the plants are mainly halophytes, including Suaeda salsa, Aeluropus sinensis (A. sinensis), and Limonium bicolor as the main herbaceous plants; Tamarix chinensis, Periploca sepium Bunge and Apocynum venetum as the main shrubs; and Robinia pseudoacacia, Fraxinus, and Populus as the main trees.
In the YRD, the severe N deposition rate of 2.3 g/m2 has attracted the attention of scholars, and this rate is always increasing. However, the rate of increase in the P input does not keep up with the rate of increase in the N input [8]. Affected by N deposition, water and sediment regulation, and land use change, the soil N and P supply in this region is rapid [8].

2.2. Experiment Design and Soil Sample

The study area is about 120 m2, and twelve sample squares (1 m × 1 m) were randomly conducted in the study area. The minimum distance between each sample square was 2 m. The dominant plant in the study area is A. sinensis. Based on previous studies, we selected one CK (adding the same volume of distilled water as in treatment group) and three N:P ratio treatments. In the three N:P ratio treatments, P was added at 10 kg h−1, and N was added at 50, 150, and 450 kg h−1, respectively [8]. The N:P addition ratios were set to 5:1, 15:1 and 45:1, respectively. The three ratios corresponded to limited N, basic N:P ratio, and limited P conditions, respectively [24]. Urea and KH2PO4 were used for nutrient addition. Nutrients were added in May 2021. Soil sampling was conducted about 3 months after nutrient addition. BS was collected from 5–10 cm soil layer without plant growth. RS was collected from the soil nearer to the root (1–2 mm). Each soil was divided into two parts, one for microbial sequencing and the other for soil environmental factor determination.

2.3. Soil Environmental Factor Determination and Sequencing Analysis

The potassium dichromate volumetric method was employed to determine the SOC content. The total N (TN) and total C (TC) content were measured by an elemental analyzer (Vario macro cube, Elementar, Langenselbold, Germany). A pH meter and conductivity meter were employed to measure the soil pH and salt content, respectively. The molybdenum blue method was utilized to determine the total P (TP) and available P (AP) contents.
The total genome DNA of samples was extracted using the CTAB method. After dilution with sterile water, primers were used to amplify the V3 and V4 variable regions by PCR amplification. Then, the PCR products were sent to the sequencing company for high-throughput sequencing. More information about high-throughput sequencing is provided in Section S1 of the Supplementary Materials.

2.4. Statistical Analysis

The original DNA data were processed by the Qiime2. R (4.1.3) software vegan package (2.6-2), which was used to calculate the α-diversity of bacterial community. The formulas are as follows.
S h a n n o n = − ∑ i n p i × log 2 ⁡ p i
s i m p s o n = − ∑ i n p i 2
where p i is the proportional abundance of species i . PICRUSt2 was used to predict the function of the bacterial community. The difference among treatments was tested using the LSD test by the agricolae package (1.3-5). Before performing the LSD test, the ANOVA test was first performed. Pearson correlation analysis was conducted to evaluate the correlations between soil physicochemical properties and bacterial community by the corrplot package (0.92). The ggplot2 package (3.3.6) was used for plotting.
The co-occurrence network was finished by the igraph package (1.3.4). There are 12 samples in each co-occurrence network. Before constructing the network, we removed OTUs that had low relative abundance (<0.01%) and disappeared in 4 samples. Connections with correlation coefficients less than 0.8 and p-values higher than 0.01 were filtered out by Spearman analysis. Finally, we used gephi software (0.9.2) for the visualization of the co-occurrence network.
With reference to [25], we performed Faprotax functional analysis based on OTU absolute abundance and annotation information. PICRUSt2 was used to analyze the KEGG pathway. Based on the KEGG Orthology, we have plotted the process of the N cycle [25].

3. Results

3.1. α-Diversity Analysis

The Shannon and Chao1 indexes of bacterial communities in the RS and BS of A. sinensis under different N:P ratio treatments are shown in Figure 2. The Shannon and Chao1 indexes of the BS bacterial community continued to decrease with increasing N:P supply ratios. The Chao1 and Shannon indexes were reduced by 10.92% and 1.76%, respectively, in the treatment with a high N:P ratio but showed an insignificant difference with CK. N and P addition increased the bacterial community diversity in the RS. Treatments with medium and high N:P ratios significantly increased the Chao1 index (by 14.89% and 8.48%, respectively) and the Shannon index (5.81% and 4.75%, respectively).

3.2. β-Diversity Analysis

Figure 3 shows the PCoA of bacterial communities at the OTUs level in the RS of A. sinensis and BS. The PCOA explained 42.5% and 39.1% of the variation in the RS and BS bacterial communities, respectively. ADONIS and ANOSIM analysis showed that N:P addition ratios had significant effects on the bacterial community of RS and BS (p < 0.01). The effect of the N:P ratio on the bacterial communities in RS was less than that of BS. In BS, the difference between N and P addition treatment and CK was gradually increased with increasing N:P supply ratio and had a significant linear relationship with the N:P ratio (Figure S1, p < 0.05).

3.3. The Dominant Phylum of the Bacterial Community

The highest relative abundance (Figure 4) was found in Proteobacteria (37.9%, 42.9%), followed by Actinobacteria (14.9% and 15.3%), Bacteroidetes (14.9%, 7.1%), Acidobacteria (7.7%, 8.1%), Gemmatimonadetes (7.5%, 7.8%), Chloroflexi (5.1%, 6.1%), Firmicutes (1.9%, 2.9%), Verrucomicrobia (2.7%, 1.1%), and Entotheonellaeota (0.5%, 0.8%). The high N:P ratio decreased the Bacteroidetes, Acidobacteria, and Chloroflexi of the BS by 44.8%, 23.7%, and 35.0%, respectively. The Actinobacteria, Acidobacteria, Chloroflexi, and Verrucomicrobia increased and then decreased with increasing N:P ratio, reaching a maximum at a low N:P ratio treatment. In RS, the Proteobacteria increased consistently with increasing N:P ratio and was significantly higher in the 15:1 and 45:1 treatments than in the CK (p < 0.05). Increasing N:P ratio decreased the relative abundance of the Actinobacteria and Chloroflexi of RS.

