Bacterial Communities and Their Predicted Functions Explain the Sediment Nitrogen Changes Along with Submerged Macrophyte Restoration

Variations in soil microbial communities in different saline soils under typical Populus spp. vegetation in alpine region of the Qaidam Basin, NW China

Salinization is a severe threat to agriculture and the environment in many areas, and the same in Qaidam Basin, Qinghai Province, Northwestern China. Microorganisms have an important influence on regulating the biochemical cycles of ecosystems; however, systematic research exploring microbial diversity and interactions with saline-soil ecosystems' environmental variables remains scarce. Thus, 16 S rRNA high-throughput sequencing was performed in this paper to characterize microbial diversity under different levels of salinized soils: non-salinized (NS, 2.25 g/L), moderately salinized (MS, 6.14 g/L) and highly salinized (HS, 9.82 g/L). The alpha diversity results showed that the HS soil was significantly different from the NS and MS soils. An analysis of similarity (ANOSIM) and a principal co-ordinates analysis (PCoA) indicated that NS and MS clustered closely while HS separated from the other two. Significant differences in microbial composition were observed at the taxonomic level. Proteobacteria (42.29-79.23 %) were the most abundant phyla in the studied soils. Gammaproteobacteria (52.49 and 66.61 %) had higher abundance in the MS and HS soils at the class level; Methylophaga and Pseudomonas were the predominant bacteria in the HS soil; and Azotobacter and Methylobacillus were abundant in the MS soil. Most genera belonging to Proteobacteria and Actinobacteria were detected via a linear discriminate analysis (LDA) effect size (LEfSe) analysis, which indicated that microbes with the ability to degrade organic matter and accomplish nutrient cycling can be well-adapted to salt conditions. Further analyses (redundancy analysis and Mantel test) showed that the microbial communities were mainly related to the soil salinity, electrical conductivity (EC1:5), total phosphorus (TP) and ammonia nitrogen (NH4+-N). Overall, the findings of the study can provide insights for better understanding the dominant indigenous microbes and their roles in biochemical cycles in different saline soils in the Qaidam Basin, Qinghai Province, China. The researches related to microbial community under typical poplar species should further clarify the mechanism of plant-microbial interaction and benefit for microbial utilization in salt soil remediation.

Enhancing phosphorus transformation in typical reddish paddy soil from China: Insights on long-term straw return and pig manure application via microbial mechanisms

Effective utilization of organic resources to activate residual phosphorus (P) in soil and enhance its availability is crucial for mitigating P resource scarcity and assessing the sustainable use of P in agricultural practices. However, the mechanisms through which organic resources affect soil P conversion via microorganisms and functional genes remain unknown, particularly in long-term organic-inorganic agricultural systems. In this study, we examined the impact of combined organic-inorganic fertilizer application on P availability, carbon (C) and P cycling genes, and microbial communities (bacterial and fungal) in reddish paddy soil based on a 42-year field experiment. The results indicated that long-term straw returning and pig manure application significantly augmented soil organic carbon (SOC), Olsen-P, microbial biomass carbon (MBC), microbial biomass phosphorus (MBP), enzyme-P, and CaCl2-P levels in paddy soils. Furthermore, these practices increased the abundance of soil C degradation genes, reduced the abundance of soil P cycling genes, and altered microbial community structure and network complexity. Notably, Module #3 ecological clusters in the fungal ecological co-occurrence network were significantly correlated with P cycling genes. Finally, our study demonstrated that long-term straw returning and pig manure application in paddy fields facilitated two robust and contrasting predictive relationships between C degradation (negative relationship) and P cycling (positive relationship) genes, respectively, and enzyme-P and HCl-P changes to improve soil P availability. This study can enhance our understanding of the role of soil microbial communities and functional genes in mediating P transformation to decipher the enhancement in P application efficiency driven by organic resources in reddish paddy soils.

