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Brief Report

Examining the Diversity of Rhizosphere Soil Bacterial Communities and Screening of Growth-Promoting Bacteria from the Rhizosphere Soil of Haloxylon ammodendron in Xinjiang

by
Xuejing Wang
1,2,3,†,
Yong Chen
4,†,
Zeyu Wang
4,
Wenfang Luo
1,
Junhui Zhou
1,
Xiaoyan Xin
1,5,
Rui Guo
1,3,
Qingyue Zhu
1,5,
Lili Wang
3,* and
Suqin Song
1,2,*
1
Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis Ministry of Agriculture, Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
2
Xinjiang Key Laboratory of Special Environmental Microbiology, Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
3
School of Agrculture, Xinjiang Agricultural University, Urumqi 830052, China
4
Institute of Soil, Fertilizer and Agricultural Water Conservation, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
5
College of Food Science and Pharmacology, Xinjiang Agricultural University, Urumqi 830052, China
*
Authors to whom correspondence should be addressed.
†
These authors are co-first authors.
Microbiol. Res. 2024, 15(3), 1346-1358; https://doi.org/10.3390/microbiolres15030091 (registering DOI)
Submission received: 29 March 2024 / Revised: 1 June 2024 / Accepted: 13 June 2024 / Published: 27 July 2024
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Abstract

:
The bacterial communities in rhizosphere soil interact with the roots of plants. This interaction is beneficial for both the bacteria and the plants, which makes it very important to identify the structure of these bacterial communities for plant growth and development. However, the composition characteristics of bacterial communities in rhizosphere soil of 2-year and 5-year Haloxylon ammodendron have not been clearly defined. The purpose of this study was to identify the diverse composition of 2-year and 5-year Haloxylon ammodendron in Turpan, Xinjiang. Thus, rhizosphere soil bacteria were analyzed by isolating, purifying, and identifying the species through high-throughput sequencing technology. The bacterial strains in the rhizosphere soil of Haloxylon ammodendron were isolated with the dilution coating method, resulting in 37 isolated strains. The selective media were used to screen the growth-promoting characteristics of the rhizosphere soil isolates of Haloxylon ammodendron. The results of high-throughput amplification sequencing showed that the rhizosphere bacteria in the 2-year rhizosphere soil belonged to 45 phyla, 109 classes, 288 orders, 451 families, 826 genera, and 404 species, and those in the 5-year rhizosphere soil belonged to 56 phyla, 148 classes, 369 orders, 601 families, 1062 genera, and 671 species. Among them, Firmicutes, Proteobacteria, Actinobacteriota, Bacteroidota, Crenarchaeota, and so on are the dominant bacteria. There were 12206 and 14,053 OTUs in the 2-year-old and 5-year-old rhizosphere soil bacteria, respectively, and 3329 OTUs in the 2-year- and 5-year-old rhizosphere soil, accounting for 16.98% of the total number of OTUs. The results showed that three strains, sg16, sg21, and ss4, had the highest inorganic phosphorus solubility index (1.58). The isolated strain did not have the ability to dissolve organophosphorus and potassium, while the screened strain sg16 had the ability to fix nitrogen. Two strains with a good iron-bearing capacity, Sg9F and Sg1, were screened, among which Sg9F had the highest D/d value and Sg9F had the strongest iron-bearing capacity. The results showed that 37 strains of rhizosphere soil bacteria belonged to six genera. They are Bacillus, Corynebacterium, Phyllobacterium, Lysinibacillus, Sinorhizobium meliloti, and Streptomyces levis. Among them are sg21 (Bacillus sp.), sg1 (Bacillus sp.), sg9F (Streptomyces levis), sg16 (Phyllobacterium phragmitis), and ss4 (Sinorhizobium meliloti). This study provides a particular research basis for the influence of Haloxylon ammodendron rhizosphere bacteria on soil nutrient release and depicts a solution for improving the yield and quality of cistanche deserticola indirectly through isolating, screening, and identifying rhizosphere soil bacteria, including screening strains with growth-promoting functions and analyzing the population structure of rhizosphere bacteria in 2- and 5-year soil in combination with high-throughput sequencing technology.