3.4. The Genus of the Bacterial Community

The top 50 genera of the relative abundance of the RS and BS bacterial communities of the A. sinensis are shown in Figure 5. Sandaracinus, bacterium_YC_LK_LKJ36, Steroidobacter, Zeaxanthiniabcter, Tunicatimonas, Ilumatobacter, Erythrobacter, and Fulvivirga had higher relative abundance in the RS, while Rubrobacter, Anearomyxobacter, Nitrospira, Subgroup_10, MND1, Bryobacter, UTCFX1, and Candidatus_Entotheonella showed higher relative abundance in the BS. The high N:P ratio significantly increased Bacillus, Rhodomicrobium, bacterium_YC_LK_LKJ35, Methyloceanibacter, and Ilumatobacter (p < 0.05), and significantly decreased the relative abundance of Pelobacter, Desulfopila, Desulfuromonas, Marinobacterium, Pseudohongiella, and Geoalkalibacter in BS (p < 0.05). The relative abundance of Geoalkalibacter, Pontibacter, Sphingomonas, Altererythrobacter, Ellin6067, Haliangium, Vibrio, Gemmatimonas, Sandaracinus, Tunicatimonas, Erythrobacter, and Fulvivirga increased with the increasing N:P ratio in RS (p < 0.05). The increasing N:P ratio significantly decreased the relative abundance of UTCFX1, Candidatus_Entotheonella, MND1, and PAUC26f of RS (p < 0.05).

3.5. Bacterial Co-Occurrence Network

The numbers of nodes were 1284 and 1484, and the numbers of edges were 6502 and 6417 in the RS and BS, respectively (Figure 6A,B, Table S1). There are higher average degrees, network densities, clustering coefficients, and modules in the BS, while the network diameters and average path lengths are higher in the RS, suggesting that the BS has a more complex network. In addition, the BS network had a higher stability (Figure S2). The SOC content was significantly and positively correlated with several modules in both soils (Figure 6C,D). The AP content was negatively correlated with several modules in RS. Despite having more modules, only 3 network hubs were found in the BS network (Figure 6E), compared to 10 in the RS network (Figure 6F). Network hubs were rare species in both soils (Table S2). Among the 10 hubs in the RS network, there were 7 hubs belonging to the Proteobacteria and 2 hubs belonging to the Bacteroidetes.

3.6. Function Analysis

Differential functional compositions were observed between RS and BS (Figure 7, Table S3). In the BS, the treatment with a high N:P ratio enriched the urea decomposition, aromatic compound degradation, chitinolysis, and nitrification more, whereas the CK showed increased methylotrophy and nitrite respiration (Figure 7A). In the RS, more functions were associated with N metabolism. The treatment with a high N:P ratio increased microbial denitrification (Figure 7B). Increasing the N:P ratio reduced the abundance of plant pathogens but increased the abundance of aerobic chemoheterotrophs in RS. In the BS, increasing the N:P ratio enhanced the nitrification process, such as the process from NH3 to NO3− (Figure 8, Table S4), but the abundance of N-fixing genes was decreased. In the RS, the high N:P ratio increased the abundance of denitrification genes (Figure 8). Additionally, functional predictions were made for 10 network hubs in the RS microbial network (Table S5). The results revealed four functions predicted, namely aerobic chemoheterotrophy, hydrocarbon degradation, iron respiration, and chemoheterotrophy. The chemoheterotrophy and aerobic chemoheterotrophy increased with the increasing N:P ratio (p < 0.05), while iron respiration exhibited the opposite trend (p < 0.05).

3.7. The Effect of Environmental Factors on Bacterial Community

The SOC and AP contents were most closely related to the bacterial community diversity of both RS and BS (Figure 9). In BS, the correlation coefficients of the SOC content with Salinimicrobium, Bacteroidetes, Acidobacteria, Chloroflexih, and Verrucomicrobiad were 0.63, 0.60, 0.77, 0.72, and 0.72 (p < 0.05), respectively. The AP content was significantly positively correlated with Acidobacteria, Chloroflex, and Verrucomicrobia (p < 0.05). In the RS, the SOC content was significantly and positively correlated with Woeseia, Proteobacteria, Acidobacteria, and Gemmatimonadetes with correlation coefficients of 0.70, 0.67, 0.72, and 0.77, respectively (p < 0.05). The AP content was negatively correlated with Subgroup_10, Firmicutes, Chao1, and Shannon in RS (p < 0.05). In both soils, the SOC content was positively correlated with the bacterial community α-diversity (p < 0.05). RDA analysis showed that the SOC content was the main environmental factor influencing the bacterial community phyla composition of BS and RS (Figure 10A,B). Except for the SOC content, the pH and AP content had significant effects on BS bacterial community’s phyla composition (Table S6). Similarly, the SOC content was the most key factor in the bacterial community diversity of both RS and BS (Figure 10C). In the RDA of both samples (Figure S3), the RS and BS bacterial community structures differed significantly, with AP explaining the most variation (R2 = 0.52, p = 0.001).