Fungal, but not bacterial, diversity and network complexity promote network stability during roadside slope restoration

To restore degraded roadside ecosystems, conventional methods such as revegetation and soil amendment are frequently employed. However, our understanding of the long-term effects of these restoration approaches on soil microbial diversity and network complexity across different vegetation types remains poor, which contributes to poor restoration outcomes. In this study, we explored the effects of roadside slope restoration on microbial communities across different vegetation types at varying stages of restoration. We found that restoration time had a more pronounced impact on microbial diversity than specific vegetation type. As restoration progressed, microbial network complexity and fungal diversity increased, but bacterial diversity declined, suggesting that keystone taxa may contribute to network complexity. Interestingly, bacterial network complexity increased concomitant with decreasing network modularity and robustness, which may compromise system stability. Distinct vegetation types were associated with restoration-sensitive microbial communities at different restoration stages. Leguminouse and nitrogen-fixing plants, such as Albiziak alkora, Ginkgo biloba, Rhus chinensis, Rhapis excels, and Rubia cordifolia exhibited such associations after five years of restoration. These keystone taxa included Proteobacteria, Actinobacteria, Chloroflexi, Gemmatimonadota, and Myxococcota. We also found that bacterial alpha diversity was significantly correlated with restoration time, soil pH, moisture, available phosphate, nitrate nitrogen, and plant height, while fungal diversity was primarily shaped by restoration time. Together, our findings suggest that soil properties, environmental factors, vegetation type, and dominant species can be manipulated to guide the trajectory of ecological recovery by regulating the abundance of certain microbial taxa.

The proliferation of beneficial bacteria influences the soil C, N, and P cycling in the soybean-maize intercropping system

Soybean-maize intercropping system can improve the utilization rate of farmland and the sustainability of crop production systems. However, there is a significant gap in understanding the interaction mechanisms between soil carbon (C), nitrogen (N), and phosphorus (P) cycling functional genes, rhizosphere microorganisms, and nutrient availability. To reveal the key microorganisms associated with soil nutrient utilization and C, N, and P cycling function in the soybean-maize intercropping system, we investigated the changes in soil properties, microbial community structure, and abundance of functional genes for C, N, and P cycling under soybean-maize intercropping and monocropping at different fertility stages in a pot experiment. We found that there was no significant difference in the rhizosphere microbial community between soybean-maize intercropping and monocropping at the seeding stage. As the reproductive period progressed, differences in microbial community structure between intercropping and monocropping gradually became significant, manifesting the advantages of intercropping. During the intercropping process of soybean and maize, the relative abundance of beneficial bacteria in soil rhizosphere significantly increased, particularly Streptomycetaceae and Pseudomonadaceae. Moreover, the abundances of C, N, and P cycling functional genes, such as abfA, mnp, rbcL, pmoA (C cycling), nifH, nirS-3, nosZ-2, amoB (N cycling), phoD, and ppx (P cycling), also increased significantly. Redundancy analysis and correlation analysis showed that Streptomycetaceae and Pseudomonadaceae were significantly correlated with soil properties and C, N, and P cycling functional genes. In brief, soybean and maize intercropping can change the structure of microbial community and promote the proliferation of beneficial bacteria in the soil rhizosphere. The accumulation of these beneficial bacteria increased the abundance of C, N, and P cycling functional genes in soil and enhanced the ability of plants to fully utilize environmental nutrients and promoted growth.