1. Introduction

Haloxylon ammodendron (C. A. Meyer) Bunge is a perennial shrub or small tree in the Chenopodiaceae family [1,2]. It is a dominant species in the desert flora of Northwest China and Inner Mongolia with a high tolerance for drought, salt and alkali, and its roots are particularly tolerant of barren soil. Moreover, its rhizosphere contains rich culturable bacteria and a large number of unique microbial resources [3,4,5,6,7]. The roots of the plant contain a very valuable Chinese medicine—cistanche. Cistanche deserticola, known as “desert ginseng”, has bowel-relaxing abilities, anti-aging effects, and liver-protecting capabilities [8]. The existing research on Haloxylon ammodendron is only focused on cultivation techniques; soil physical and chemical properties; and resistance to drought, high-temperature, cold, salty, and alkaline conditions. Studies of the molecular biology and molecular genetics of stress resistance have also attracted attention from researchers [1,2,3,4]. However, there are relatively few studies on the rhizosphere bacterial community and rhizosphere growth-promoting bacteria.
Rhizosphere microorganisms are a very important part of soil ecosystems and are essential for plant health and growth [9]. At present, research on rhizosphere microorganisms focuses on the function of the rhizosphere microbial community [10], and there are relatively few research studies on how rhizosphere microorganisms regulate the quality and yield of medicinal plants. Rhizosphere microorganisms could be helpful for solving practical production and application problems, such as disease prevention and the control of medicinal plants and continuous cropping obstacles, and for improving the quality and yield of medicinal plants [11].
Plant rhizosphere growth-promoting bacteria (PGPR) can improve the utilization efficiency of nitrogen, phosphorus, and potassium fertilizers; promote plant growth in soil lacking nitrogen, phosphorus, and potassium; and regulate the microbial community structure of rhizosphere soil [12]. They can also inhibit the adverse effects of harmful pathogens on plant growth, development, and yield [13,14], accelerate the cycle of rhizosphere nutrient elements, and provide help to regulate soil fertility and plant health [15]. In recent years, high-throughput sequencing technology has been widely used in the study of plant rhizospheres and phyllosphere microbial community structures. Cao et al. [16] used real-time fluorescent quantitative PCR combined with MiSeq amplicon sequencing to compare their effects on microbial abundance and community structure in the rhizosphere at three soil depths (0–20, 20–40, and 40–60 cm). It was found that eutrophic bacteria (Firmicutes, Proteobacteria, and Bacteroidota), nitrogen-fixing bacteria, and ammonia-oxidizing bacteria exist in the rhizosphere of Haloxylon ammodendron, with strong microbial activity. Shen Liang et al. studied and analyzed the correlation between cistanche parasitism and rhizosphere microorganisms with regard to their effects on the environmental factors of Halaxel [17].
In this study, high-throughput sequencing technology was used to study the diversity of bacterial microbial community structures in 2-year and 5-year Haloxylon ammodendron rhizosphere soil in Turpan, Xinjiang. At the same time, Haloxylon ammodendron rhizosphere growth-promoting bacteria capable of phosphorous solubilization, nitrogen fixation, and stimulating iron-producing carriers were also screened from the culturable bacteria in the rhizosphere soil, providing a research basis for exploring the composition of bacteria in the rhizosphere soil and promoting the growth of Cistanola deserticola.

2. Materials and Methods

2.1. Test Materials

A five-point sampling method was used to collect 2-year and 5-year Haloxylon ammodendron rhizosphere soil samples from Gaochang, Turpan City, Xinjiang, whereby 3 samples were collected from each of the 10 regions. The collected soil was quickly transported to the laboratory, mixed with a 2 mm sieve, labeled, and stored in the refrigerator at 4 °C and −80 °C, respectively.

2.2. Analysis of Bacterial Microbial Diversity in Rhizome Soil of Haloxylon ammodendron via High-Throughput Sequencing

2.2.1. Data Processing of High-Throughput Sequencing Information

A small fragment library was constructed according to the characteristics of the amplified region, and double-terminal sequencing was performed using the Illumina NovaSeq sequencing platform. After the splicing and filtering of reads, OTU (operational taxonomic unit) clustering or ASV (amplicon sequence variant) noise reduction, species annotation, and abundance analysis were all performed on the obtained valid data, thus revealing the species composition of the sample [18].