4. Discussion

In this study, N:P addition ratios increased the diversity of RS bacterial communities, which is inconsistent with most studies about the effect of N addition on bacterial communities. A previous study found that the N addition decreased the α-diversity of soil bacterial communities mainly by decreasing the soil pH [26]. In this study, a positive but insignificant correlation was found between the pH and α-diversity of the RS bacterial community. This may be due to the uptake of soil N by plants, which mitigates the effect of N addition on the soil [27]. In BS, the α-diversity decreased with increasing N:P ratio and was negatively correlated with pH, although insignificant, which demonstrated that the effects of N addition on the α-diversity of the RS and BS bacterial communities were different. On the one hand, P addition usually has insignificant effects on soil pH and is less likely to cause soil acidification [28]. In addition, the soils of the YRD are severely salinized and dominated by alkaline soils. And the present study was conducted in summer, when the BS evaporates severely and the pH does not easily decrease. On the other hand, P addition alleviated the P limitation of bacterial community under N addition and might have increased the threshold at which N addition induced a decrease in the bacterial community diversity [2]. Liu et al. [29] found that N input exceeding 32 g/m2 resulted in a decrease in the diversity of the RS bacterial community. In this study, there is a threshold between 15 g/m2 and 45 g/m2 of N addition that resulted in a change in the linear relationship between the RS bacterial community and the N addition gradient. In contrast, diversity was still increased compared to the CK, which further supports our previous conclusion that P addition may increase the threshold for the decrease in bacterial community diversity caused by N addition. Unfortunately, only three N:P addition gradient ratios were set in this study, and it was unable to further investigate the key turning threshold for decreasing the bacterial community diversity.
A negative correlation was found between α-diversity and AP content in the RS, but this phenomenon was not observed in the BS, which further indicates that nutrient addition has different effects on the RS and BS bacterial communities. The decrease in AP content was caused by an N-P imbalance that increased soil N availability, which in turn increased plant P demand. However, this may not be the main reason for the increased α-diversity of the RS bacterial community. In both soils, the bacterial community’s α-diversity showed a significant positive correlation with soil SOC content, which was similar to the findings of previous studies [30]. The N addition contributed to plants’ primary productivity [31], which in turn increased the root secretion release and apoplast production and alleviated microbial C limitation. In addition, the input of N and P contributed more to SOC than N addition alone [32]. N and P input can alleviate the N and P limitation in bacterial growth, thus reducing the N excavation and P excavation to SOC [33,34]. However, in BS, the continued utilization of bacterial communities can limit growth due to the absence of a stable C input.
The N:P ratio significantly altered the structure of the RS and BS bacterial communities, indicating that the bacterial community structures of both RS and BS were sensitive to changes in the N:P ratio. When under the treatment with a high N:P ratio, the most pronounced differentiation in bacterial community structure was observed, which is similar to the findings of the study by [35]. The higher N:P addition would promote great niche differentiation [35]. The bacterial community structure of BS is more sensitive to the N:P ratio than that of RS. More opportunities can be provided for different species that exhibit mutual adaptation to environmental stresses through such interactions [36].
There was a difference in the response of the dominant bacterial community phylum between the RS and BS to the N:P addition ratios, which was similar to the findings of previous studies [36]. The Proteobacteria had the highest abundance, which indicates its better adaptation to the environment [37,38]. The relative abundance of Proteobacteria in the RS bacterial community increased gradually with the increasing N:P ratio, while in the BS, the low- and high-N:P treatments were significantly lower than in the CK. Proteobacteria, Actinobacteria, and Bacteroidetes can grow rapidly in an environment with sufficient C content [39,40]. The N and P addition increased C release from plant roots, providing abundant C sources, which in turn promoted the growth of eutrophic taxa. The relative abundance of Bacteroidetes in BS decreased with increasing N:P ratios. The N and P addition alleviated the N limitation and P limitation during the growth of Bacteroidetes, but its growth was still C-limited. The relative abundance of the Bacteroidetes in RS was higher than in the BS, further indicating that plant root C sources limit the growth of eutrophic taxa. The medium and high N:P ratios significantly decreased the relative abundance of Acidobacteria, which is similar to the findings of a previous study [41]. The Acidobacteria belongs to the oligotrophic group [42], which mainly uses recalcitrant C in the soil. The nutrient addition may inhibit its ability to use recalcitrant C.
The relative abundance of Ilumatobacter, Halomonas, Erythrobacter, Fulvivirga, and Haliangium was significantly higher in the RS than in the BS. Halomonas, Fulvivirga, and Ilumatobacter were found to be plant-growth-promoting rhizobacteria. Ilumatobacter can help plants to suppress pathogenic bacteria and usually has a higher relative abundance in the RS [43]. Halomonas can increase soil permeability, improve soil structure, and provide nutrients to promote root and shoot growth and nutrient use efficiency [44]. Haliangium and Erythrobacter have the ability to decompose complex organic compounds [45]. The abundance of secretions in the RS promotes the growth of both. [29] found that the relative abundance of Fulvivirga was higher at low P effectiveness. In this study, the relative abundance of Fulvivirga increased with the increasing N:P ratio. Fulvivirga can promote the decomposition of organic P to satisfy the growth requirements of plants and itself. Higher levels of N input induce P limitation and promote the growth of Fulvivirga [29]. Wang et al. [30] found that vegetation cover reduced the relative abundance of Rubrobacter, which is consistent with the results of this study. Anaeromyobacter is an anaerobic bacterium, and its activity can be inhibited by root oxygenation [46]. The main function of Nitrospira is nitrification. On the one hand, root secretion inhibits nitrification, and on the other hand, nitrifying bacteria are less competitive for NH4+ compared to plant roots, which makes the relative abundance of Nitrospira lower in RS [47]. Our results showed that Subgroup_10 was higher in BS, while Fu et al. [48](2022) found that Sugroup_10 is the dominant genera using root secretion and has a higher relative abundance in the RS. We speculate that the salinity resulted in a higher relative abundance of Subgroup_10 in the BS. Subgroup_10 was found to be suitable for living in environments with higher salinity [49]. A. sinensis is a salt-secreting plant that can absorb salt from the soil and thus causes a decrease in soil salinity, which in turn changes the abundance of Subgroup_10.
In the BS, the relative abundance of Bacillus increased in the treatment with a high N:P ratio. Bacillus has good N-removal capacity and is therefore unaffected by increasing N levels [50]. In addition, Bacillus has the function of decomposing insoluble inorganic phosphorus minerals [51]. The P limitation of microorganisms also increased with the increasing N:P ratio; thus, the relative abundance of Bacillus with P-acquisition capacity increased. Sulfate-reducing bacteria (Desulfuromonas, Desulfopila) are important components that constitute nitrogen-fixing bacteria, and their abundance is affected by the N:P ratio, which is consistent with a previous study [52]. The relative abundance of Sphingomonas gradually increased with increasing N:P. Sphingomonas can decompose cellulose, alkanes, and aromatic hydrocarbons and can secrete carbohydrate hydrolases [53]. The increased N:P ratio caused an increase in root abscission and secretion in the RS, which promoted the growth of Sphingomonas.
The complexity of microbial co-occurrence networks is usually characterized by topological parameters, such as the number of nodes and edges [54]. We found that the co-occurrence network of the RS bacterial community has more nodes and edges, which suggests that there is higher diversity in the RS and more bacteria for coexistence. The enriched C of RS is suitable for the growth of microorganisms. Higher proportions of negative edges were found in BS, suggesting that BS bacteria are closer to a competitive relationship than a complementary relationship [55]. Soil nutrients are altered by the change in the N:P ratio. The bacteria better adapt to the environment and thus enhance their competitive advantage [56]. The bacterial community in the BS is more environmentally constrained than that in the RS [57]. Unlike RS, BS has no plant root system to transport the C source; thus, there is more competition for microbial available C. In RS, the selective effect of the altered N:P ratio on bacteria was mitigated by plants’ acquisition of nutrients. There were higher clustering coefficients and lower average path lengths in the BS co-occurrence network, suggesting closer communication between the nodes of the RS network. Microbial core groups are highly interconnected taxa in microbial communities, and changes in their abundance have important impacts on the structure and function [58]. More network hubs were found in the RS bacterial symbiotic network. The network hubs were all rare species, and most of them belonged to Proteobacteria and Bacteroidetes. It has been found that rare taxa of bacterial communities tend to be more closely linked to other members, occupy unique ecological niches, and are more sensitive to environmental changes [59,60]. Thus, although there are more nodes and edges in the RS bacterial co-occurrence network, its stability is more fragile compared to BS. We conducted the functional annotation for hubs and found that the functions were mainly focused on C utilization. The abundance of these functions was increased with the increasing N:P ratio. The abundance of several modules in the RS network was positively correlated with SOC content. Influenced by the N:P ratio, the release of organic matter from the plant root system increased, which enriched the microbially available C source [61].
Nutrient changes lead to changes in the soil microbial community structure, which in turn alters soil elemental cycling [55]. Nutrient inputs typically affect functional taxa involved in the C and N cycles. The increased N:P addition ratio increased the abundance of N-fixing genes and increased nitrification processing genes in BS, which is consistent with previous studies [62,63]. The abundance of denitrifying functional taxa increased in RS, along with the abundance of the chemoheterotrophy and aerobic chemoheterotrophy functions. In N-sufficient soils, the bacterial community increases the denitrification process as reactive N is released again during the decomposition of SOC content.