Impact of Ecological Restoration on the Physicochemical Properties and Bacterial Communities in Alpine Mining Area Soils

Ecological restoration has notably impacted microbe and soil characteristics in abandoned open pit mines, especially in alpine regions. Yet, the adaptive responses of microbial communities in the initial years of mine site restoration remain largely unexplored. This study endeavors to offer a thorough comprehension of soil properties and microbial dynamics during the initial phases of alpine mining land reclamation. It places emphasis on physicochemical properties and microbial community composition and evaluates the feasibility of phytoremediation, along with proposing subsequent measures. Our study employs spatial sequence instead of time-sequenceal sequence to investigate early-stage changes in soil microbes and physicochemical properties in alpine mining land reclamation. We used high-throughput sequencing for the 16S rRNA amplicon study. Over time, soil physicochemical properties improved noticeably. Soil pH shifted from neutral to alkaline (7.04-8.0), while soil electrical conductivity (EC) decreased to 77 μS·cm-1 in R_6a. Cation exchange capacity (CEC) initially decreased from R_2a (12.30-27.98 cmol·kg-1) and then increased. Soil organic matter increased from 17.7 to 43.2 g·kg-1 over time during mine reclamation and restoration. The dominant bacterial community consisted of Proteobacteria (33.94% to 52.09%), Acidobacteriota (4.94% to 15.88%), Bacteroidota (6.52% to 11.15%), Actinobacteriota (7.18% to 9.61%), and Firmicutes (4.52% to 16.80%) with varying relative abundances. Gene annotation of sequences from various reclamation years revealed general function prediction, translation, ribosome structure, cell wall/membrane/envelope biogenesis, nucleotide translocation, and metabolism, along with other related functions. Mine reclamation improved soil fertility and properties, with the R_6a treatment being the most effective. Starting in the 2nd year of reclamation, the effective phosphorus content and the dominance of microbial bacteria, notably the Bacillus content, decreased. Firmicute fertilization promoted phosphorus and bacterial growth. In conclusion, employing a blend of sequencing and experimental approaches, our study unveils early-stage enhancements in soil microbial and physicochemical properties during the reclamation of alpine mining areas. The results underscore the beneficial impacts of vegetation restoration on key properties, including soil fertility, pore structure, and bacterial community composition. Special attention is given to assessing the effectiveness of the R_6a treatment and identifying deficiencies in the R_2a treatment. It serves as a reference for addressing the challenges associated with soil fertility and microbial community structure restoration in high-altitude mining areas in Qinghai-Tibet. This holds great significance for soil and water conservation as well as vegetation restoration in alpine mining regions. Furthermore, it supports the sustainable restoration of local ecosystems.

Burial or mineralization: Origins and fates of organic matter in the water-suspended particulate matter-sediment of macrophyte- and algae-dominated areas in Lake Taihu

Increased algal blooms and loss of aquatic vegetation are critical environmental issues associated with shallow lakes worldwide. The increase in organic matter (OM) in both macrophyte-dominated areas (MDAs) and algae-dominated areas (ADAs) has exacerbated these problems. Most OM in water is concentrated as suspended particulate matter (SPM), which eventually migrates to the sediment. However, the detailed origins and fates of OM in water-SPM-sediment systems with coexisting MDAs and ADAs remain unclear. Therefore, in this study, we conducted monthly field investigations in Lake Taihu, focusing on OM-migration patterns in an MDA and an ADA. The C/N mass ratios, δ13C contents, and OM compositions of the water, SPM, and sediment were analyzed. Our findings revealed that autochthonous sources of OM prevailed in water, whereas terrestrial sources prevailed in SPM and sediment. Rapid decomposition processes of microbial- and algae-derived dissolved OM were discovered along the water-SPM-sediment pathways in both areas. A trend towards a shift from macrophytes to algae in the MDA was also discovered. Overall, the entire lake underwent a burial process of OM in both types of areas, with mineralization mostly occurring during the algal-bloom seasons and more strongly in the ADA. Furthermore, we deduced that a decrease in the OM-burial rate, but an increase in the mineralization rate, might occur after a complete shift from a macrophyte- to an algae-dominated status. Such a shift might change the carbon-cycle process in eutrophic shallow lakes and should be given more attention in future research.

Response of dissolved organic matter (DOM) and microbial community to submerged macrophytes restoration in lakes: A review

Microorganisms play a crucial role in the biogeochemical processes of Dissolved Organic Matter (DOM), and the properties of DOM also significantly influence changes in microbial community characteristics. This interdependent relationship is vital for the flow of matter and energy within aquatic ecosystems. The presence, growth state, and community characteristics of submerged macrophytes determine the susceptibility of lakes to eutrophication, and restoring a healthy submerged macrophyte community is an effective way to address this issue. However, the transition from eutrophic lakes dominated by planktic algae to medium or low trophic lakes dominated by submerged macrophytes involves significant changes. Changes in aquatic vegetation have greatly affected the source, composition, and bioavailability of DOM. The adsorption and fixation functions of submerged macrophytes determine the migration and storage of DOM and other substances from water to sediment. Submerged macrophytes regulate the characteristics and distribution of microbial communities by controlling the distribution of carbon sources and nutrients in the lake. They further affect the characteristics of the microbial community in the lake environment through their unique epiphytic microorganisms. The unique process of submerged macrophyte recession or restoration can alter the DOM-microbial interaction pattern in lakes through its dual effects on DOM and microbial commu-----nities, ultimately changing the stability of carbon and mineralization pathways in lakes, such as the release of methane and other greenhouse gases. This review provides a fresh perspective on the dynamic changes of DOM and the role of the microbiome in the future of lake ecosystems.

A limited overlap of interactions between the bacterial community of water and sediment in wetland ecosystem of the Yellow River floodplain

Introduction

Aquatic ecosystems in floodplains provide homes for a variety of active bacterial populations. However, the coexistence pattern of bacterial communities of water and sediment in these ecosystems is unclear.

Methods

In the present study, Illumina Mi-Seq sequencing were to assess bacteria's co-occurrence patterns in the water and sediment of different time dynamics and plant communities of the Yellow River floodplain ecosystem.

Results and discussion

The results showed that compared to water, the α-diversity of the bacterial community was way greater in sediment. The bacterial community structure significantly differed between water and sediment, and there was a limited overlap of interactions between the bacterial community of water and sediment. In addition, bacteria in water and sediment coexisting show different temporal shifts and community assembly patterns. The water was selected for specific groups of microorganisms that assemble over time in a non-reproducible and non-random way, whereas the sediment environment was relatively stable, and the bacterial communities were gathered randomly. The depth and plant cover significantly influenced the structure of a bacterial community in the sediment. The bacterial community in sediment formed a more robust network than those in water to cope with external changes. These findings improved our comprehension of the ecological trends of water and sediment bacterium colonies coexisting enhanced the biological barrier function, and the capacity of floodplain ecosystems to provide services and offered support for doing so.

Community structure and function of epiphytic bacteria attached to three submerged macrophytes

In aquatic ecosystems, large amounts of epiphytic bacteria living on the leaf surfaces of submerged macrophytes play important roles in affecting plant growth and biogeochemical cycling. The restoration of different submerged macrophytes has been considered an effective measure to improve eutrophic lakes. However, the community ecology of epiphytic bacteria is far from well understood for different submerged macrophytes. In this study, we used quantitative PCR, 16S rRNA gene high-throughput sequencing and functional prediction analysis to explore the structure and function of epiphytic bacteria in an aquatic ecosystem recovered by three submerged macrophytes (Hydrilla verticillata, Vallisneria natans and Potamogeton maackianus) during two growth periods. The results showed that the community compositions and functions of epiphytic bacterial communities on the submerged macrophyte hosts were different from those of the planktonic bacterial communities in the surrounding water. The alpha diversity of the epiphytic bacterial community was significantly higher in October than in July, and the community compositions and functions differed significantly in July and October. Among the three submerged macrophytes, the structures and functions of the epiphytic bacterial community exhibited obvious differences, and some specific taxa were enriched on the biofilms of the three plants. The alpha diversity and the abundance of functions related to nitrogen and phosphorus transformation were higher in the epiphytic bacteria of P. maackianus. In summary, these results provide clues for understanding the distribution and formation mechanisms of epiphytic bacteria on submerged macrophyte leaves and their roles in freshwater ecosystems.

Variation of soil bacterial communities in a chronosequence of citrus orchard

Purpose

Soil microorganisms are vital for soil ecosystems through bioconversion of soil nutrients and maintenance of soil fertility to promoting the growth and development of citrus. However, understanding of how different planting years affect the soil bacterial community structures as related to nutrient availability in citrus orchards is limited.

Methods

Here, Illumina MiSeq technology was used to investigate changes in bacterial community structures with different ages of citrus orchards that were 2, 5, 10, 15, and 18 years old.

Results

The data showed that (1) soil bacterial community structures changed over the different growth stages of citrus orchards. With the extension of plantation age, the microbial diversity of citrus orchards increased gradually so that it was highest in 10-year-old citrus plantations but then decreased where the diversity of 18-year-old citrus ages was significantly lower than that of 10 and 15-year-old ones. Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi were the four dominant phyla in soil of citrus orchards, accounting for 30.85%, 24.89%, 14.27%, and 14.05% of the total soil bacterial communities, respectively. (2) Soil bacterial community structures in different succession stages were affected by soil pH and nutrients, in particular available potassium (AK).

Conclusion

This study advances the understanding of soil microbiota of orchards and their interactions related to environmental factors in citrus orchard, which will improve our ability to promote the function of soil bacteria, so as to improve soil pH and reduce potassium (K) fertilizer input and improve the fruit quality.

Response of sediment and water microbial communities to submerged vegetations restoration in a shallow eutrophic lake

Submerged macrophytes are the main primary producers in shallow lakes and play an important role in structuring communities. Aquatic microbes are also an important component of aquatic ecosystems and play important roles in maintaining the health and stability of ecosystems. However, little is known about the interactions between macrophytes and microbes during the reintroduction of submerged vegetation. Here, we chose restored zones dominated by four different submerged vegetations and a bare zone in a shallow eutrophic lake to unveil the microbial diversity, composition and structure changes in sediment and water samples after submerged macrophytes were recovered for one and a half years (July 2019) and two years (April 2020). We found that the recovery of submerged vegetations decreased phosphorus content in water and sediments but increased nitrogen and carbon content in sediments. We observed that the transparency of water in the restored zones was significantly higher than that in the bare zone in July. The recovery of submerged vegetations significantly influenced the alpha diversity of bacterial communities in sediments, with higher values observed in restored zones than in bare zones, whereas no significant influence was found in the water samples. In July, the macrophyte species showed strong effects on the bacterial community composition in water and relatively little effect in sediment. However, a strong effect of the macrophyte species on the composition of bacterial communities in sediments was observed in April, which may be related to the decomposition of plant litter and the decay of detritus. Additionally, the dissimilarity of the sedimentary bacterial community may increase more slowly with environmental changes than the planktonic bacterial community dissimilarity. These results suggest that the large-scale restoration of aquatic macrophytes can not only improve water quality and change sediment characteristics but can also affect the diversity and compositions of bacterial communities, and these effects seem to be very long-lasting.

Responses of the Soil Microbial Community to Salinity Stress in Maize Fields

To investigate the diversity and structure of soil bacterial and fungal communities in saline soils, soil samples with three increasing salinity levels (S1, S2 and S3) were collected from a maize field in Yanqi, Xinjiang Province, China. The results showed that the K⁺, Na⁺, Ca²⁺ and Mg²⁺ values in the bulk soil were higher than those in the rhizosphere soil, with significant differences in S2 and S3 (p < 0.05). The enzyme activities of alkaline phosphatase (ALP), invertase, urease and catalase (CAT) were lower in the bulk soil than those in the rhizosphere. Principal coordinate analysis (PCoA) demonstrated that the soil microbial community structure exhibited significant differences between different salinized soils (p < 0.001). Data implied that the fungi were more susceptible to salinity stress than the bacteria based on the Shannon and Chao1 indexes. Mantel tests identified Ca²⁺, available phosphorus (AP), saturated electrical conductivity (EC_e) and available kalium (AK) as the dominant environmental factors correlated with bacterial community structures (p < 0.001); and AP, urease, Ca²⁺ and EC_e as the dominant factors correlated with fungal community structures (p < 0.001). The relative abundances of Firmicutes and Bacteroidetes showed positive correlations with the salinity gradient. Our findings regarding the bacteria having positive correlations with the level of salinization might be a useful biological indicator of microorganisms in saline soils.

Effects of different vegetable rotations on the rhizosphere bacterial community and tomato growth in a continuous tomato cropping substrate

In this study, High throughput sequencing was used to analyze the effects of different vegetable rotations on the rhizosphere bacterial diversity and community structure in a substrate that was used for continuous tomato cropping (CK). The vegetable rotations tested were cabbage/tomato (B), kidney bean/tomato (D), and celery/tomato (Q). The results revealed that the substrate bacterial diversity and richness of each crop rotation were higher than those of CK. The highest bacterial diversity was found in the B substrate, followed by the Q and D substrates. Further comparison showed that the rhizosphere bacterial community structure of Q substrate was significantly different to that of CK. Compared with the CK, the Q substrate had a significantly higher relative abundance of several dominant microflora, such as Acidobacteria, Chloroflexi, and Firmicutes. Additionally, the Q rotation significantly increased the abundance of beneficial bacteria, such as Actinobacteria_unclassified and Anaerolineaceae_unclassified. A redundancy analysis showed that Most dominant bacteria correlated positively with the substrate pH, total N, and alkali-hydrolyzable N but negatively with the available P, available K, total P, total K, and organic matter contents and substrate EC. The substrates after crop rotation improved the growth and physiological condition of the subsequent tomato plants, among which those from the Q rotation performed the best. Therefore, celery rotation not only increased the richness and diversity of bacterial communities in the substrate but also significantly increased the richness of the beneficial bacterial communities, allowing better maintenance of the substrate microenvironment for the healthy growth of crops.

Sediments nitrogen cycling influenced by submerged macrophytes growing in winter

Restoration of submerged macrophytes is one of the important measures for ecological treatment of eutrophic lakes. The changes in physical and chemical conditions caused by submerged macrophytes also affect the process of benthic nitrogen cycling. The growth period of Potamogeton crispus is mainly in winter. In order to understand the effect of submerged macrophytes growing in winter on nitrification rate and denitrification rate in the process of nitrogen cycling, experiments were carried out from winter to summer with vegetated and non-vegetated treatments. The results showed that the effect of submerged macrophytes on water temperature was not significant in winter. The nitrogen cycling was mainly affected by variables, which were inorganic nitrogen and dissolved oxygen. Submerged macrophytes had little effect on nitrification rate, but had a certain inhibition on denitrification rate by providing oxygen from photosynthesis. In total, submerged macrophytes growing in winter have little effect on nitrogen cycling in sediment. However, submerged macrophytes growing in winter can increase the attachment surface of microbes and inhibit resuspension of sediment, which play a complementary role to submerged macrophytes growing in summer for maintaining stability of eutrophic lakes.

Sediment Bacterial Community Structure Under the Influence of Different Domestic Sewage Types

Sediment bacterial communities are critical to the biogeochemical cycle in river ecosystems, but our understanding of the relationship between sediment bacterial communities and their specific input streams in rivers remains insufficient. In this study, we analyzed the sediment bacterial community structure in a local river receiving discharge of urban domestic sewage by applying Illumina MiSeq high-throughput sequencing. The results showed that the bacterial communities of sediments samples of different pollution types had similar dominant phyla, mainly Proteobacteria, Actinobacteria, Chloroflexi and Firmicutes, but their relative abundances were different. Moreover, there were great differences at the genus level. For example, the genus Bacillus showed statistically significant differences in the hotel site. The clustering of bacterial communities at various sites and the dominant families (i.e., Nocardioidaceae, and Sphingomonadaceae) observed in the residential quarter differed from other sites. This result suggested that environmentally induced species sorting greatly influenced the sediment bacterial community composition. The bacterial cooccurrence patterns showed that the river bacteria had a nonrandom modular structure. Microbial taxonomy from the same module had strong ecological links (such as the nitrogenium cycle and degradation of organic pollutants). Additionally, PICRUSt metabolic inference analysis showed the most important function of river bacterial communities under the influence of different types of domestic sewage was metabolism (e.g., genes related to xenobiotic degradation predominated in residential quarter samples). In general, our results emphasize that the adaptive changes and interactions in the bacterial community structure of river sediment represent responses to different exogenous pollution sources.

Bacterial community responses to tourism development in the Xixi National Wetland Park, China

A large number of urban wetland parks have been established, but knowledge about the effects of tourism development on the microbial diversity and ecosystem functioning remains limited. This study aimed to clarify the responses of bacterial communities to tourism development targeted the Xixi National Wetland Park, China. By analyzing the diversity, composition, assembly pattern, and environmental drivers of bacterial communities, we found that tourism development considerably affected the water quality, which further decreased the α-diversity but increased the β-diversity in open areas for landscaping and recreation. Specifically, there was higher Simpson dissimilarity across functional wetland areas, indicating that species replacement mainly explained β-diversity patterns of bacterial communities. RDA analysis and ecological processes quantification further suggested that TOC and TC were the major factors in the open areas driving bacterial communities in water and sediment, respectively. Also, typical anti-disturbance taxa (Gammaproteobacteria) and potential pathogens (Bacillus) were enriched in the wetlands under more anthropogenic disturbances. Findings of the present study highlighted the effects of tourism development on bacterial communities resulted in obvious spatial variation in the Xixi National Wetland Park. This study gives us useful information for ecological assessments of urban wetlands, and further can provide references in making appropriate strategies to manage wetland ecosystems.

Variations in pH significantly affect cadmium uptake in grafted muskmelon (Cucumis melo L.) plants and drive the diversity of bacterial communities in a seedling substrate

Substrates are fundamental prerequisites for growing grafted seedlings. In this study, substrates with different pH levels (5.0, 5.5, 6.0, 6.5, 7.0, and 8.0) were set up to elucidate the effect of pH on cadmium (Cd) uptake in grafted muskmelon (Cucumis melo L.) plants. Bacterial diversity was also investigated. Results showed that pH and high Cd concentration greatly affected the growth of grafted plants. The chlorophyll content of the muskmelon leaves decreased at 100 μM Cd. The majority of the Cd ions accumulated in the rootstock rather than in the shoot tissue in all of the treatments. The shoots and roots showed the highest Cd content at pH 5.5 and the lowest Cd content at pH 8.0 regardless of the Cd concentration. The operational taxonomic units belonging to Proteobacteria and Bacteroidetes were significantly (p < 0.05) enriched at different substrate pH levels compared with those at pH 5.0. The operational taxonomic units belonging to the phyla Firmicutes, Acidobacteria, and Chloroflexi were significantly decreased. The available nitrogen, phosphorus, Cd, and pH were strongly linked to bacterial community compositions. On the contrary, the available potassium was weakly correlated with the bacterial structure. This study demonstrates that pH greatly affects Cd uptake in grafted muskmelon plants and predicts microbial community structures in breeding substrates with different pH levels. Our results suggest that Cd accumulation in grafted plants can be reduced by setting the appropriate substrate pH. This work can serve as a reference for growing high-quality grafted plants and ensuring food safety in the presence of Cd contamination.