2.2.2. Data Analysis

The final valid data were grouped into operational taxonomic units (OTUs) with UCLUS in QIIME software [19] at a 97% similarity level, and OTUs were annotated based on bacterial NCBI and fungal UNITE taxonomic databases. Then, the species composition and diversity index of OTUs were analyzed [20].

2.3. Separation and Purification of Rhizome Soil Strains of Haloxylon Ammodendron

The collected rhizosphere soil was air-dried under natural conditions and refined with a sterile mortar. Then, 1 g of rhizosphere soil was weighed and 9 mL of sterile water was added. This was subsequently mixed with a vortex, left for 30 min, and finally diluted with a gradient of 10−2, 10−3, 10−4, 10−5, and 10−6 times through a dilution coating method. A total volume of 100 μL of suspension was coated on LB, PDA, and Gau I media [21] and cultured at 28 °C for 7 days. Single colonies on the media were selected, purified, and then stored in the refrigerator at 4 °C on an inclined surface.

2.4. Analysis of 16S rDNA Sequence of Rhizosphere Soil Bacteria

The 16S rDNA sequence determination was conducted as follows: Bacterial strain DNA was extracted by freezing the solution [22]. The purified and cultured bacteria were selected with an aseptic inoculation ring and placed into an aseptic centrifuge tube containing 30 μL of aseptic water. The bacteria and aseptic water in the centrifuge tube were thoroughly mixed with oscillators. Then, the centrifuge tube containing the bacterial solution was frozen in liquid nitrogen for 10 min, removed, and immediately placed on a floating tray in boiling water for 5 min. After removal, centrifugation was conducted at 12,000 r/min for 2 min. The supernatant in the centrifuge tube, the DNA template, and the major instruments and equipment used are listed in Table S1. According to the bacterial genomic DNA kit method of Shenggong Bioengineering (Shanghai) Co., Ltd., Shanghai, China, DNA was extracted as the template, and the bacterial universal primers 27F and 1492R were used for PCR amplification (Table S2) [23]. The PCR system was as shown in Table S3, and with PCR conditions (Table S4). The PCR products were detected using 1.0% agarose gel electrophoresis. They were determined by personnel from Xinjiang Youkang Biotechnology Co., Ltd., Urumqi, China. The sequencing results were blasted on the NCBI website, and a phylogenetic tree was constructed using MEGA 5 software.

2.5. Growth-Promoting Bacteria Screening

2.5.1. Screening of Phosphorus-Solubilizing Bacteria

The inorganic phosphorus [24] and organophosphorus [25] media were divided into 6 regions on average. Sterile toothpicks were used to inoculate the isolated and purified rhizosphere soil bacteria in these 6 regions, respectively, which was repeated 3 times for each group before they were incubated at 28 °C at constant temperature. After 7 days, the diameters of the phosphorus-solubilizing circle (D) and the colony (d) were measured, respectively, and the ratio of the diameter of the phosphorus-solubilizing circle and the colony was calculated to determine the strength of the phosphorus-solubilizing ability [26].

2.5.2. Screening of Potassium-Solubilizing Bacteria

The strain was inoculated on the silicate bacteria medium [27] via the dot method and cultured at 28 °C for 7 days. The yellow halo of the colony was observed every 24 h. After 7 days, the potassium solubility of the strain was determined according to the halo size.

2.5.3. Nitrogen-Fixing Bacteria Screening

The isolated strains were connected to six regions of Ashby medium [28] with sterile toothpicks and cultured at 28 °C for 7 days. The bacterial colonies with viscous, translucent growth and white, brown, or dark brown color were considered to have nitrogen-fixing ability, which was determined according to the growth diameter of the bacterial colonies.

2.5.4. Screening of Iron-Producing Carrier Strains

The isolated strain was connected to the chromium azurin (CAS) medium [29] and cultured in an incubator at 28 °C for 7 days. The CAS plate changed from blue to orange, indicating that the strain produced a ferriferous carrier. The strength of the strain’s ferriferous carrier-producing capacity was judged according to the size of the orange ferriferous carrier halo measured.