5. Conclusions

The N deposition caused by human activities has changed the N:P input ratio in terrestrial ecosystems. The Yellow River Delta, with its fragile habitats, is experiencing greater rates of N deposition and rapidly changing the N:P input–input ratio. In this study, we investigated the effect of N and P input ratios on bacterial communities in RS and BS. The N:P addition ratio significantly increased the community α-diversity of the plant RS community. Increasing the N:P ratio relieved N limitation and accelerated the process of soil nitrification in the BS and accelerated the denitrification process in the RS. The co-occurrence network of the RS bacterial community is more complex but has lower robustness compared to the BS. The response of the BS and RS bacterial communities to the N:P ratio differed, as influenced by SOC content in terms of diversity, community composition, mutualistic networks, and functional composition. This study illustrated that there are differences in the response of soil bacterial communities to N:P ratios as influenced by plant roots. This study emphasized that the interaction between environmental changes and plant root systems on soil microorganisms should be considered in future studies.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/microorganisms12122419/s1, Figure S1. Linear regression of Bray-Curtis distance. BS, bulk soil. RS, rhizosphere soil. Figure S2. Network robustness analysis. Figure S3. RDA of all samples. Table S1. Basic topological properties of co-occurrence networks in bulk and rhizosphere soil. Table S2. The network hubs in bulk and rhizosphere soil bacterial community. Table S3. The function of bulk and rhizosphere soil bacterial community. The lowercase letter indicates that the difference is significant at 0.05 level. Table S4. The pathway of N cycle of bulk and rhizosphere soil bacterial community. The lowercase letter indicates that the difference is significant at 0.05 level. Table S5. Rhizosphere soil bacterial community network hubs. The lowercase letter indicates that the difference is significant at 0.05 level. Table S6. Monte Carlo test (per = 999) for top 10 phyla composition.

Author Contributions

Investigation, T.L., Z.F., R.H. and Y.Z.; Data curation, Z.Z.; Writing—original draft, J.M.; Project administration, J.S. All authors have read and agreed to the published version of the manuscript.

Funding

The funding was supported by the National Key Research and Development Program of China (2022YFF1303203), the National Natural Science Foundation of China (41971119, 42171059 and 41871089), the Natural Science Foundation of Shandong Province (ZR2019MD024), the Science and Technology Support Plan for Youth Innovation of Colleges and Universities (2019KJD010), and the Binzhou Youth Science and Technology Rising Star Program Project (QMX2023001).

Data Availability Statement

The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number can be found below: https://www.ncbi.nlm.nih.gov/, PRJNA949158 (accessed on 1 May 2020).

Conflicts of Interest

The authors declare no conflicts of interest.

