Diversity Of Soil Microbial Communities Research Articles

Diversity and Structure of Soil Microbial Communities in Chinese Fir Plantations and Cunninghamia lanceolata–Phoebe bournei Mixed Forests at Different Successional Stages

Cunninghamia lanceolata is an important species in plantations and is widely planted in sub-tropical regions of China because of its fast-growing and productive characteristics. However, the monoculture planting is carried out in the pursuit of economic value. This planting mode has led to problems such as the exhaustion of soil fertility, decrease in vegetation diversity, and decrease in woodland productivity. In order to restore soil fertility and increase timber production, the introduction of broad-leaved tree species to plantations is an effective transformation model. Understanding how forest age changes and stand structure differences drive the composition and diversity of soil microbial communities is helpful in understanding the trend of soil–microbial changes in plantations and evaluating the effects of the introduction of broad-leaved tree species in soil–plant–microbial ecosystems in plantations. Therefore, the purpose of our study is to investigate the effects of forest age and pure forest conversion on C. lanceolata–P. bournei-mixed forest soil microbial community structure and diversity by detecting soil nutrients, enzyme activities, and soil microbial 16S and ITS rRNA gene sequencing. According to the findings, the diversity and abundance of bacterial communities in C. lanceolata plantations of different ages increased first and then decreased with the increase in forest age, and the max value was in the near-mature forest stage. The fungal abundance decreased gradually with stand age, with the lowest fungal diversity at the near-mature stand stage. During the whole growth process, the bacterial community was more limited by soil pH, nitrogen, and phosphorus. After introducing P. bournei into a Chinese fir plantation, the abundance and diversity of the bacterial community did not improve, and the abundance of the fungal community did not increase. However, soil nutrients, pH, and fungal community diversity were significantly improved. The results of these studies indicate that the introduction of broad-leaved tree species not only increased soil nutrient content, but also had a significant effect on the increase in the diversity of soil fungal communities, making the microbial communities of mixed forests more diverse.

Effects of historical agricultural crops on the soil microbiome of a living agricultural museum in the Sonoran Desert

AbstractAlthough soil has been a central piece in agricultural knowledge for most of recorded history, introductions of exotic plant assemblages can produce loss of soil quality, especially in more fragile ecosystems such as drylands. Here, we investigate the impact of indigenous and introduced plant assemblages associated with ethno‐agricultural traditions of Tucson, AZ, on soil microbial communities using 16S rRNA gene (bacteria and archaea) and internal transcribed spacer region (fungi) metabarcoding. We found differences in soil microbial community diversity and composition across plant assemblages associated with ethno‐agricultural traditions. However, we found the largest community structure differences between managed cultivated plots and not cultivated desert soils. Managed cultivated plots were characterized by higher diversity (23% increment for bacteria/archaea, and 40% for fungi) and a higher abundance of nitrifying bacteria (19% higher) and cellulolytic bacteria (39% higher) relative to minimally disturbed plots, suggesting higher rates of decomposition and nitrogen cycling. Given the observed influence of management on soil microbial communities, we conclude that efforts to build arid‐specific sustainable agricultural solutions would benefit from the use of adapted plants that require minimal management.

Microbiome Reveals the Effects of Biogas Fertilizer on Soil Microbial Community Structure and Diversity in Perennial Apple Orchards

Fruit trees are perennial crops that grow in one place for their whole lives, which leads to the deterioration of the soil as well as a decline in fruit quality and yield. Microbial diversity and community structure are important soil factors affecting stress resistance and the quality of fruit trees. Additionally, biogas fertilizer also plays an important role in improving fruit quality. Whether biogas fertilizer can improve continuous cropping barriers by affecting microbial diversity and community structure remains to be further investigated. Therefore, 7-year-old Fuji apples were used as material, and biogas fertilizer was applied continuously for three years. The results show that the contents of soil organic matter (SOM), available nitrogen (AN), available phosphorus (AP), and soil porosity (SP) increased by 0.712, 0.217, 1.089, and 0.401 after applying biogas fertilizer, respectively. The concentrations of vitamin C, titratable acid, and soluble solids also significantly increased. We also found that the relative abundance of dominant soil flora significantly increased, such as Sphingomonas (g_Sphingomonas), Chlamydomonas (g_Chlamydomonas), and Stachybotry (g_Stachybotry), while the relative abundance of inferior flora significantly decreased, such as Cryptococcus (g_Cryptococcus) and Alternaria (g_Alternaria). In summary, biogas fertilizer can improve the physicochemical properties of the soil as well as the structure and diversity of the microbial communities in rainfed orchards, resulting in higher fruit quality.

Different responses of soil fungal and bacterial communities to nitrogen addition in a forest grassland ecotone.

Continuous nitrogen deposition increases the nitrogen content of terrestrial ecosystem and affects the geochemical cycle of soil nitrogen. Forest-grassland ecotone is the interface area of forest and grassland and is sensitive to global climate change. However, the structure composition and diversity of soil microbial communities and their relationship with soil environmental factors at increasing nitrogen deposition have not been sufficiently studied in forest-grassland ecotone. In this study, experiments were carried out with four nitrogen addition treatments (0 kgN·hm-2·a-1, 10 kgN·hm-2·a-1, 20 kgN·hm-2·a-1 and 40 kgN·hm-2·a-1) to simulate nitrogen deposition in a forest-grassland ecotone in northwest Liaoning Province, China. High-throughput sequencing and qPCR technologies were used to analyze the composition, structure, and diversity characteristics of the soil microbial communities under different levels of nitrogen addition. The results showed that soil pH decreased significantly at increasing nitrogen concentrations, and the total nitrogen and ammonium nitrogen contents first increased and then decreased, which were significantly higher in the N10 treatment than in other treatments (N:0.32 ~ 0.48 g/kg; NH4+-N: 11.54 ~ 13 mg/kg). With the increase in nitrogen concentration, the net nitrogen mineralization, nitrification, and ammoniation rates decreased. The addition of nitrogen had no significant effect on the diversity and structure of the fungal community, while the diversity of the bacterial community decreased significantly at increasing nitrogen concentrations. Ascomycetes and Actinomycetes were the dominant fungal and bacterial phyla, respectively. The relative abundance of Ascomycetes was negatively correlated with total nitrogen content, while that of Actinomycetes was positively correlated with soil pH. The fungal community diversity was significantly negatively correlated with nitrate nitrogen, while the diversity of the bacterial community was significantly positively correlated with soil pH. No significant differences in the abundance of functional genes related to soil nitrogen transformations under the different treatments were observed. Overall, the distribution pattern and driving factors were different in soil microbial communities in a forest-grassland ecotone in northwest Liaoning. Our study enriches research content related to factors that affect the forest-grassland ecotone.

Remediation of the microecological environment of heavy metal-contaminated soil with fulvic acid, improves the quality and yield of apple

The excessive application of chemical fertilizers and pesticides in apple orchards is responsible for high levels of manganese and copper in soil, and this poses a serious threat to soil health. We conducted a three-year field experiment to study the remediation effect and mechanism of fulvic acid on soil with excess manganese and copper. The exogenous application of fulvic acid significantly reduced the content of manganese and copper in soil and plants; increased the content of calcium; promoted the growth of apple plants; improved the fruit quality and yield of apple; increased the content of chlorophyll; increased the activity of superoxide dismutase, peroxidase, and catalase; and reduced the content of malondialdehyde. The number of soil culturable microorganisms, soil enzyme activity, soil microbial community diversity, and relative abundance of functional bacteria were increased, and the detoxification of the glutathione metabolism function was enhanced. The results of this study provide new insights that will aid the remediation of soil with excess manganese and copper using fulvic acid.

Metagenomic analysis of soybean endosphere microbiome to reveal signatures of microbes for health and disease

BackgroundSoil metagenomics is a cultivation-independent molecular strategy for investigating and exploiting the diversity of soil microbial communities. Soil microbial diversity is essential because it is critical to sustaining soil health for agricultural productivity and protection against harmful organisms. This study aimed to perform a metagenomic analysis of the soybean endosphere (all microbial communities found in plant leaves) to reveal signatures of microbes for health and disease. ResultsThe dataset is based on the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) release “microbial diversity in soybean”. The quality control process rejected 21 of the evaluated sequences (0.03% of the total sequences). Dereplication determined that 68,994 sequences were artificial duplicate readings, and removed them from consideration. Ribosomal Ribonucleic acid (RNA) genes were present in 72,747 sequences that successfully passed quality control (QC). Finally, we found that hierarchical classification for taxonomic assignment was conducted using MG-RAST, and the considered dataset of the metagenome domain of bacteria (99.68%) dominated the other groups. In Eukaryotes (0.31%) and unclassified sequence 2 (0.00%) in the taxonomic classification of bacteria in the genus group, Streptomyces, Chryseobacterium, Ppaenibacillus, Bacillus, and Mitsuaria were found. We also found some biological pathways, such as CMP-KDO biosynthesis II (from D-arabinose 5-phosphate), tricarboxylic acid cycle (TCA) cycle (plant), citrate cycle (TCA cycle), fatty acid biosynthesis, and glyoxylate and dicarboxylate metabolism. Gene prediction uncovered 1,180 sequences, 15,172 of which included gene products, with the shortest sequence being 131 bases and maximum length 3829 base pairs. The gene list was additionally annotated using Integrated Microbial Genomes and Microbiomes. The annotation process yielded a total of 240 genes found in 177 bacterial strains. These gene products were found in the genome of strain 7598. Large volumes of data are generated using modern sequencing technology to sample all genes in all species present in a given complex sample. ConclusionsThese data revealed that it is a rich source of potential biomarkers for soybean plants. The results of this study will help us to understand the role of the endosphere microbiome in plant health and identify the microbial signatures of health and disease. The MG-RAST is a public resource for the automated phylogenetic and functional study of metagenomes. This is a powerful tool for investigating the diversity and function of microbial communities.

Changes in soil microbial communities after exposure to neonicotinoids: A systematic review.

Neonicotinoids are a group of nicotine-related chemicals widely used as insecticides in agriculture. Several studies have shown measurable quantities of neonicotinoids in the environment but little is known regarding their impact on soil microbial populations. The purpose of this systematic review was to clarify the effects of neonicotinoids on soil microbiology and to highlight any knowledge gaps. A formal systematic review was performed following PRISMA (Preferred Reporting Items for Systematic Review and Meta-Analyses) guidelines using keywords in PubMed, SCOPUS and Web of Science. This resulted in 29 peer-reviewed articles, whose findings diverged widely because of variable methodologies. Field-based studies were few (28%). Imidacloprid was the most widely used (66%) and soil microbial communities were most sensitive to it. Spray formulations were used in 83% of the studies and seed treatments in the rest. Diversity indices were the most frequently reported soil microbial parameter (62%). About 45% of the studies found that neonicotinoids had adverse impacts on soil microbial community structure, composition, diversity, functioning, enzymatic activity and nitrogen transformation. Interactions with soil physicochemical properties were poorly addressed in all studies. The need for more research, particularly field-based research on the effects of neonicotinoids on soil microorganisms was highlighted by this review.

Response of soil microbial community diversity to continuous cucumber cropping in facilities along the Yellow River irrigation area.

Cucumber is an important cash crop; however, continuous cropping obstacles readily occur within the intensive production processes of facility horticulture. This study aimed to determine the effects of continuous cropping on soil quality and the microbial community in the rhizosphere soil of cucumbers. Rhizosphere soil of cucumber planted continuously for 4, 8, and 12 years was investigated, and soil that was not continuously planted was used as the control. Soil physicochemical properties, enzyme activity, microbial diversity, and richness were determined. The results showed that with the increase in continuous cropping years (0, 4, 8, and 12 years), soil total salt content continuously increased, while the pH value significantly decreased. Compared with the control, soil organic matter, alkali-hydrolyzed nitrogen, available phosphorus, available potassium, and nitrate nitrogen contents increased significantly after 4 and 8 years of continuous cropping. Spearman correlation analysis showed that pH was negatively correlated with sucrase or sucrose and available phosphorus was positively correlated with alkaline phosphatase. Compared with the control, the diversity and abundance of bacterial and fungal communities in cucumber rhizosphere soil decreased after 4 and 12 years of continuous cropping. Continuous cropping led to a significant increase in the richness of the dominant phylum of cucumber rhizosphere soil. Principal coordinates analysis showed that, compared with the control, the soil microbial community structure was significantly separated after 4, 8, and 12 years of continuous cropping, and the microbial community structure was most similar after 4 and 8 years of continuous cropping. In addition, redundancy analysis showed that pH was the main driver of soil microbial dominance. In conclusion, continuous cropping of cucumber along the Yellow River irrigation area has led to the deterioration of soil nutrients and microbial communities in that region. This experiment provides a theoretical foundation for addressing the challenges associated with continuous cropping in cucumber cultivation.

Effects of Soil Microbiological Properties on the Fractional Distribution and Stability of Soil Organic Carbon under Different N Addition Treatments

Soil organic carbon (SOC) fractions are influenced by inputs of nitrogen (N) from globally rising N deposition; however, the mechanisms of how soil microbiological properties are influenced by N deposition and its impact on the fractional distribution and stability of SOC remain unclear. In this study, we assessed the effects on SOC fraction distribution and stability from four aspects of soil microbiological properties: soil microbial biomass (SMB), soil microbial activity, structure diversity, and functional diversity of soil microbial community in a Pinus tabuliformis plantation, which received four N addition levels (0 g N m−2 y−1 (N0), 3 g N m−2 y−1 (N3, low N addition), 6 g N m−2 y−1 (N6, mid-N addition), and 9 g N m−2 y−1 (N9, high N addition)) for 2 years. The N inputs did significantly affect some soil microbiological properties, like SMB, soil phospholipid fatty acid (PLFA), and soil microbial functional diversity. Mid- and high N addition decreased the richness (HPLFA) and evenness (EPLFA) index of the soil microbial community, from 3.24 to 2.91 and 0.93 to 0.87, respectively. In addition, the low N addition promoted the carbon management index (CMI) to 141.35, i.e., higher than the CMIs in the mid- and high-level treatments. The SOC stability also showed significant differences among N addition treatments, and SOC could be the most stable at the mid-N addition level. Regarding the effects of the four soil microbiological attributes on the CMI and stability, SMB and soil respiration positively impacted the CMI, but did not significantly affect the stability. In addition, EPLFA had positive effects, but EBIOLOG had negative effects on CMI and lability. Our findings indicate that soil microbiological properties are essential in SOC fractional distributions and stability. Further identification and study of soil microbial species used to change SOC fractions would help to clarify the detailed mechanisms involved.

Variations in diversity, composition, and species interactions of soil microbial community in response to increased N deposition and precipitation intensity in a temperate grassland

BackgroundGlobal climate change has resulted in precipitation regimes exhibiting an increasing trend in rainfall intensity but a reduction in frequency. In addition, nitrogen (N) deposition occurs simultaneously in arid and semi-arid regions. Microbial biomass, diversity, composition, and species interactions are key determinants of ecological functions. We examined the effects of changes in precipitation intensity and N addition on the soil bacterial and fungal communities in a semi-arid grassland in Inner Mongolia, China.MethodsThe microbial biomass (bacterial PLFAs and fungal PLFAs) was determined through phospholipid fatty acid (PLFA) analysis, and microbial diversity (Shannon index and evenness index) was determined with high-throughput sequencing (16S and ITS). Species interactions were determined using a molecular ecological network analysis. The relationships between microbial community (bacterial community and fungal community) and environmental variables were examined by Mantel tests.ResultsWe found that N addition decreased fungal PLFA under moderate, high, and extreme precipitation intensity treatments and increased fungal community complexity under the high precipitation intensity treatment. Furthermore, N addition increased bacterial diversity under moderate and high precipitation intensity treatments. N addition caused greater environmental stress to the fungal community, which was dominated by deterministic processes.ConclusionsThe effects of N deposition on soil bacterial and fungal communities were altered by precipitation intensity. The changes in soil bacterial and fungal communities were different, implying that composition and functional traits adapt differently to projected global changes at a regional scale.

Linking soil depth to aridity effects on soil microbial community composition, diversity and resource limitation

With ongoing climate change, aridity is increasing worldwide, affecting biodiversity and ecosystem function in drylands. However, how the depth-profile microbial community structure and metabolic limitations change along aridity gradients are still poorly explored. Here, 16S rRNA and ITS amplicon sequencing and ecoenzymatic stoichiometry analysis were used to investigate both bacterial and fungal diversities and resource limitations in 1 m depth profiles across a wide aridity gradient (0.51–0.78) in a semiarid region. Results showed a sharp decrease in microbial diversity with soil depth, accompanied by an increase in microbial phosphorus (P) vs. N (nitrogen) limitation and a decrease in microbial carbon (C) vs. nutrient limitation. Aridity led to a strong shift in microbial community composition, but aridity has a threshold effect on microbial resource limitation through impacts on soil pH and C/P or N/P. When the aridity threshold (1-precipitation/evapotranspiration) exceeds 0.65, relationship between aridity and microbial resource demand was decoupled; but at aridity threshold = 0.65, microbial relative C limitation and C-acquiring enzyme activity dropped. These results suggest that aridity might have a stronger influence on microbial community composition, than on diversity, shaped by inherent soil biotic factors (i.e., MBC:MBP or MBN:MBP). These findings suggest that soil microbial diversity or enzymatic stoichiometry may be not necessary to mirror changes in water availability in the drylands, while aridity would be well explained by microbial community composition.

Earthworm activity effectively mitigated the negative impact of microplastics on maize growth

Microplastic pollution can have detrimental effects on soil environments and inhibit crop growth. Earthworms, known as soil engineers, promote crop growth, but their role and impact on the amelioration of microplastic-polluted soil is not yet clear. In this study, we investigated the impact and pathways of earthworm activity on microplastic-contaminated soil by introducing varying densities (without earthworm:0, low-density: 1, medium-density: 2, high-density: 5 ind column−1) of earthworms (epi-endogeic) into soil contaminated with two types of microplastics: polyethylene and polyvinyl chloride. Our results showed that earthworms all survived in soil polluted with two types of microplastics. Meanwhile, earthworm activity increased nutrient content and enzyme activity by 0.2–36.1% and 2.9–34.3%, respectively, and significantly increased soil microbial biomass and community diversity index. Earthworm activity also decreased antioxidant enzyme activity and promoted maize plant growth, including agronomic traits such as plant height, biomass, root length, and root surface area. Furthermore, the nutrient content of maize organs increased by 1.1–29.7%. Partial least squares models confirmed that earthworm activity alleviated the stress effect of microplastic pollution on plant growth by improving soil structure, fertility, and microbial abundance and diversity. The greatest effect on maize growth was observed with the improvement of soil physical-chemical properties. Our results suggest that medium densities of earthworms have the greatest soil improvement effect and provide an important basis for bioremediation of farmland contaminated by microplastics and promoting green and efficient development in agriculture.

Dual effects of plant growth-promoting rhizobacteria (PGPR) on the Moso bamboo-soil system: Plant growth promotion and microbial community stability

Understanding the effects of plant growth-promoting rhizobacteria (PGPR) on Moso bamboo (Phyllostachys edulis) growth, soil nutrient and microbial community will help to improve the growth of Moso bamboo. In this study, an experiment was established to quantify the effects of PGPR inoculation on Moso bamboo growth. Soil phosphorus fraction, nutrient content, enzyme activity, microbial community and copy numbers of the phoA, phoD and phoN genes were also analyzed. The PGPR inoculations significantly increased the Moso bamboo biomass by 34.2 %− 108.9 % and improved soil nutrient contents and enzyme activities. In addition, the applications of PGPR significantly increased the diversity of soil microbial community but decreased the relative abundance of Bacteroidetes. The mixed bacterial inoculants helped to stabilize the soil microbial community. The functional genes related to phosphorus solubilization (phoA, phoD and phoN) had substantial effects on the activation of soil phosphorus fractions. The study showed that the applications of PGPR inoculations effectively improved microbial community stabilities and promoted the growth of Moso bamboo.

Effects of Grazing Exclusion on Microbial Community Diversity and Soil Metabolism in Desert Grasslands

In this study, the effect of 14 years of GE exclusion in a desert grassland on soil microbial community diversity and metabolites was examined. GE changed the bacterial community structure, the alpha diversity of the bacterial community, and the total phosphorus (TP) and total potassium (TK) content in the soil. More specifically, the relative abundance of Actinobacteria, Proteobacteria, and Chloroflexi increased with GE. In contrast, the relative abundance of Acidobacteria was higher during grazing (G), so it is believed that soil bacteria adapt to environmental changes. Both amino acid and carbohydrate metabolism were enhanced, while lipid metabolism was decreased under GE. It was concluded that GE could trigger changes in both bacterial diversity and soil metabolites, increase the energy supply, and regulate ecosystem function. Consequently, GE would have positive effects on the restoration of desert grasslands by altering the soil microbial community. This work provides new insights into the response of soil microbes to GE.

Composition and Diversity of Soil Microbial Communities in Walnut Orchards at Different Altitudes in Southeastern Tibet

To understand the distribution of the soil microbial community in natural walnut orchards at different altitude gradients (3000–3500 m) and to reveal the mechanism of the soil microbial activity in natural walnut orchards adapting to high-altitude environments, soil samples from four groups of natural walnut orchards in Gyaca County, southeast Tibet, were studied. Illumina MiSeq sequencing technology was used to analyze the community composition and diversity of soil bacteria and fungi and their responses to the altitudes. The alpha diversity results showed that the vertical distribution pattern of the fungal community was more obvious than that of the bacterial community and the bacterial community diversity first increased (~3364 m) and then decreased with altitude. The number of amplicon sequence variants (ASVs) in the soil bacterial community was significantly higher than that in the fungal community, but soil bacterial and fungal communities in walnut orchards at different altitudes exhibited both inheritance and uniqueness. At the phylum level, the dominant bacterial phyla at different altitudes were Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi (relative abundances > 10.0% in each treatment). With the increase in altitude, the relative abundance of Actinobacteria increased gradually while that of Acidobacteria and Proteobacteria decreased gradually. The dominant fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota (relative abundances >5.0% in each treatment). With the increase in altitude, the relative abundance of Ascomycota increased significantly. At the genus level, the number of dominant bacteria and fungi in the soil decreased gradually with increased altitude and showed anisotropic distribution characteristics. The relative abundances of Actinobacteria among the bacterial phyla—and Olpidiomycota and Zoopagomycota among the fungal phyla—were positively correlated with the altitude (p < 0.05). Most dominant bacterial and fungal phyla were highly significantly (p < 0.01) or significantly (p < 0.05) negatively correlated with the altitude. Soil nitrogen and phosphorus availabilities are the main limiting factors of microbial community diversity. Therefore, altitude caused changes in soil physicochemical properties which directly or indirectly affected the composition and diversity of soil bacterial and fungal communities, and our study provides a theoretical basis for the altitudinal pattern and succession changes in soil microbial communities in the natural walnut orchards of southeast Tibet.

The effect of plant compartment and geographical location on shaping microbiome of Pulsatilla chinensis.

The plant-associated microbiome has an effect on plant growth. Pulsatilla chinensis (Bge.) Regel is an important Chinese medicinal plant. Currently, there is little understanding of the P. chinensis-associated microbiome and its diversity and composition. Here, the core microbiome associated with the root, leaf, and rhizospheric soil compartments of P. chinensis from five geographical locations was analyzed by the metagenomics approach. The alpha and beta diversity analysis showed that the microbiome associated with P. chinensis was shaped by the compartment, especially in the bacterial community. The geographical location had little influence on microbial community diversity associated with root and leaf. Hierarchical clustering distinguished the microbial communities of rhizospheric soil based on their geographical location and among the soil properties, pH was showed the more stronger effect on the diversity of rhizospheric soil microbial communities. Proteobacteria was the most dominant bacterial phylum in the root, leaf, and rhizospheric soil. Ascomycota and Basidiomycota were the most dominant fungal phyla in different compartments. Rhizobacter, Anoxybacillus, and IMCC26256 were the most important marker bacterial species for root, leaf, and rhizospheric soil screened by random forest, respectively. The fungal marker species for root, leaf, and rhizospheric soil were not only different across the compartments but also the geographical locations. Functional analysis showed that P. chinensis-associated microbiome had the similar function which had no obvious relationship with geographical location and compartment. The associated microbiome indicated in this study can be used for identifying microorganisms related to the quality and growth of P. chinensis. KEY POINTS: • Microbiome associated with P. chinensis was shaped by the compartment • Microbiome composition and abundance associated with rhizospheric soil were affected by the geographical location • Compared with fungi, bacterial associated with P. chinensis composition and diversity were more stable in different geographical locations and compartments.

Environmental Parameters Determine the Structure of Soil Bacteria under Different Land use Types in Tailings Area

Soil microorganisms contribute substantially to a wide range of services and thereby improve recovery in ecosystem restoration. However, there is relatively limited information on how microbial communities respond to different land-use types with similar plant species and their potential roles in supporting soil restoration in mine tailings. To understand the importance of the response of soil microbial communities to the stress of tailings area in different soil habitats, this article selected three different land use types (Tailings area, Buffer zone and Vegetable field) as the variables in the Yanzibian tailings area in Ningqiang, Shaanxi Province, China. Soil physicochemical properties and heavy metal concentrations of the different land use types were compared. Illumina MiSeq. 2500 Sequencing Technology was used to analyze the abundance and structural diversity of the microbial community in soil samples. The results showed that most of the soil samples were unsafe with multiple metals. All soil samples in the buffer zone and tailings ponds were acidic. With the acidity decreased, bacterial community richness and diversity increased significantly. Briefly, different environmental factors and soil microbial communities were significantly distinct across different land-use types. Cu, Zn, Pb, pH, MC (Moisture content), TN (Total nitrogen), TP (Total phosphorus), and TK (Total potassium) were essential factors affecting the abundance and structural diversity of soil microbial communities across three different land-use types. As a result, Actinobacteria, Alphaproteobacteria, and Gammaproteobacteria were the top dominant classes in the buffer zone and Vegetable field soils, while Sulfobacillia dominated in tailings pond soils. Further, we found that with the continuous decline of the pH, the dominant genera transferred from norank_f__norank_o__Vicinamibacterales, Bacillus and Nocardioides to the norank_f__norank_o__Gaiellales and norank_f__norank_o__Acidobacteriales, then to Sulfobacillus. These confirmed that the responses of microbiota to heavy metals stress varied in different land-use types. Together, this study provides important information on the occurrence and distribution of soil microbiomes in tailings areas and their potentially beneficial roles in soil restoration.

Soil microbiomes of hardwood‐ versus pine‐dominated stands: Linkage with overstory species

AbstractBiodiversity in forest ecosystems is paradoxical. Whereas their most apparent component—the woody overstory—is the least diverse with respect to numbers of species, the least apparent component is the biotic community of highest diversity—the soil microbiome. Numerous factors influence the composition and diversity of soil microbial communities, which in turn exert a profound impact on plant species occupying the soil and the biogeochemistry of essential plant nutrients. Of interest in forest ecosystems is how the soil microbiome interacts with the overstory, a phenomenon referred to as linkage. This study compared the soil microbiome of two adjacent stand types—hardwood‐ and longleaf pine (Pinus palustris)‐dominated—and addressed the following questions: (1) How does soil microbiome vary with stand type? (2) Do the forest overstory community and soil microbiome exhibit linkage? Twelve 0.04‐ha circular plots were established in each stand type to assess tree community composition and structure and to sample mineral soil for three separate analyses: assessment of soil fertility, measurement of total carbon and nitrogen (N), and extraction of genomic DNA for assessment of microbiome communities. All live stems ≥2.5 cm dbh in each plot were identified to species and measured for dbh to the nearest 0.1 cm. Mineral soil was taken from a depth of 5 cm and oven‐dried at 38°C prior to analyses. Hardwood stands were dominated by flowering magnolia (Magnolia grandiflora) and southern evergreen oaks, whereas pine stands were dominated by longleaf pine and live oak (Quercus virginiana). Although soils of both stand types were highly acidic, the hardwood stands were generally higher in fertility, especially for total and available N. The overstory and soil microbial communities exhibited evidence of linkage among all sample plots combined. When assessed separately by stand type, only hardwood‐dominated stands displayed evidence of overstory/microbial linkage. These results have broader implications for future scenarios given the sensitivity of soil microbes to climate change.

Soil microbial community characteristics and the influencing factors at different elevations on the eastern slope of Helan Mountain, Northwest China.

As an important bridge connecting aboveground communities and belowground biological processes, soil microorganisms play an important role in regulating belowground ecological processes. The altitudinal changes and driving factors of soil microbial community in mountain ecosystem in arid region are still unclear. We measured soil physicochemical properties at seven altitudes in the range of 1300-2800 m in Helan Mountains, and investigated the understory community composition, soil physicochemical properties, and soil microbial community. The driving factor for soil microbial community was explored by variance partitioning analysis and redundancy analysis. The results showed that the total amount of soil microorganisms and bacterial biomass first increased and then decreased with the increases of altitude, fungi, actinomyces, arbuscular mycorrhizal fungi, Gram-positive bacteria, and Gram-negative bacteria groups showed a gradual increase. The variation of fungal-to-bacterial ratio (F/B) along the altitude showed that the cumulative ability of soil bacteria was stronger than that of fungi at low altitudes, while the pattern is opposite at high altitudes. The ratio of Gram-positive bacteria to Gram-negative bacteria (GP/GN) showed an overall decreasing trend with the increases of altitude, indicating that soil bacteria and organic carbon availability changed from "oligotrophic" to "eutrophication" and from "low" to "high" transition as the altitude increased. Vegetation properties, soil physical and chemical properties jointly accounted for 95.7% of the variation in soil microbial community. Soil organic carbon (SOC), soil water content (SWC), and total nitrogen (TN) were significantly correlated with soil microbial community composition. Our results revealed the distribution pattern and driving factors of soil microbial communities at different elevations on the eastern slope of Helan Mountain, which would provide theoretical basis and data support for further understanding the interaction between plant-soil-microorganisms in arid areas.

Effects of grazing intensity on diversity and composition of rhizosphere and non-rhizosphere microbial communities in a desert grassland.

Overgrazing-induced grassland degradation has become a serious ecological problem worldwide. The diversity and composition of soil microbial communities are sensitive to grazing disturbances. However, our understanding is limited with respect to the effects of grazing intensity on bacterial and fungal communities, especially in plant rhizosphere. Using a long-term grazing experiment, we evaluated the diversity and composition of microbial communities in both rhizosphere and non-rhizosphere soils under three grazing intensities (light, moderate, and heavy grazing) in a desert grassland and examined the relative roles of grazing-induced changes in some abiotic and biotic factors in affecting the diversity and composition of microbial communities. Our results showed that soil bacteria differed greatly in diversity and composition between rhizosphere and non-rhizosphere zones, and so did soil fungi. Moderate and heavy grazing significantly reduced the rhizosphere bacterial diversity. Grazing intensity substantially altered the bacterial composition and the fungal composition in both zones but with different mechanisms. While root nitrogen and soil nitrogen played an important role in shaping the rhizosphere bacterial composition, soil-available phosphorus greatly affected the non-rhizosphere bacterial composition and the fungal composition in both soils. This study provides direct experimental evidence that the diversity and composition of microbial communities were severely altered by heavy grazing on a desert grassland. Thus, to restore the grazing-induced, degraded grasslands, we should pay more attention to the conservation of soil microbes in addition to vegetation recovery.