3. Results

3.1. In-Depth Analysis of Sequencing

Whether the amount of sample sequencing data is reasonable can be reflected through the rarefaction curve. The results of the bacterial sample dilution curve, which are shown in Figure 1, demonstrate that the 2-year and 5-year dilution curves of soil samples sequenced in this time gradually leveled off as the sequencing depth increased. This indicates that the amount of data sequenced in this time was sufficient and the sequencing results were reasonable and representative, and could be used for subsequent analysis [30].

3.2. Comparative Analysis of Phylum Level

The results of high-throughput amplification sequencing showed that the rhizosphere soil bacteria belonged to 45 phyla, 109 classes, 288 orders, 451 families, 826 genera, and 404 species. The rhizosphere bacteria belonging to 56 bacterial phyla, 148 classes, 369 orders, 601 families, 1062 genera, and 671 species were distributed in the rhizosphere soil over a period of 5 years. The dominant bacterial phyla are Firmicutes, Proteobacteria, Actinobacteriota, Bacteroidota, Crenarchaeota, Patescibacteria, Chloroflexi, Gemmatimonadota, Myxococcota, Acidobacteriota, etc. The relative abundance of bacteria in the rhizosphere soil was 31.59%, 36.24%, 3.67%, 5.45%, 0.81%, 3.01%, 4.21%, 4.12%, 1.41%, and 2.26%, respectively. The relative abundance of bacteria in rhizosphere soil after 5 years was 27.73%, 33.36%, 13.61%, 7.16%, 2.57%, 2.01%, 3.51%, 1.47%, 1.33%, and 1.69%, respectively. There was no significant difference between 2 and 5 years at door level. The sum of relative abundance of Firmicutes, Proteobacteria, Actinobacteriota, and Bacteroidota is over 70%. Firmicutes and Proteobacteria decreased with an increase in tree age, while Bacteroidota decreased with an increase in tree age. Actinobacteriota, Bacteroidota, and Crenarchaeota increased with an increase in tree age (Figure 2).

3.3. Comparative Analysis of Genus Level

The composition of the rhizosphere soil bacterial community of Haloxylon ammodendron was analyzed. The dominant bacterial genera are Pseudomonas, Bacillus, Acinetobacter, Nitrosopumilaceae, Lactobacillus, Ralstonia, Marinobacter, Viridibacillus, Pseudarthrobacter, Achromobacter, etc. The relative abundance of bacteria in the rhizosphere soil of Haloxylon ammodendron after 2 years was 9.32%, 11.68%, 2.71%, 0.24%, 2.71%, 1.34%, 0.94%, 1.64%, 0.04%, and 1.70%, respectively. The relative abundance of bacteria in the rhizosphere soil after 5 years was 1.16%, 10.18%, 2.74%, 1.71%, 1.47%, 1.51%, 1.26%, 1.61%, 2.61%, and 2.49%, respectively (Figure 3).

3.4. Species Distribution of Rhizosphere Soil Bacteria in 2-Year and 5-Year Haloxylon ammodendron Soil at Taxonomic Level

The rhizosphere soil bacteria in the two-year period belonged to 45 phyla, 109 classes, 288 orders, 451 families, 826 genera, and 404 species, and the rhizosphere soil bacteria in the five-year period belonged to 53 phyla, 139 classes, 345 orders, 555 families, 1062 genera, and 513 species, respectively (Table 1).

3.5. OTU Clustering

The results of difference analysis show differences between the rhizosphere bacterial communities of 2- and 5-year-old Haloxylon ammodendron. There were 12,206 and 14,053 OTUs, respectively, in the rhizosphere soil bacteria of 2- and 5-year-old Haloxylon ammodendron, and 3329 OTUs in the rhizosphere soil bacteria of different tree ages, accounting for 16.98% of the total number of OTUs (Figure 4).

3.6. Diversity of Rhizosphere Bacterial Microbial Community α

It can be seen from the coverage index that the sequenced soil bacterial samples reached more than 98% among the bacterial groups, indicating the rhizosphere bacterial diversity of Haloxylon ammodendron. The diversity (Shannon) and richness (Chao1) indexes of rhizosphere bacteria of 5 years were higher than those of 2 years (Table 2).