References

  1. Zong, N.; Shi, P.L. Differential responses of community structure and production. and the sensitivities of different alpine grasslands tonitrogen addition. Acta Ecol. Sin. 2020, 40, 4000–4010. [Google Scholar] [CrossRef]
  2. Hao, J.H.; Han, H.K.; Liu, Y.; Li, J.H.; Yang, J.Y.; Ren, B.H.; Bai, L. Phosphorus addition alleviates the inhibition of nitrogen deposition on photosynthesis of Potentilla tanacetifolia. Front. Environ. Sci. 2023, 11, 3389. [Google Scholar] [CrossRef]
  3. Wang, X.; Li, S.; Zhu, B.; Homyak, P.M.; Chen, G.; Yao, X.; Wu, D.; Yang, Z.; Lyu, M.; Yang, Y. Long-term nitrogen deposition inhibits soil priming effects by enhancing phosphorus limitation in a subtropical forest. Glob. Chang. Biol. 2023, 29, 4081–4093. [Google Scholar] [CrossRef] [PubMed]
  4. Penuelas, J.; Sardans, J. The global nitrogen-phosphorus imbalance. Science 2022, 375, 266–267. [Google Scholar] [CrossRef] [PubMed]
  5. Yu, G.; Jia, Y.; He, N.; Zhu, J.; Chen, Z.; Wang, Q.; Piao, S.; Liu, X.; He, H.; Guo, X.; et al. Stabilization of atmospheric nitrogen deposition in China over the past decade. Nat. Geosci. 2019, 12, 424–429. [Google Scholar] [CrossRef]
  6. Dong, C.; Wang, W.; Liu, H.; Xu, X.; Zeng, H. Temperate grassland shifted from nitrogen to phosphorus limitation induced by degradation and nitrogen deposition: Evidence from soil extracellular enzyme stoichiometry. Ecol. Indic. 2019, 101, 453–464. [Google Scholar] [CrossRef]
  7. Penuelas, J.; Poulter, B.; Sardans, J.; Ciais, P.; van der Velde, M.; Bopp, L.; Boucher, O.; Godderis, Y.; Hinsinger, P.; Llusia, J.; et al. Human-induced nitrogen-phosphorus imbalances alter natural and managed ecosystems across the globe. Nat. Commun. 2013, 4, 2934. [Google Scholar] [CrossRef]
  8. Liu, X.; Wang, G.; Ran, Y.; Qi, D.; Han, G.; Guan, B.; Hao, C. Overall supply level, not the relative supply of nitrogen and phosphorus, affects the plant community composition of a supratidal wetland in the Yellow River Delta. Sci. Total Environ. 2019, 695, 133866. [Google Scholar] [CrossRef]
  9. Yang, W.; Cai, X.W.; Wang, Y.Q.; Diao, L.F.; Xia, L.; An, S.Q.; Luo, Y.Q.; Cheng, X.L. Increased Soil Bacterial Abundance but Decreased Bacterial Diversity and Shifted Bacterial Community Composition Following Secondary Succession of Old-Field. Forests 2022, 13, 1628. [Google Scholar] [CrossRef]
  10. Liu, J.; Ma, Q.; Hui, X.; Ran, J.; Ma, Q.; Wang, X.; Wang, Z. Long-term high-P fertilizer input decreased the total bacterial diversity but not phoD-harboring bacteria in wheat rhizosphere soil with available-P deficiency. Soil Biol. Biochem. 2020, 149, 107918. [Google Scholar] [CrossRef]
  11. Wang, X.; Feng, J.; Ao, G.; Qin, W.; Han, M.; Shen, Y.; Liu, M.; Chen, Y.; Zhu, B. Globally nitrogen addition alters soil microbial community structure, but has minor effects on soil microbial diversity and richness. Soil Biol. Biochem. 2023, 179, 108982. [Google Scholar] [CrossRef]
  12. Hu, J.X.; Huang, C.D.; Zhou, S.X.; Kuzyakov, Y. Nitrogen addition to soil affects microbial carbon use efficiency: Meta-analysis of similarities and differences in C-13 and O-18 approaches. Glob. Chang. Biol. 2022, 28, 4977–4988. [Google Scholar] [CrossRef] [PubMed]
  13. Huang, J.S.; Hu, B.; Qi, K.B.; Chen, W.J.; Pang, X.Y.; Bao, W.K.; Tian, G.L. Effects of phosphorus addition on soil microbial biomass and community composition in a subalpine spruce plantation. Eur. J. Soil Biol. 2016, 72, 35–41. [Google Scholar] [CrossRef]
  14. Wang, H.; Liu, S.; Zhang, X.; Mao, Q.; Li, X.; You, Y.; Wang, J.; Zheng, M.; Zhang, W.; Lu, X.; et al. Nitrogen addition reduces soil bacterial richness, while phosphorus addition alters community composition in an old-growth N-rich tropical forest in southern China. Soil Biol. Biochem. 2018, 127, 22–30. [Google Scholar] [CrossRef]
  15. Zhu, J.; Wang, Q.; He, N.; Smith, M.D.; Elser, J.J.; Du, J.; Yuan, G.; Yu, G.; Yu, Q. Imbalanced atmospheric nitrogen and phosphorus depositions in China: Implications for nutrient limitation. J. Geophys. Res. Biogeosci. 2016, 121, 1605–1616. [Google Scholar] [CrossRef]
  16. Luo, M.; Moorhead, D.L.; Ochoa-Hueso, R.; Mueller, C.W.; Ying, S.C.; Chen, J. Nitrogen loading enhances phosphorus limitation in terrestrial ecosystems with implications for soil carbon cycling. Funct. Ecol. 2022, 36, 2845–2858. [Google Scholar] [CrossRef]
  17. Peng, Y.; Peng, Z.; Zeng, X.; Houx, J.H. Effects of nitrogen-phosphorus imbalance on plant biomass production: A global perspective. Plant Soil 2019, 436, 245–252. [Google Scholar] [CrossRef]
  18. Peng, Y.F.; Guo, D.L.; Yang, Y.H. Global patterns of root dynamics under nitrogen enrichment. Glob. Ecol. Biogeogr. 2017, 26, 102–114. [Google Scholar] [CrossRef]
  19. Liu, W.; Liu, L.; Yang, X.; Deng, M.; Wang, Z.; Wang, P.; Yang, S.; Li, P.; Peng, Z.; Yang, L.; et al. Long-term nitrogen input alters plant and soil bacterial, but not fungal beta diversity in a semiarid grassland. Glob. Chang. Biol. 2021, 27, 3939–3950. [Google Scholar] [CrossRef] [PubMed]
  20. Zhang, X.; Wang, G.; Xue, B.; Zhang, M.; Tan, Z. Dynamic landscapes and the driving forces in the Yellow River Delta wetland region in the past four decades. Sci. Total Environ. 2021, 787, 147644. [Google Scholar] [CrossRef]
  21. Li, H.G.; Li, X.R.; Xu, Z.H.; Liang, S.K.; Ding, Y.; Song, D.H.; Guo, H. Nutrient budgets for the Bohai Sea: Implication for ratio imbalance of nitrogen to phosphorus input under intense human activities. Mar. Pollut. Bull. 2022, 179, 113665. [Google Scholar] [CrossRef] [PubMed]
  22. Liu, X.L.; Wang, G.M.; Yu, J.B.; Ran, Y.N.; Guan, B.; Han, G.X. Effects of nitrogen and phosphorus supply on plant community structure of coastal wetland in the Yellow River Delta. Chin. J. Ecol. 2018, 37, 801–809. [Google Scholar] [CrossRef]
  23. Finks, S.S.; Weihe, C.; Kimball, S.; Allison, S.D.; Martiny, A.C.; Treseder, K.K.; Martiny, J.B.H. Microbial community response to a decade of simulated global changes depends on the plant community. Elem. Sci. Anthr. 2021, 9, 00124. [Google Scholar] [CrossRef]
  24. Venterink, H.O.; Güsewell, S. Competitive interactions between two meadow grasses under nitrogen and phosphorus limitation. Funct. Ecol. 2010, 24, 877–886. [Google Scholar] [CrossRef]
  25. Gao, Y.; Zhang, G.; Jiang, S.; Liu, Y.-X. Wekemo Bioincloud: A user-friendly platform for meta-omics data analyses. iMeta 2024, 3, e175. [Google Scholar] [CrossRef]
  26. Zhao, X.C.; Du, Z.W.; Liu, S.E.; Wang, Q.K. Effects of nitrogen addition on soil microbial respiration and its temperature sensitivity in a Duolun grassland ecosystem. Acta Ecol. Sin. 2020, 40, 1551–1561. [Google Scholar] [CrossRef]
  27. Wang, Q.; Ma, M.; Jiang, X.; Guan, D.; Wei, D.; Zhao, B.; Chen, S.; Cao, F.; Li, L.; Yang, X.; et al. Impact of 36 years of nitrogen fertilization on microbial community composition and soil carbon cycling-related enzyme activities in rhizospheres and bulk soils in northeast China. Appl. Soil Ecol. 2019, 136, 148–157. [Google Scholar] [CrossRef]
  28. Feng, J.; Zhu, B. Global patterns and associated drivers of priming effect in response to nutrient addition. Soil Biol. Biochem. 2021, 153, 108118. [Google Scholar] [CrossRef]
  29. Liu, W.X.; Jiang, L.; Yang, S.; Wang, Z.; Tian, R.; Peng, Z.Y.; Chen, Y.L.; Zhang, X.X.; Kuang, J.L.; Ling, N.; et al. Critical transition of soil bacterial diversity and composition triggered by nitrogen enrichment. Ecology 2020, 101, e03053. [Google Scholar] [CrossRef]
  30. Wang, Y.J.; Huang, Q.Q.; Gao, H.; Zhang, R.Q.; Yang, L.; Guo, Y.R.; Li, H.K.; Awasthi, M.K.; Li, G.C. Long-term cover crops improved soil phosphorus availability in a rain-fed apple orchard. Chemosphere 2021, 275, 130093. [Google Scholar] [CrossRef]
  31. Xu, C.H.; Xu, X.; Ju, C.H.; Chen, H.Y.H.; Wilsey, B.J.; Luo, Y.Q.; Fan, W. Long-term, amplified responses of soil organic carbon to nitrogen addition worldwide. Glob. Chang. Biol. 2021, 27, 1170–1180. [Google Scholar] [CrossRef] [PubMed]
  32. Yue, K.; Fornara, D.A.; Yang, W.Q.; Peng, Y.; Peng, C.H.; Liu, Z.L.; Wu, F.Z. Influence of multiple global change drivers on terrestrial carbon storage: Additive effects are common. Ecol. Lett. 2017, 20, 663–672. [Google Scholar] [CrossRef] [PubMed]
  33. Manzoni, S.; Taylor, P.; Richter, A.; Porporato, A.; Agren, G.I. Environmental and stoichiometric controls on microbial carbon-use efficiency in soils. New Phytol. 2012, 196, 79–91. [Google Scholar] [CrossRef]
  34. Spohn, M.; Potsch, E.M.; Eichorst, S.A.; Woebken, D.; Wanek, W.; Richter, A. Soil microbial carbon use efficiency and biomass turnover in a long-term fertilization experiment in a temperate grassland. Soil Biol. Biochem. 2016, 97, 168–175. [Google Scholar] [CrossRef]
  35. Li, Y.; Yang, H.; Su, Y.; Gong, X.; Yao, B.; Cheng, L. Phosphorus Coupled with High Nitrogen Addition Exerts a Great Influence on Soil Bacterial Community in a Semiarid Grassland. Microb. Ecol. 2023, 86, 2993–3002. [Google Scholar] [CrossRef]
  36. Wang, J.; Liao, L.; Ye, Z.; Liu, H.; Zhang, C.; Zhang, L.; Liu, G.; Wang, G. Different bacterial co-occurrence patterns and community assembly between rhizosphere and bulk soils under N addition in the plant–soil system. Plant Soil 2022, 471, 697–713. [Google Scholar] [CrossRef]
  37. Li, W.; Lv, X.; Ruan, J.; Yu, M.; Song, Y.B.; Yu, J.; Dong, M. Variations in Soil Bacterial Composition and Diversity in Newly Formed Coastal Wetlands. Front Microbiol. 2018, 9, 3256. [Google Scholar] [CrossRef]
  38. Shao, P.; Liang, C.; Rubert-Nason, K.; Li, X.; Xie, H.; Bao, X. Secondary successional forests undergo tightly-coupled changes in soil microbial community structure and soil organic matter. Soil Biol. Biochem. 2019, 128, 56–65. [Google Scholar] [CrossRef]
  39. Li, X.M.; Chen, Q.L.; He, C.; Shi, Q.; Chen, S.C.; Reid, B.J.; Zhu, Y.G.; Sun, G.X. Organic Carbon Amendments Affect the Chemodiversity of Soil Dissolved Organic Matter and Its Associations with Soil Microbial Communities. Environ. Sci. Technol. 2019, 53, 50–59. [Google Scholar] [CrossRef]
  40. Wang, L.; Zhang, H.; Wang, J.; Wang, J.D.; Zhang, Y.C. Long-term fertilization with high nitrogen rates decreased diversity and stability of diazotroph communities in soils of sweet potato. Appl. Soil Ecol. 2022, 170, 104266. [Google Scholar] [CrossRef]
  41. Wang, C.; Liu, D.; Bai, E. Decreasing soil microbial diversity is associated with decreasing microbial biomass under nitrogen addition. Soil Biol. Biochem. 2018, 120, 126–133. [Google Scholar] [CrossRef]
  42. Sha, M.H.; Xu, J.; Zheng, Z.C.; Fa, K.Y. Enhanced atmospheric nitrogen deposition triggered little change in soil microbial diversity and structure in a desert ecosystem. Glob. Ecol. Conserv. 2021, 31, e01879. [Google Scholar] [CrossRef]
  43. Zhao, F.Y.; Zhang, Y.Y.; Dong, W.G.; Zhang, Y.Q.; Zhang, G.X.; Sun, Z.P.; Yang, L.J. Vermicompost can suppress Fusarium oxysporum f. sp. lycopersici via generation of beneficial bacteria in a long-term tomato monoculture soil. Plant Soil 2019, 440, 491–505. [Google Scholar] [CrossRef]