3.7. PCA

PCA was used to investigate the structural differences of rhizosphere bacterial communities of Haloxylon ammodendron at 2 and 5 years, and the interpretation of PC1 (principal component 1) and PC2 (principal component 2) was 7.89% and 5.83%, respectively, and the total interpretation of the two was 13.72% (Figure 5). Through calculating the binary Jaccard distance matrix for principal coordinate axis analysis (PCoA), the partition was found to be not obvious, indicating that there was no significant difference in the bacterial microbial community structure of the rhizosphere soil of Haloxylon ammodendron in 2 and 5 years.

3.8. Analysis of 16Sr DNA Sequence in Rhizosphere Soil Bacteria of Haloxylon ammodendron

A total of 37 strains were isolated from the rhizosphere soil bacteria of Haloxylon ammodendron. Universal primers were used for the amplification of the isolated strains, obtaining 16S rDNA sequencing with a length of 1500 bp. The results showed that 37 strains of rhizosphere soil bacteria belonged to six genera: Bacillus, Corynebacterium, Phyllobacterium, Lysinibacillus, Sinorhizobium meliloti, and Streptomyces levis. Among them, sg21 and Bacillus sp. reached 100%, sg1 and Bacillus sp. reached 100%, and sg9F and Streptomyces levis reached 100%. sg16 and Phyllobacterium phragmitis formed a cluster with 99.85% similarity, and ss4 formed a cluster with Sinorhizobium meliloti with 99.75% similarity (Figure 6).

3.9. Screening of Growth-Promoting Bacteria in the Rhizosphere soil of Haloxylon ammodendron

3.9.1. Phosphorus Solubilization Capacity

The phosphorus-solubilizing cycle method was used to screen the phosphorus-solubilizing ability of soil rhizosphere bacteria isolated from Haloxylon ammodendron [26]. The experimental results showed that there were four strains of bacteria that produced phosphorus-solubilizing circles, namely Sg16, sg21, ss4, and ss5, among which sg16 had the highest (1.58), ss4 had the second highest (1.34), and sg21 had the lowest inorganic phosphorus soluble index (1.23) (Table 3). At the same time, these strains did not show the ability to dissolve organophosphorus.

3.9.2. Potassium Capacity

Yellow halos were not observed in the culture medium of the isolated strains, indicating that these strains did not have the ability to dissolve potassium.

3.9.3. Nitrogen-Fixing Capacity

One strain, sg16, was screened on Ashby medium. The round surface of the sg16 colony was viscous, shiny, and translucent (Figure 7).

3.9.4. Iron-Bearing Capacity

Strains with a siderophore-producing ability were screened according to whether each strain produced orange siderophore halos in the CAS medium. A total of two strains with good iron-bearing capacity were screened from the isolated bacteria. The D/d value of Sg9F was up to 6.94, and the solubility index of sg1 was 1.56, indicating that Sg9F had the strongest iron-bearing capacity (Table 4).

4. Discussion

Soil microorganisms are the key drivers of plant productivity in the terrestrial ecosystem. Therefore, we studied and analyzed the Cistanche deserticola–Haloxylon ammodendron bacterial community structure of rhizosphere soil bacteria and the screening of growth-promoting bacteria. This study is of great significance for the influence of rhizosphere bacteria on soil nutrient release, improvement of cistanche yield and quality, and access to nutrient elements [31]. Therefore, we studied and analyzed the bacterial microbial community structure in the rhizosphere soil as well as the screening of growth-promoting bacteria.
The number of bacteria in plant rhizosphere microorganisms is the largest, and the types of soil microorganisms will also change when the external environment changes [32,33]. The variation in bacterial diversity in the rhizosphere soil of Cistanche deserticola-Haloxylon ammodendron in Gaochang District of Turpan City, Xinjiang Province, was studied for the first time in this study using high-throughput amplification sequencing. The dominant rhizosphere soil bacteria in 2 and 5 years were Firmicutes, Proteobacteria, Actinobacteriota, and Bacteroidota, and the total relative abundance of these four groups was over 70%. This is consistent with the research results of Wang Anlin, who showed that Proteobacteria, Actinomycetes, Cyanobacteria, and Chloromycetes accounted for 76.05% of the relative abundance of soil bacteria in the forest, belonging to the dominant bacteria in soil [34].
It was found that the relative abundance of Firmicutes, Proteobacteria, and Patescibacteria in two years was higher than that in five years. The relative abundance of 5-year-old Actinobacteriota, Bacteroidota, and Crenarchaeota is higher than that of 2-year-old Haloxylon ammodendron, but the relative abundance difference is between 1 and 10%, which is not significant. Studies have shown that Proteobacteria is widely distributed, among which Rhizobium sp., Shinella zoogloeoides, Pseudomonas fluorescens, Pseudomonas extremaustralis, Sphingomonas paucimobilis, Stenotrophomonas sp., and others have strong nitrogen fixation ability and exceptional morphological and physiological characteristics, resulting in considerable competitive advantages in the ecological niche [35]. In addition, the relative abundance of actinomycetes in the rhizosphere soil of Haloxylon is significantly higher because actinomycetes are Gram-positive bacteria, which not only have strong drought resistance, but also participate in the complex decomposition process of organic matter, providing favorable conditions for the growth and development of plants [36]. Chloroflexi is a phototrophic microorganism that is mainly involved in microbial photosynthesis [37].
In this study, the relative abundance of Pseudomonas, Bacillus, and Lactobacillus was higher in the 2-year-old species than in the 5-year-old species, while Acinetobacter, Nitrosopumilaceae and Ralstonia were higher after 5 years than after 2 years. Pseudomonas and Bacillus are basophilic bacteria whose living environment is alkaline soil, carbonate lake, and a high-pH environment [38].
Studies have shown that the number of microorganisms in the rhizosphere soil of Haloxylon ammodendron in different growth years are different to varying degrees, which is related to the species and content of root exudates of Haloxylon ammodendron growing under different environmental conditions [39]. In this study, there were differences between the rhizosphere bacterial communities of 2- and 5-year-old Haloxylon haloxylon. There were 10,724 unique OTUs in the rhizosphere soil of 5-year-old Haloxylon ammodendron and 3329 OTUs in the rhizosphere soil of different tree ages, accounting for 16.98% of the total number of OTUs. It can be seen that the microbial species in the rhizosphere soil of 5-year-old Haloxylon ammodendron were significantly higher than those in the rhizosphere soil of 2-year-old Haloxylon ammodendron. Different years of Haloxylon ammodendron can also change the underground rhizosphere flora, affecting the scale of soil rhizosphere effect and special rhizosphere microorganisms. This study also concluded that the haloxylon of different years affected the rhizosphere effect and changed the number of microorganisms [40].
The number of inorganic phosphorus bacteria, iron-bearing bacteria, and azotobacter increased in the rhizosphere soil of Haloxylon ammodendron, while the number of potassium-solubilizing bacteria and organophosphorus bacteria decreased in the rhizosphere soil. The inorganic phosphorus bacteria in this study belong to Phyllobacterium, Bacillus, and Sinorhizobium meliloti, respectively. There have been many studies on the growth-promoting effect of Bacillus on plants [41,42]. The isolated bacillus sg16 has the dual characteristics of phosphorus solubilizing and nitrogen fixation. The synthesis and release of low-molecular-weight organic acids by Bacillus can promote the dissolution of inorganic phosphorus in soil. The hydroxyl and carboxyl groups in organic acids chelate phosphates to bind cations and ultimately convert phosphates into soluble forms [43].
In this study, the microbial community structure of the rhizosphere soil bacteria in the 2-year and 5-year rhizosphere soil in Turpan, Xinjiang was analyzed. Through the isolation, purification, and identification of the dominant microorganisms in the roots of Haloxylon ammodendron, combined with high-throughput sequencing technology, the main microbial groups and diversity of the rhizosphere soil of Haloxylon ammodendron were analyzed. It should be noted that there are, nonetheless, shortcomings in the process of this experiment. This study did not include the bacterial diversity in different growth periods, different ecological niches, and different years of Haloxylon ammodendron. The IAA production ability of the isolated strains was not tested, but can be tested later, and the bacterial diversity of different growth periods, ecological niches, and different years can be studied.

5. Conclusions

The results of high-throughput sequencing showed that Firmicutes, Proteobacteria, and Actinobacteriota were the main bacterial phyla in the rhizosphere soil of Haloxylon ammodendron. The results of the promoting efficiency analysis of 37 species of bacteria isolated from the rhizosphere soil of Haloxylon ammodendron showed that three strains of bacteria could produce phosphorus solubilization circles, namely Sg16, sg21, and ss4, among which the sg16 strain had the highest inorganic phosphorus solubility index (1.58). The isolated strains had no ability to dissolve organophosphorus and potassium. At the same time, the strain sg16 was screened for nitrogen fixation ability. Two strains with good iron-bearing capacity were screened: Sg9F and Sg1, of which Sg9F had both the highest D/d value and the strongest iron-bearing capacity. The results of 16S rDNA sequencing showed that 37 strains of rhizosphere soil bacteria belonged to six genera, including Bacillus, Corynebacterium, Phyllobacterium, Lysinibacillus, Sinorhizobium meliloti, and Streptomyces levis. Among them, sg21 is Bacillus sp, sg1 is Bacillus sp, sg9F is Streptomyces levis, sg16 is Phyllobacterium phragmitis, and ss4 is Sinorhizobium meliloti.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/microbiolres15030091/s1. Table S1: The main instruments and equipment used in this experiment; Table S2: Strain identification and related primers sequence; Table S3: PCR system; Table S4: PCR conditions.

Author Contributions

S.S. and Y.C. designed the study. Z.W. collected the plant materials. X.W. and W.L. isolated and identified the plant endophytic fungi. J.Z., X.W., X.X., R.G., Q.Z. isolated the endophytic fungi and performed the antifungal activity evaluation of the extracts. X.W. and S.S. interpreted the data and wrote the manuscript. L.W. reviewed and edited the manuscript. All authors have read and agreed to the published version of the manuscript.

Funding

This research was found by the Xinjiang Uygur Autonomous Region key research and development project: Study on key technology of “inoculation” of Cistanche deserticola (2022B02012-03). Research and application of high-quality and efficient production technology and equipment of Vaccinium myrtillus L. and Helichrysum arenarium (2023B02023-2).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The original data presented in the study are included in the article.

Acknowledgments

This study was supported by the Xinjiang Uygur Autonomous Region key research and development project: Study on key technology of “inoculation” of Cistanche deserticola (2022B02012-03).

Conflicts of Interest

The authors declare no conflicts of interest.

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Figure 1. Sequence dilution curve of bacterial samples. sg2.1.1: The first sample from the first zone of 2-year-old Haloxylon ammodendron; sg5.1.1: the first sample from the first zone of 5-year-old Haloxylon ammodendron.
Figure 1. Sequence dilution curve of bacterial samples. sg2.1.1: The first sample from the first zone of 2-year-old Haloxylon ammodendron; sg5.1.1: the first sample from the first zone of 5-year-old Haloxylon ammodendron.
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Figure 2. Composition of rhizosphere soil bacterial community in 2-year and 5-year horizontal phyla Haloxylon ammodendron. sg2.1.1: The first sample from the first zone of 2-year-old Haloxylon ammodendron; sg5.1.1: the first sample from the first zone of 5-year-old Haloxylon ammodendron.
Figure 2. Composition of rhizosphere soil bacterial community in 2-year and 5-year horizontal phyla Haloxylon ammodendron. sg2.1.1: The first sample from the first zone of 2-year-old Haloxylon ammodendron; sg5.1.1: the first sample from the first zone of 5-year-old Haloxylon ammodendron.
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Figure 3. Composition of rhizosphere soil bacterial community in 2-year and 5-year genus Haloxylon ammodendron. sg2.1.1: The first sample from the first zone of 2-year-old Haloxylon ammodendron; sg5.1.1: the first sample from the first zone of 5-year-old Haloxylon ammodendron.
Figure 3. Composition of rhizosphere soil bacterial community in 2-year and 5-year genus Haloxylon ammodendron. sg2.1.1: The first sample from the first zone of 2-year-old Haloxylon ammodendron; sg5.1.1: the first sample from the first zone of 5-year-old Haloxylon ammodendron.
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Figure 4. Venn diagram of OTU distribution of bacteria in rhizosphere soil of Haloxylon ammodendron in 2 and 5 years. sg2: Two-year rhizosphere soil bacteria sample; sg5: five-year rhizosphere soil bacteria sample.
Figure 4. Venn diagram of OTU distribution of bacteria in rhizosphere soil of Haloxylon ammodendron in 2 and 5 years. sg2: Two-year rhizosphere soil bacteria sample; sg5: five-year rhizosphere soil bacteria sample.
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Figure 5. Principal component analysis of bacterial communities in rhizosphere soil of 2- and 5-year-old Haloxylon ammodendron.
Figure 5. Principal component analysis of bacterial communities in rhizosphere soil of 2- and 5-year-old Haloxylon ammodendron.
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Figure 6. Phylogenetic tree of Haloxylon ammodendron rhizosphere growth promoters based on 16S rDNA homologous sequences collected from NCBI. MEGA7.0 software was used to construct the phylogenetic tree.
Figure 6. Phylogenetic tree of Haloxylon ammodendron rhizosphere growth promoters based on 16S rDNA homologous sequences collected from NCBI. MEGA7.0 software was used to construct the phylogenetic tree.
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Figure 7. Colony morphology of sg16 nitrogen fixation medium.
Figure 7. Colony morphology of sg16 nitrogen fixation medium.
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Table 1. Species distribution of rhizosphere soil bacteria in 2-year and 5-year Haloxylon ammodendron soil at taxonomic level.
Table 1. Species distribution of rhizosphere soil bacteria in 2-year and 5-year Haloxylon ammodendron soil at taxonomic level.
ComponentKingdomPhylumClassOrderFamilyGenusSpecies
Sg2145109288451826404
Sg51531393455551062513
sg2: Two-year rhizosphere soil bacteria sample; sg5: five-year rhizosphere soil bacteria sample.
Table 2. α Diversity of bacterial microbial community in rhizosphere soil of Haloxylon ammodendron in 2 and 5 years.
Table 2. α Diversity of bacterial microbial community in rhizosphere soil of Haloxylon ammodendron in 2 and 5 years.
GroupChao1DominanceGoods_CoverageOTUPielou_eShannonSimpson
sg21720.8250.02370.99812,2060.7838.3600.977
sg51745.8830.01570.99814,0530.7918.4700.984
sg2: Two-year rhizosphere soil bacteria sample; sg5: five-year rhizosphere soil bacteria sample.
Table 3. The ability of the strain to dissolve inorganic phosphorus.
Table 3. The ability of the strain to dissolve inorganic phosphorus.
Strain NumberColony Diameter (d)/cmHydrolytic Ring Diameter (D)/cmSolubility Index (D/d)
Sg160.430.681.58
Sg210.590.731.23
Ss40.470.631.34
Table 4. Ability of strain to produce iron carriers.
Table 4. Ability of strain to produce iron carriers.
Strain NumberColony Diameter (d)/cmHydrolysis Circle Diameter (D)/cmSolubility Index (D/d)
Sg9F0.171.186.94
Sg10.410.641.56
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Wang, X.; Chen, Y.; Wang, Z.; Luo, W.; Zhou, J.; Xin, X.; Guo, R.; Zhu, Q.; Wang, L.; Song, S. Examining the Diversity of Rhizosphere Soil Bacterial Communities and Screening of Growth-Promoting Bacteria from the Rhizosphere Soil of Haloxylon ammodendron in Xinjiang. Microbiol. Res. 2024, 15, 1346-1358. https://doi.org/10.3390/microbiolres15030091

AMA Style

Wang X, Chen Y, Wang Z, Luo W, Zhou J, Xin X, Guo R, Zhu Q, Wang L, Song S. Examining the Diversity of Rhizosphere Soil Bacterial Communities and Screening of Growth-Promoting Bacteria from the Rhizosphere Soil of Haloxylon ammodendron in Xinjiang. Microbiology Research. 2024; 15(3):1346-1358. https://doi.org/10.3390/microbiolres15030091

Chicago/Turabian Style

Wang, Xuejing, Yong Chen, Zeyu Wang, Wenfang Luo, Junhui Zhou, Xiaoyan Xin, Rui Guo, Qingyue Zhu, Lili Wang, and Suqin Song. 2024. "Examining the Diversity of Rhizosphere Soil Bacterial Communities and Screening of Growth-Promoting Bacteria from the Rhizosphere Soil of Haloxylon ammodendron in Xinjiang" Microbiology Research 15, no. 3: 1346-1358. https://doi.org/10.3390/microbiolres15030091

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