  44. Gou, Y.C.; Wang, Z.K.; Zhang, Z.P.; Wei, H.; Meng, P.P.; Zeng, Y.H. Advance in role mechanisms of plant growth promoting rhizobacteria. Chin. J. Appl. Environ. Biol. 2022, 1, 1–19. [Google Scholar] [CrossRef]
  45. Chen, W.; Gao, Y.; Yang, J.; Fan, F.J.; Zhang, W.G.; Li, J.Y.; Zhou, C.; Shi, G.L.; Tong, F.; Fan, G.P. Taxonomical and functional bacterial community selection in the rhizosphere of the rice genotypes with different nitrogen use efficiencies. Plant Soil 2022, 470, 111–125. [Google Scholar] [CrossRef]
  46. Duan, X.; Yu, X.F.; Li, Z.; Wang, Q.G.; Liu, Z.P.; Zou, Y.C. Iron-bound organic carbon is conserved in the rhizosphere soil of freshwater wetlands. Soil Biol. Biochem. 2020, 149, 107949. [Google Scholar] [CrossRef]
  47. Chai, Y.N.; Schachtman, D.P. Root exudates impact plant performance under abiotic stress. Trends Plant Sci. 2022, 27, 80–91. [Google Scholar] [CrossRef]
  48. Fu, Y.; Luo, Y.; Tang, C.; Li, Y.; Guggenberger, G.; Xu, J. Succession of the soil bacterial community as resource utilization shifts from plant residues to rhizodeposits. Soil Biol. Biochem. 2022, 173, 108785. [Google Scholar] [CrossRef]
  49. Loganathachetti, D.S.; Alhashmi, F.; Chandran, S.; Mundra, S. Irrigation water salinity structures the bacterial communities of date palm (Phoenix dactylifera)-associated bulk soil. Front. Plant Sci. 2022, 13, 944637. [Google Scholar] [CrossRef]
  50. Xie, Y.M.; Tian, X.L.; Liu, Y.; Zhao, K.; Li, Y.M.; Luo, K.; Wang, B.; Dong, S.L. Nitrogen removal capability and mechanism of a novel heterotrophic nitrifying-aerobic denitrifying strain H1 as a potential candidate in mariculture wastewater treatment. Environ. Sci. Pollut. Res. 2023, 48, 106366–106377. [Google Scholar] [CrossRef]
  51. Wang, H.Y.; Wang, R.F.; Zhong, W.; Kong, Q.; Ma, Q.L.; Zong, K.J. Advance in Structural Characteristics and lnfluence Factors of Functional Microbial Communities in the Soils of the Wetlands in the Yellow River Delta. Wetl. Sci. 2022, 20, 111–118. [Google Scholar] [CrossRef]
  52. Zhou, W.G.; Ding, D.W.; Yang, Q.S.; Ling, J.; Ahmad, M.; Lin, X.C.; Lin, L.Y.; Zhang, Y.; Dong, J.D. Diversity and abundance of diazotrophic communities of seagrass Halophila ovalis based on genomic and transcript level in Daya Bay, South China Sea. Arch. Microbiol. 2021, 203, 5577–5589. [Google Scholar] [CrossRef] [PubMed]
  53. Ma, X.D.; Wang, K.; Li, M.D.; Duan, C.J. Genome Sequencing and Analysis of Sphingobium sp. LF-16. Genom. Appl. Biol. 2020, 39, 599–605. [Google Scholar] [CrossRef]
  54. Mo, Y.Y.; Peng, F.; Gao, X.F.; Xiao, P.; Logares, R.; Jeppesen, E.; Ren, K.X.; Xue, Y.Y.; Yang, J. Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir. Microbiome 2021, 9, 128. [Google Scholar] [CrossRef]
  55. Sun, M.Y.; Li, M.C.; Zhou, Y.Q.; Liu, J.I.; Shi, W.C.; Wu, X.L.; Xie, B.H.; Deng, Y.; Gao, Z. Nitrogen deposition enhances the deterministic process of the prokaryotic community and increases the complexity of the microbial co-network in coastal wetlands. Sci. Total Environ. 2023, 856, 158939. [Google Scholar] [CrossRef]
  56. Madhaiyan, M.; Poonguzhali, S.; Lee, J.S.; Lee, K.C.; Sundaram, S. Flavobacterium glycines sp. nov., a facultative methylotroph isolated from the rhizosphere of soybean. Int. J. Syst. Evol. Microbiol. 2010, 60, 2187–2192. [Google Scholar] [CrossRef]
  57. Tian, G.L.; Qiu, H.S.; Li, D.W.; Wang, Y.T.; Zhen, B.; Li, H.Z.; Niu, Q.L.; Qi, D.L.; Zhou, X.G. Little environmental adaptation and high stability of bacterial communities in rhizosphere rather than bulk soils in rice fields. Appl. Soil Ecol. 2022, 169, 104183. [Google Scholar] [CrossRef]
  58. Yan, K.; Lu, D.S.; Ding, C.J.; Wang, Y.; Tian, Y.R.; Su, X.H.; Dong, Y.F.; Wang, Y.P. Rare and abundant bacterial communities in poplar rhizosphere soils respond differently to genetic effects. Sci. Total Environ. 2024, 908, 168216. [Google Scholar] [CrossRef]
  59. Jousset, A.; Bienhold, C.; Chatzinotas, A.; Gallien, L.; Gobet, A.; Kurm, V.; Küsel, K.; Rillig, M.C.; Rivett, D.W.; Salles, J.F.; et al. Where less may be more: How the rare biosphere pulls ecosystems strings. ISME J. 2017, 11, 853–862. [Google Scholar] [CrossRef]
  60. Pan, C.C.; Feng, Q.; Li, Y.L.; Li, Y.Q.; Liu, L.D.; Yu, X.Y.; Ren, S.L. Rare soil bacteria are more responsive in desertification restoration than abundant bacteria. Environ. Sci. Pollut. Res. 2022, 29, 33323–33334. [Google Scholar] [CrossRef]
  61. Capek, P.T.; Manzoni, S.; Kastovská, E.; Wild, B.; Diáková, K.; Bárta, J.; Schnecker, J.; Blasi, C.; Martikainen, P.J.; Alves, R.J.E.; et al. A plant-microbe interaction framework explaining nutrient effects on primary production. Nat. Ecol. Evol. 2018, 2, 1588–1596. [Google Scholar] [CrossRef] [PubMed]
  62. Sun, R.B.; Wang, F.H.; Hu, C.S.; Liu, B.B. Metagenomics reveals taxon-specific responses of the nitrogen-cycling microbial community to long-term nitrogen fertilization. Soil Biol. Biochem. 2021, 156, 108214. [Google Scholar] [CrossRef]
  63. Song, L.; Niu, S.L. Increased soil microbial AOB, amoA and narG abundances sustain long-term positive responses of nitrification and denitrification to N deposition. Soil Biol. Biochem. 2022, 166, 108539. [Google Scholar] [CrossRef]
Microorganisms 12 02419 g001
Figure 1. Location of the YRD and experimental site.
Figure 1. Location of the YRD and experimental site.
Microorganisms 12 02419 g001
Microorganisms 12 02419 g002
Figure 2. The Shannon and Chao1 indexes of bacterial communities in the RS and BS under different N:P ratio treatments. Different lowercase and uppercase letters indicate that the difference between N:P ratio treatments is significant at 0.05 level in the RS and BS, respectively. CK indicates the addition of distilled water.
Figure 2. The Shannon and Chao1 indexes of bacterial communities in the RS and BS under different N:P ratio treatments. Different lowercase and uppercase letters indicate that the difference between N:P ratio treatments is significant at 0.05 level in the RS and BS, respectively. CK indicates the addition of distilled water.
Microorganisms 12 02419 g002
Microorganisms 12 02419 g003
Figure 3. PCoA of bacterial communities in the rhizosphere soil and bulk soil. CK indicates the addition of distilled water.
Figure 3. PCoA of bacterial communities in the rhizosphere soil and bulk soil. CK indicates the addition of distilled water.
Microorganisms 12 02419 g003
Microorganisms 12 02419 g004
Figure 4. The dominant phylum of bacterial communities in the RS and BS communities. Different lowercase letters indicate that the difference is significant. CK indicates the addition of distilled water.
Figure 4. The dominant phylum of bacterial communities in the RS and BS communities. Different lowercase letters indicate that the difference is significant. CK indicates the addition of distilled water.
Microorganisms 12 02419 g004
Microorganisms 12 02419 g005
Figure 5. The dominant genera in the RS and BS communities. Different lowercase letters indicate that the difference is significant in the same soil. CK indicates the addition of distilled water.
Figure 5. The dominant genera in the RS and BS communities. Different lowercase letters indicate that the difference is significant in the same soil. CK indicates the addition of distilled water.
Microorganisms 12 02419 g005
Microorganisms 12 02419 g006
Figure 6. (A,B) Co-occurrence network of the RS and BS bacterial communities (12 samples). (C,D) Correlation between network modules and soil environmental factors in RS and BS. (E,F) Zi-Pi analysis of RS and BS. *, ** and *** indicate that the correlation coefficients are significant at the 0.05, 0.01, and 0.001 levels, respectively.
Figure 6. (A,B) Co-occurrence network of the RS and BS bacterial communities (12 samples). (C,D) Correlation between network modules and soil environmental factors in RS and BS. (E,F) Zi-Pi analysis of RS and BS. *, ** and *** indicate that the correlation coefficients are significant at the 0.05, 0.01, and 0.001 levels, respectively.
Microorganisms 12 02419 g006
Microorganisms 12 02419 g007
Figure 7. Faprotax functional analysis of the BS (A) and RS (B) bacterial communities. Different lowercase letters indicate that the difference is significant at a 0.05 level. CK indicates the addition of distilled water.
Figure 7. Faprotax functional analysis of the BS (A) and RS (B) bacterial communities. Different lowercase letters indicate that the difference is significant at a 0.05 level. CK indicates the addition of distilled water.
Microorganisms 12 02419 g007
Microorganisms 12 02419 g008
Figure 8. The pathway of N cycle of the BS (top) and RS (bottom) bacterial communities. CK indicates the addition of distilled water.
Figure 8. The pathway of N cycle of the BS (top) and RS (bottom) bacterial communities. CK indicates the addition of distilled water.
Microorganisms 12 02419 g008
Microorganisms 12 02419 g009
Figure 9. The correlation analysis between the physical and chemical properties and the bacterial community.
Figure 9. The correlation analysis between the physical and chemical properties and the bacterial community.
Microorganisms 12 02419 g009
Microorganisms 12 02419 g010
Figure 10. RDA analysis and multiple regression analysis. (A) RDA analysis for BS bacterial phlya. (B) RDA analysis for RS bacterial phlya. (C) Effect of the environmental factors on soil bacterial community Shannon diversity in BS and RS from multiple regression models. CK indicates the addition of distilled water.
Figure 10. RDA analysis and multiple regression analysis. (A) RDA analysis for BS bacterial phlya. (B) RDA analysis for RS bacterial phlya. (C) Effect of the environmental factors on soil bacterial community Shannon diversity in BS and RS from multiple regression models. CK indicates the addition of distilled water.
Microorganisms 12 02419 g010
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Ma, J.; Zhang, Z.; Sun, J.; Li, T.; Fu, Z.; Hu, R.; Zhang, Y. Effects of Increasing the Nitrogen–Phosphorus Ratio on the Structure and Function of the Soil Microbial Community in the Yellow River Delta. Microorganisms 2024, 12, 2419. https://doi.org/10.3390/microorganisms12122419

AMA Style

Ma J, Zhang Z, Sun J, Li T, Fu Z, Hu R, Zhang Y. Effects of Increasing the Nitrogen–Phosphorus Ratio on the Structure and Function of the Soil Microbial Community in the Yellow River Delta. Microorganisms. 2024; 12(12):2419. https://doi.org/10.3390/microorganisms12122419

Chicago/Turabian Style

Ma, Jinzhao, Zehao Zhang, Jingkuan Sun, Tian Li, Zhanyong Fu, Rui Hu, and Yao Zhang. 2024. "Effects of Increasing the Nitrogen–Phosphorus Ratio on the Structure and Function of the Soil Microbial Community in the Yellow River Delta" Microorganisms 12, no. 12: 2419. https://doi.org/10.3390/microorganisms12122419

APA Style

Ma, J., Zhang, Z., Sun, J., Li, T., Fu, Z., Hu, R., & Zhang, Y. (2024). Effects of Increasing the Nitrogen–Phosphorus Ratio on the Structure and Function of the Soil Microbial Community in the Yellow River Delta. Microorganisms, 12(12), 2419. https://doi.org/10.3390/microorganisms12122419

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop