Variations of soil microbial communities accompanied by different vegetation restoration in an open-cut iron mining area

Soil Fungal Community Diversity, Co-Occurrence Networks, and Assembly Processes under Diverse Forest Ecosystems

Fungal communities are critical players in the biogeochemical soil processes of forest ecosystems. However, the factors driving their diversity and community assembly are still unclear. In the present study, five typical vegetation types of soil fungal communities in Liziping Nature Reserve, China, were investigated using fungal ITS sequences. The results show that the topsoil fungal community is mainly dominated by the phyla Ascomycota, Basidiomycota, and Mortierellomycota. Although there was no significant difference in α diversity (Shannon, Simpson, and Pielou evenness indices) among different forest types, there was a significant difference in β diversity (community composition). This study found that soil pH, soil organic carbon, total nitrogen (TN), total phosphorus (TP), and the total nitrogen/total phosphorus (N/P) ratio are the main environmental factors that affect soil fungal communities. Each forest type has a specific co-occurrence network, indicating that these community structures have significant specificities and complexities. Deciduous evergreen broad-leaved forests as well as deciduous broad-leaved and evergreen broad-leaved mixed forests showed high modularity and average path lengths, indicating their highly modular nature without distinct small-scale characteristics. Furthermore, our findings indicate that the structures of topsoil fungal communities are mainly shaped by stochastic processes, with the diffusion limitation mechanism playing a particularly significant role.

Characteristics and driving forces of the soil microbial community during 35 years of natural restoration in abandoned areas of the Daxin manganese mine, China

The restoration of mining wastelands, particularly in karst regions contaminated by heavy metals, is an environmental challenge in need of urgent attention. Soil microbes play a vital role in nutrient cycling and ecosystem recovery, yet the long-term evolution of soil microbial communities in such settings remains poorly understood. This study explored the dynamics and influencing factors of soil microbial communities during 35 years of natural restoration in abandoned manganese (Mn) mine areas in Guangxi Province, China. The results revealed that the concentrations of Mn, Cd, Zn, and Cu were significantly (p < 0.05) reduced by 80.4-85.3%, 55.3-70.0%, 21.0-38.1%, and 29.4-49.4%, respectively, in the mid-late restoration periods (R19 and R35) compared with R1. The α diversities of the bacterial and fungal communities significantly increased in the middle-late restoration periods (R19 and R35), indicating increased microbial diversity as restoration progressed. The bacterial community structure exhibited more pronounced changes than did the fungal community structure, with significant shifts observed in dominant phyla such as Proteobacteria, Actinobacteria, Acidobacteriota, and Ascomycota. Notably, the relative abundances of Rhizobiales, Burkholderiales, and Hypocreales increased gradually with succession. Co-occurrence network analysis revealed that bacterial interactions became stronger over time, whereas interactions between bacteria and fungi weakened. Mantel tests and partial least squares path modeling (PLS‒PM) identified soil pH, heavy metals (Mn, Cd, Zn, and Cu), and nutrients (SOM and TN) as key drivers shaping the microbial community composition. These factors were more strongly correlated with bacterial communities than with fungal communities, underscoring the different responses of microbial groups to environmental changes during natural restoration. These findings enhance our understanding of the ecological processes governing microbial community succession in heavy metal-contaminated soils undergoing natural restoration.

Diversity of soil fungi and entomopathogenic fungi in subtropical mountain forest in southwest China

Till now, the diversity of entomopathogenic fungi in subtropical mountain forest was less studied. Here, the vertical distribution of forest soil fungi, entomopathogenic fungi, and their environmental influencing factors in a subtropical mountain in western China were investigated. Soil samples were collected from four elevations in a subtropical forest in Shaanxi. The results indicated a greater richness of soil fungi at middle elevations and soil fungi were more even at low elevation. Soil pH, available iron, available potassium, total potassium, and available zinc were the most important influencing factors affecting this vertical distribution of fungi. Interestingly, the Isaria genus was predominant while Metarhizium and Beauveria showed decreasing abundance. The presence of Isaria showed a significant positive correlation with both total phosphorus and available iron, while, available zinc was negatively correlated. Metarhizium was influenced by elevation, pH, available phosphorus, and available copper and Beauveria was influenced by soil organic carbon, total nitrogen, total potassium, available potassium, and available zinc. Overall, as environmental factors affecting soil fungi, elevation, and plant species diversity were less important than soil physical and chemical properties. The virulence of isolated entomopathogenic fungi were tested against larvae of Tenebrio molitor, with mortality ranging from 31.11% to 100%. The above findings provide valuable data to deepen our understanding of the diversity of entomopathogenic fungi in subtropical mountain forests.

Biochar dose-dependent impacts on soil bacterial and fungal diversity across the globe

Biochar, a widely used material for soil amendment, has been found to offer numerous advantages in improving soil properties and the habitats for soil microorganisms. However, there is still a lack of global perspectives on the influence of various levels of biochar addition on soil microbial diversity and primary components. Thus, in our study, we performed a global meta-analysis of studies to determine how different doses of biochar affect soil total carbon (C), nitrogen (N), pH, alpha- and beta-diversity, and the major phyla of both bacterial and fungal communities. Our results revealed that biochar significantly increased soil pH by 4 %, soil total C and N by 68 % and 22 %, respectively, in which the positive effects increased with biochar doses. Moreover, biochar promoted soil bacterial richness and evenness by 3-8 % at the biochar concentrations of 1-5 % (w/w), while dramatically shifting bacterial beta-diversity at the doses of >2 % (w/w). Specifically, biochar exhibited significantly positive effects on bacterial phyla of Acidobacteria, Bacteroidetes, Gemmatimonadetes, and Proteobacteria, especially Deltaproteobacteria and Gammaproteobacteria, by 4-10 % depending on the concentrations. On the contrary, the bacterial phylum of Verrucomicrobia and fungal phylum of Basidiomycota showed significant negative responses to biochar by -8 % and -24 %, respectively. Therefore, our meta-analysis provides theoretical support for the development of optimized agricultural management practices by emphasizing biochar application dosing.

The Impact of Artificial Restoration of Alpine Grasslands in the Qilian Mountains on Vegetation, Soil Bacteria, and Soil Fungal Community Diversity

To understand how the soil microbial community structure responds to vegetation restoration in alpine mining areas, this study specifically examines the grassland ecosystem in the Qianmalong mining area of the Qilian Mountains after five years of artificial restoration. High-throughput sequencing methods were employed to analyze soil bacteria and fungi microbial characteristics in diverse grassland communities. Combined with modifications in vegetation diversity as well as soil physicochemical properties, the impact of vegetation restoration on soil microbiome diversity in this alpine mining area was investigated. The findings indicated that the dominant plants were Cyperus rotundus, Carex spp., and Elymus nutans. As the extent of the grassland's restoration increased, the number of plant species, importance values, and plant community diversity showed an increasing trend. The plant functional groups were mainly dominated by Cyperaceae, followed by Poaceae. Plant height, density, plant cover, frequency, and aboveground biomass showed an increasing trend, and soil water content (SWC) increased. While soil pH and soil electrical conductivity (EC) exhibited a declining trend, available phosphorus (AP), total phosphorus (TP), total nitrogen (TN), nitrate nitrogen (NO3-N), soil organic carbon (SOC), and soil water content (SWC) showed an increasing trend. The dominant bacterial communities were Actinobacteriota, Proteobacteria, Acidobacteriota, Chloroflexi, Firmicutes, and Gemmatimonadota, while the dominant fungal communities were Ascomycota, Mortierellomycota, Basidiomycota, unclassified_k_Fungi, and Glomeromycota. Significant differences were detected within soil microbial community composition among different degrees of restoration grasslands, with bacteria generally dominating over fungi. SWC, TP, and TN were found to be the main soil physicochemical factors affecting the distribution of soil bacterial communities' structure; however, SOC, TN, and NO3-N were the primary factors influencing the soil distribution of fungal communities. The results of this study indicate that different degrees of vegetation restoration in alpine mining areas can significantly affect soil bacterial and fungal communities, and the degree of restoration has varying effects on the soil bacteria and fungi community structure in alpine mining areas.

Vegetation communities and soil properties along the restoration process of the Jinqianghe mine site in the Qilian Mountains, China

The study explores the impact of mine grassland restoration on plant communities and soil properties in alpine grasslands, a subject of significant interest due to the observed relationship between grassland changes, plant communities, and soil properties. While prior research has mainly focused on the consequences of grassland degradation on plant diversity and soil characteristics, the specific effects of varying restoration degrees in alpine mining grasslands at the regional scale remain poorly understood. To address this knowledge gap, we established 15 sampling plots (0.5m×0.5m) across five different restoration degrees within alpine mining grasslands in the Qilian Mountains, China. Our objective was to assess the variations in plant diversity and soil properties along these restoration gradients. We conducted comprehensive analyses, encompassing soil properties [soil water content (SWC), available nitrogen (AN), total phosphorus (TP), nitrate nitrogen (NO3-N), ammonium nitrogen (NH4-N), total nitrogen (TN), available phosphorus (AP), soil organic carbon (SOC), nitrate nitrogen, soil pH, and electrical conductivity (EC)], plant characteristics (height, density, frequency, coverage, and aboveground biomass), and plant diversity indices (Simpson, Shannon-Wiener, Margalef, Dominance, and Evenness indexes). Our findings included the identification and collection of 18 plant species from 11 families and 16 genera across the five restoration degrees: Very Low Restoration Degree (VLRD), Low Restoration Degree (LRD), Moderate Restoration Degree (MRD), High Restoration Degree (HRD), and Natural Grassland (NGL). Notably, species like Carex duriuscula, Cyperus rotundus, and Polygonum viviparum showed signs of recovery. Principal component analysis and Pearson correlation analysis revealed that soil pH, SWC, SOC, NO3-N, and AN were the primary environmental factors influencing plant communities. Specifically, soil pH and EC decreased as restoration levels increased, while SWC, AN, TP, NH4-N, TN, AP, SOC, and NO3-N exhibited a gradual increase with greater restoration efforts. Furthermore, the HRD plant community demonstrated similarities to the NGL, indicating the most effective natural recovery. In conclusion, our study provides valuable insights into the responses of plant community characteristics, plant diversity, and soil properties across varying restoration degrees to environmental factors. It also elucidates the characteristics of plant communities along recovery gradients in alpine grasslands.

Effects of coastal saline-alkali soil on rhizosphere microbial community and crop yield of cotton at different growth stages

Soil salinization is a global constraint that significantly hampers agricultural production, with cotton being an important cash crop that is not immune to its detrimental effects. The rhizosphere microbiome plays a critical role in plant health and growth, which assists plants in resisting adverse abiotic stresses including soil salinization. This study explores the impact of soil salinization on cotton, including its effects on growth, yield, soil physical and chemical properties, as well as soil bacterial community structures. The results of β-diversity analysis showed that there were significant differences in bacterial communities in saline-alkali soil at different growth stages of cotton. Besides, the more severity of soil salinization, the more abundance of Proteobacteria, Bacteroidota enriched in rhizosphere bacterial composition where the abundance of Acidobacteriota exhibited the opposite trend. And the co-occurrence network analysis showed that soil salinization affected the complexity of soil bacterial co-occurrence network. These findings provide valuable insights into the mechanisms by which soil salinization affects soil microorganisms in cotton rhizosphere soil and offer guidance for improving soil salinization using beneficial microorganisms.

Characteristics of bacterial communities in rhizosphere and bulk soil in Fe-deficient citrus growing in coastal saline-alkali land

Aims

Citruses often occur with imbalance in iron nutrition in coastal saline-alkali lands, which severely limits the yield and quality of the fruit. In the rhizosphere, the salt content plays a crucial role in reducing uptake of iron, as well as the activity and abundance of bacteria. However, few studies have explored how salt content affects the effectiveness of iron and the community structure of bacteria across different vertical spatial scales.

Methods

We investigated the citrus rhizosphere (0-30 cm) and bulk (0-60 cm) soil microenvironments of the coastal saline soil were analyzed using the 16S rRNA amplicon and inductively coupled plasma-optical emission spectroscopy.

Results

We found that the nutrient-related elements in the rhizosphere and bulk soil decreased with increasing soil depth, while the salinity-related elements showed the opposite trend. The nutrient-related element content in the rhizosphere was higher than that in the bulk, whereas the salinity-alkaline-related element content was lower than that in the bulk. The structure and diversity of bacterial communities are affected by the rhizosphere and soil depth. In the bulk, there are enriched bacteria such as WB1-A12, Nitrospiraceae and Anaerolineae that are tolerant to salt-alkali stress. In the rhizosphere, bacteria that promote plant nutrient absorption and secretion of iron carriers, such as Pseudomonas, Streptomyces, and Duganella, are prominent.

Conclusions

The soil depth and rhizosphere affect soil nutrients and saline alkali-related factors. Changes in soil depth and rhizosphere determine the structure and diversity of bacterial communities. Rhizosphere enhances iron absorption promoting bacteria to alleviate iron deficiency stress in saline-alkali soils. Our results indicate that citrus roots maybe can resist the stress of iron deficiency in saline-alkali soils by enhancing iron absorption promoting bacteria.

Assessment of metal pollution and effects of physicochemical factors on soil microbial communities around a landfill

The physicochemical properties, chemical fractions of six metals (Cu, Zn, Pb, Cd, Cr, and Mn), and microbial communities of soil around a typical sanitary landfill were analyzed. The results indicate that soils around the landfill were from neutral to weak alkalinity. The contents of organic matter (OM), total nitrogen (TN), total phosphorous (TP), and activities of catalase, cellulase, and urease were significantly higher in landfill soils than those in background soils. Negative correlations were found between pH and metals. Cr was the dominant metal. Cu, Pb, Cr, and Mn were accumulated in the nearby farmland soils. Cd had the highest percentage of exchangeable fraction (33.7%-51.8%) in landfill and farmland soils, suggesting a high bioavailability to the soil environment affected by the landfill. Pb, Cr, and Mn existed mostly in oxidable fraction, and Cu and Zn were dominant in residual fraction. There was a low risk of soil metals around the landfill based on the RI values, while according to RAC classification, Cd had high to very high environmental risk. The MisSeq sequencing results showed that Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria were the dominant phyla of bacteria, and the most abundant phylum of fungi was Ascomycota. The NMDS analysis revealed that the landfill could influence soil fungal communities more intensely than bacterial communities. TN, cellulase, and bioavailable metals (Pb-Bio and Cr-Bio) were identified to have main influences on microbial communities. Pb-Bio was the most dominant driving factor for bacterial community structures. For fungi, Pb-Bio was significantly negatively related to Olpidiomycota and Cr-Bio had a significantly negative correlation with Ascomycota. It manifests that bioavailable metals play important roles in assessing environmental risks and microbial community structures of soil around landfill.

Replacing traditional pretreatment in one-step UF with natural short-distance riverbank filtration: Continuous contaminants removal and TMP increase relief

Scientists have been focusing on applying more natural processes instead of industrial chemicals in drinking water treatment to achieve the purpose of carbon emissions reduction. In this study, we shortened the infiltration range of riverbank filtration, a natural water purification process, to form the short-distance riverbank filtration (sRBF) which retained its ability in water quality improvement and barely influenced the groundwater environment, and integrated it with ultrafiltration (UF) to form a one-step sRBF-UF system. This naturalness-artificiality combination could realize stable contaminants removal and trans-membrane pressure (TMP) increase relief for over 30 days without dosing chemicals. Generally, both sRBF and UF played the important role in river water purification, and the interaction between them made the one-step sRBF-UF superior in long-term operation. The sRBF could efficiently remove contaminants (90 % turbidity, 60 % total nitrogen, 30 % ammonia nitrogen, and 25 % total organic carbon) and reduce the membrane fouling potential of river water under its optimum operation conditions, i.e., a hydraulic retention time of 48 h, an operation temperature of 20 °C, and a synergistic filter material of aquifer and riverbank soil. Synergistic adsorption, interception, and microbial biodegradation were proved to be the mechanisms of contaminants and foulants removal for sRBF. The sequential UF also participated in the reduction of impurities and especially played a role in intercepting microbial metabolism products and possibly leaked microorganisms from sRBF, assuring the safety of product water. To date, the one-step sRBF-UF was a new attempt to combine a natural process with an artificial one, and realized a good and stable product quality in long-term operation without doing industrial chemicals, which made it a promised alternative for water purification for cities alongside the river.

Chitosan-Se Engineered Nanomaterial Mitigates Salt Stress in Plants by Scavenging Reactive Oxygen Species

Soil salinity seriously hinders the sustainable development of green agriculture. The emergence of engineered nanomaterials has revolutionized agricultural research, providing a new means to overcome the limitations associated with current abiotic stress management and achieve highly productive agriculture. Herein, we synthesized a brand-new engineered nanomaterial (Cs-Se NMs) through the Schiff base reaction of oxidized chitosan with selenocystamine hydrochloride to alleviate salt stress in plants. After the addition of 300 mg/L Cs-Se NMs, the activity of superoxide dismutase, catalase, and peroxidase in rice shoots increased to 3.19, 1.79, and 1.85 times those observed in the NaCl group, respectively. Meanwhile, the MDA levels decreased by 63.9%. Notably, Cs-Se NMs also raised the transcription of genes correlated with the oxidative stress response and MAPK signaling in the transcriptomic analysis. In addition, Cs-Se NMs augmented the abundance and variety of rhizobacteria and remodeled the microbial community structure. These results provide insights into applying engineered nanomaterials in sustainable agriculture.

Defined synthetic microbial communities colonize and benefit field-grown sorghum

The rhizosphere constitutes a dynamic interface between plant hosts and their associated microbial communities. Despite the acknowledged potential for enhancing plant fitness by manipulating the rhizosphere, the engineering of the rhizosphere microbiome through inoculation has posed significant challenges. These challenges are thought to arise from the competitive microbial ecosystem where introduced microbes must survive, and the absence of adaptation to the specific metabolic and environmental demands of the rhizosphere. Here, we engineered a synthetic rhizosphere community (SRC1) with the anticipation that it would exhibit a selective advantage in colonizing the host Sorghum bicolor, thereby potentially fostering its growth. SRC1 was assembled from bacterial isolates identified either for their potential role in community cohesion through network analysis or for their ability to benefit from host-specific exudate compounds. The growth performance of SRC1 was assessed in vitro on solid media, in planta under gnotobiotic laboratory conditions, and in the field. Our findings reveal that SRC1 cohesion is most robust when cultivated in the presence of the plant host under laboratory conditions, with lineages being lost from the community when grown either in vitro or in a native field setting. We establish that SRC1 effectively promotes the growth of both above- and below-ground plant phenotypes in both laboratory and native field contexts. Furthermore, in laboratory conditions, these growth enhancements correlate with the transcriptional dampening of lignin biosynthesis in the host. Collectively, these results underscore the potential utility of synthetic microbial communities for modulating crop performance in controlled and native environments alike.

Soil microbial community composition and co-occurrence network responses to mild and severe disturbances in volcanic areas

Soil physicochemical properties and vegetation types are the main factors affecting soil microorganisms, but there are few studies on the effects of the disturbance following volcanic eruption. To make up for this lack of knowledge, we used Illumina Miseq high-throughput sequencing to study the characteristics of soil microorganisms on both shores of a volcanically disturbed lake. Soil microorganisms in the two sites were subjected to different degrees of volcanic disturbance and showed significant heterogeneity. Mild volcanic disturbance area had higher enrichment of prokaryotic community. Co-occurrence network analysis showed that a total of 12 keystone taxa (9 prokaryotes and 3 fungi) were identified, suggesting that soil prokaryote may play a more significant role than fungi in overall community structure and function. Compared with severe volcanic disturbance area, the soil microbial community in mild volcanic disturbance area had the higher modular network (0.327 vs 0.291). The competition was stronger (positive/negative link ratio, P/N: 1.422 vs 1.159). Random forest analysis showed that soil superoxide dismutase was the most significant variable associated with soil microbial community. Structural equation model (SEM) results showed that keystone had a directly positive effect on prokaryotic (λ = 0.867, P < 0.001) and fungal (λ = 0.990, P < 0.001) multifunctionality while had also a directly positive effect on fungal diversity (λ = 0.553, P < 0.001), suggesting that keystone taxa played a key role in maintaining ecosystem stability. These results were important for understanding the effects of different levels of volcanic disturbance on soil ecosystems.

Soil nutrients, enzyme activities, and bacterial communities in varied plant communities in karst rocky desertification regions in Wushan County, Southwest China

Vegetation restoration has become a common practice in karst rocky desertification (KRD) areas of southwestern China. The bacteria, which have made a connection between soil and plants, have been an important role in regulating the succession and restoration of karst vegetation. However, it is still unclear how soil bacterial communities and soil properties respond to natural vegetation restoration processes in karst areas. To address this gap, we investigated the soil nutrients, enzyme activity, and soil bacterial community among various plant communities, including farmland (FL), land with herbs only (SSI), herb-and-shrub land (SSII), woody thickets (SSIII), coniferous forest (SSIV), coniferous and broad-leaved mixed forest (SSV), and evergreen broad-leaved forest (SSVI). Our results found that SSII had the highest levels of soil organic matter, total nitrogen, available phosphorus, available nitrogen, sucrase, and β-glucosidase among all the plant communities. These results indicated that herb-and-shrub land have contributed to the rapid restoration of vegetation in KRD regions. FL exhibited the lowest levels of soil nutrients and enzyme activities, while showing the highest bacterial richness and diversity among all the plant communities. This suggested that appropriate human intervention can increase bacterial diversity and richness in the area. The predominant bacterial phylum also varied among the different plant communities, with Actinobacteria being the most abundant in SSI, SSII, SSIII, and SSIV, while Proteobacteria were the most abundant in SSV and SSVI. Furthermore, PCoA analysis demonstrated significant changes in the soil bacterial community structure, with SSI, SSII, SSIII, and SSIV had shared similar structures, while SSV and SSVI had comparable structures. As for soil characteristics, total phosphorus (TP) and total potassium (TK) were the primary factors affecting the soil bacterial community. SSV and SSVI had the most complex bacterial networks and were more stable than other groups. The genera Ktedonobacter, norank_f_Anaerolineaceae, and Vicinamibacter had the highest betweenness centrality scores and were identified as keystone genera in the co-occurrence network in KRD areas. In summary, our results have demonstrated that herb-and-shrub can promote community succession and increase soil nutrient levels in KRD regions.

Effects of Mineral on Taxonomic and Functional Structures of Microbial Community in Tengchong Hot Springs via in-situ cultivation

Diverse mineralogical compositions occur in hot spring sediments, but the impact of minerals on the diversity and structure of microbial communities remains poorly elucidated. In this study, different mineral particles with various chemistries (i.e., hematite, biotite, K-feldspar, quartz, muscovite, aragonite, serpentine, olivine, barite, apatite, and pyrite) were incubated for ten days in two Tengchong hot springs, one alkaline (pH ~ 8.34) with a high temperature (~ 82.8 °C) (Gumingquan, short as GMQ) and one acidic (pH ~ 3.63) with a relatively low temperature (~ 43.3 °C) (Wenguangting, short as WGT), to determine the impacts of minerals on the microbial communities taxonomic and functional diversities. Results showed that the mineral-associated bacterial taxa differed from those of the bulk sediment samples in the two hot springs. The relative abundance of Proteobacteria, Euryarchaeota, and Acidobacteria increased in all minerals, indicating that these microorganisms are apt to colonize on solid surfaces. The α-diversity indices of the microbial communities on the mineral surfaces in the WGT were higher than those from the bulk sediment samples (p < 0.05), which may be caused by the stochastically adhering process on the mineral surface during 10-day incubation, different from the microbial community in sediment which has experienced long-term environmental and ecological screening. Chemoheterotrophy increased with minerals incubation, which was high in most cultured minerals (the relative contents were 5.8 - 21.4%). Most notably, the sulfate respiration bacteria (mainly related to Desulfobulbaceae and Syntrophaceae) associated with aragonite in the acidic hot spring significantly differed from other minerals, possibly due to the pH buffering effect of aragonite providing more favorable conditions for their survival and proliferation. By comparison, aragonite cultured in the alkaline hot spring highly enriched denitrifying bacteria and may have promoted the nitrogen cycle within the system. Collectively, we speculated that diverse microbes stochastically adhered on the surface of minerals in the water flows, and the physicochemical properties of minerals drove the enrichment of certain microbial communities and functional groups during the short-term incubation. Taken together, these findings thereby provide novel insights into mechanisms of community assembly and element cycling in the terrestrial hydrothermal system associated with hot springs.

Woody plants have the advantages in the phytoremediation process of manganese ore with the help of microorganisms

The serious ecological damage caused by mining activities cannot be ignored. The use of an environmentally friendly restoration method to rebuild the vegetation and soil environment in the mining area has attracted more and more attention. This paper aims to study soil quality as well as vegetation characteristics of four woody species including Pinus massoniana (P. massoniana), Broussonetia papyrifera (B. papyrifera), Koelreuteria paniculata (K. paniculata), Osmanthus fragrans (O. fragrans), and two herbaceous species including Setaria viridis (S. viridis) and Cynodon dactylon (C. dactylon). In addition, we further clarified the effects of B. papyrifera and K. paniculata on soil nutrients and microbial communities after restoration. The results showed that the vegetation restoration area had better soil quality and plant community diversity, and the woody plants restoration effect were better. Compared with slag, B. papyrifera and K. paniculata remediation could improve soil pH and mitigate heavy metal contamination in mining areas, but was not effective in enhancing Soil Organic Matter (SOM), Total Nitrogen (TN), Total Potassium (TK) and Total Phosphorus (TP). In addition, the abundance and diversity of soil bacterial communities were increased. Of all the study sites, Proteobacteria had the greatest dominance. Vegetation restoration resulted in an increase in the relative abundance of Acidobacteria, while a decrease in Actinobacteria, Cyanobacteria and Firmicutes. With the restoration of vegetation, the increase of pH, the change of TN, SOM, TK, TP and the mitigation of Manganese (Mn) pollution were the main reasons affecting the soil microbial community. This study has great significance for understanding the ecological changes in the mining area after artificially mediated vegetation restoration, including changes in soil environment, plant community and microbial community, and woody plants will be more encouraged for the restoration of manganese mining areas.

Evaluation of efficacy and mechanism of Bacillus velezensis CB13 for controlling peanut stem rot caused by Sclerotium rolfsii

Peanut stem rot, caused by Sclerotium rolfsii, considerably affects crop productivity. Application of chemical fungicides harms the environment and induces drug resistance. Biological agents are valid and eco-friendly alternatives to chemical fungicides. Bacillus spp. are important biocontrol agents that are now widely used against several plant diseases. This study aimed to evaluate the efficacy and mechanism of a potential biocontrol agent Bacillus sp. for controlling peanut stem rot caused by S. rolfsii. Here, we isolated a strain of Bacillus from pig biogas slurry that considerably inhibits the radial growth of S. rolfsii. The strain CB13 was identified as Bacillus velezensis on the basis of morphological, physiological, biochemical characteristics and phylogenetic trees based on the 16S rDNA and gyrA, gyrB, and rpoB gene sequences. The biocontrol efficacy of CB13 was evaluated on the basis of colonization ability, induction of defense enzyme activity, and soil microbial diversity. The control efficiencies of B. velezensis CB13-impregnated seeds in four pot experiments were 65.44, 73.33, 85.13, and 94.92%. Root colonization was confirmed through green fluorescent protein (GFP)-tagging experiments. The CB13-GFP strain was detected in peanut root and rhizosphere soil, at 104 and 108 CFU/g, respectively, after 50 days. Furthermore, B. velezensis CB13 enhanced the defense response against S. rolfsii infection by inducing defense enzyme activity. MiSeq sequencing revealed a shift in the rhizosphere bacterial and fungal communities in peanuts treated with B. velezensis CB13. Specifically, the treatment enhanced disease resistance by increasing the diversity of soil bacterial communities in peanut roots, increasing the abundance of beneficial communities, and promoting soil fertility. Additionally, real-time quantitative polymerase chain reaction results showed that B. velezensis CB13 stably colonized or increased the content of Bacillus spp. in the soil and effectively inhibited S. rolfsii proliferation in soil. These findings indicate that B. velezensis CB13 is a promising agent for the biocontrol of peanut stem rot.

Deciphering the role of non-Frankia nodular endophytes in alder through in vitro and genomic characterization

Endophytic bacterial populations are well-positioned to provide benefits to their host plants such as nutrient acquisition and plant hormone level manipulation. Actinorhizal plants such as alders are well known for their microbial symbioses that allow them to colonize harsh environments whether natural or anthropized. Although the nitrogen-fixing actinobacterium Frankia sp. is the main endophyte found in alder root nodules, other bacterial genera, whose roles remain poorly defined, inhabit this niche. In this study, we isolated a diverse panel of non-Frankia nodular endophytes (NFNE). Some NFNE were isolated from alders grown from surface-sterilized seeds and maintained in sterile conditions, suggesting these may have been seed-borne. In vitro testing of 24 NFNE revealed some possessed putative plant growth promotion traits. Their genomes were also sequenced to identify genes related to plant growth promotion traits. This study highlights the complexity of the alder nodular microbial community. It paves the way for further understanding of the biology of nodules and could help improve land reclamation practices that involve alders.

The Effects of Shrub Removal on Soil Microbial Communities in Primary Forest, Secondary Forest and Plantation Forest on Changbai Mountain

Shrub removal is a common management method in forest ecosystems, but comparatively little is known regarding the effects of shrub removal on soil microbial communities among primary forest, secondary forest, and plantation forests in temperate forests, which limits our accurate assessment of sustainable management of understory vegetation removal. Given this, we used a long-term operation experiment across a contrasting mixed broadleaved-Pinus koraiensis forest, Betula platyphylla forest, and Larix gmelinii plantation forest to explore the variations of soil properties and microbial community after 5 years of shrub removal on Changbai Mountain, as well as the contribution of the soil properties and understory plant diversity to the soil microbial community. The results demonstrated that shrub removal could significantly alter soil SWC and TN, TP, and AP contents of the L. gmelinii, as well as N/P of B. platyphylla. Moreover, shrub removal also clearly improved soil bacterial Pielou_e index and Simpson index of mixed broadleaved-P. koraiensis and soil bacterial Simpson index of L. gmelinii, and decreased soil fungal Pielou_e index and Shannon index of L. gmelinii and soil bacterial Pielou_e index and soil fungal Shannon index of B. platyphylla. Identically, shrub removal notably altered the soil bacterial community composition. Soil characteristics and understory plant diversity accounted for 48.02% and 26.88%, and 45.88% and 27.57% of the variance in the bacterial and fungal community composition, respectively. This study aimed to provide an important scientific basis for the restoration and sustainable management of temperate forests in the Changbai Mountain region.

Coriander (Coriandrum sativum) Cultivation Combined with Arbuscular Mycorrhizal Fungi Inoculation and Steel Slag Application Influences Trace Elements-Polluted Soil Bacterial Functioning

The cultivation of aromatic plants for the extraction of essential oils has been presented as an innovative and economically viable alternative for the remediation of areas polluted with trace elements (TE). Therefore, this study focuses on the contribution of the cultivation of coriander and the use of arbuscular mycorrhizal fungi (AMF) in combination with mineral amendments (steel slag) on the bacterial function of the rhizosphere, an aspect that is currently poorly understood and studied. The introduction of soil amendments, such as steel slag or mycorrhizal inoculum, had no significant effect on coriander growth. However, steel slag changed the structure of the bacterial community in the rhizosphere without affecting microbial function. In fact, Actinobacteria were significantly less abundant under slag-amended conditions, while the relative proportion of Gemmatimonadota increased. On the other hand, the planting of coriander affects the bacterial community structure and significantly increased the bacterial functional richness of the amended soil. Overall, these results show that planting coriander most affected the structure and functioning of bacterial communities in the TE-polluted soils and reversed the effects of mineral amendments on rhizosphere bacterial communities and their activities. This study highlights the potential of coriander, especially in combination with steel slag, for phytomanagement of TE-polluted soils, by improving soil quality and health.

Distribution characteristics of soil microbial communities and their responses to environmental factors in the sea buckthorn forest in the water-wind erosion crisscross region

Soil microorganisms are an important part of forest ecosystems, and their community structure and ecological adaptations are important for explaining soil material cycles in the fragile ecological areas. We used high-throughput sequencing technology to examine the species composition and diversity of soil bacterial and fungal communities in sea buckthorn forests at five sites in the water-wind erosion crisscross in northern Shaanxi (about 400 km long). The results are described as follows: (1) The soil bacterial community of the sea buckthorn forest in the study region was mainly dominated by Actinobacteria, Proteobacteria, and Acidobacteria, and the fungi community was mainly dominated by Ascomycota. (2) The coefficient of variation of alpha diversity of microbial communities was higher in the 0-10 cm soil layer than in the 10-20 cm soil layer. (3) Soil electrical conductivity (36.1%), available phosphorous (AP) (21.0%), available potassium (16.2%), total nitrogen (12.7%), and the meteorological factors average annual maximum temperature (33.3%) and average annual temperature (27.1%) were identified as the main drivers of structural changes in the bacterial community. Available potassium (39.4%), soil organic carbon (21.4%), available nitrogen (AN) (13.8%), and the meteorological factors average annual maximum wind speed (38.0%) and average annual temperature (26.8%) were identified as the main drivers of structural changes in the fungal community. The explanation rate of soil factors on changes in bacterial and fungal communities was 26.6 and 12.0%, respectively, whereas that of meteorological factors on changes in bacterial and fungal communities was 1.22 and 1.17%, respectively. The combined explanation rate of environmental factors (soil and meteorological factors) on bacterial and fungal communities was 72.2 and 86.6%, respectively. The results of the study offer valuable insights into the diversity of soil microbial communities in the water-wind erosion crisscross region and the mechanisms underlying their interaction with environmental factors.

Characterization of ectomycorrhizal fungal communities associated with tree species on an iron tailings deposit undergoing restoration

Vegetation restoration is an effective method to improve the ecological environment of mine tailings, which has a profound impact on the potential ecological functions of soil fungal communities; yet, little is known about its beneficial effect on soil ectomycorrhizal fungal community. In this study, the responses of soil characteristics and soil ectomycorrhizal fungal community diversity and structure to different revegetation, as well as the contribution of soil factors to soil ectomycorrhizal community were investigated in Liaoning Province, China. As we anticipated, the presence of vegetation significantly improved most soil properties we studied. What's more, compared to Korean pine (Pinus koraiensis Sieb. et Zucc.), Chinese poplar (Populus simonii Carr), and black locust (Robinia pseudoacacia L) could better improve soil total carbon, total nitrogen, total phosphorus, and available phosphorus. In addition, soil ectomycorrhizal fungal community diversity in black locust was greater than Korean pine and Populus simonii. Nonmetric multidimensional scaling analyses indicated that soil ectomycorrhizal community significantly differed depending on different revegetation types. Thus, these results indicated that black locust could be a suitable species for the revegetation of iron mine tailings. The study provided theoretical basis for ecological restoration of iron mine tailings using local plant species.

Bacterial Community with Plant Growth-Promoting Potential Associated to Pioneer Plants from an Active Mexican Volcanic Complex

Microorganisms in extreme volcanic environments play an important role in the development of plants on newly exposed substrates. In this work, we studied the structure and diversity of a bacterial community associated to Andropogon glomeratus and Cheilanthes aemula at El Chichón volcano. The genetic diversity of the strains was revealed by genomic fingerprints and by 16S rDNA gene sequencing. Furthermore, a metagenomic analysis of the rhizosphere samples was carried out for pioneer plants growing inside and outside the volcano. Multifunctional biochemical tests and plant inoculation assays were evaluated to determine their potential as plant growth-promoting bacteria (PGPB). Through metagenomic analysis, a total of 33 bacterial phyla were identified from A. glomeratus and C. aemula rhizosphere samples collected inside the volcano, and outside the volcano 23 bacterial phyla were identified. For both rhizosphere samples, proteobacteria was the most abundant phylum. With a cultivable approach, 174 bacterial strains were isolated from the rhizosphere and tissue of plants growing outside the volcanic complex. Isolates were classified within the genera Acinetobacter, Arthrobacter, Bacillus, Burkholderia, Cupriavidus, Enterobacter, Klebsiella, Lysinibacillus, Pantoea, Pseudomonas, Serratia, Stenotrophomonas and Pandoraea. The evaluated strains were able to produce indole compounds, solubilize phosphate, synthesize siderophores, showed ACC deaminase and nitrogenase activity, and they had a positive effect on the growth and development of Capsicum chinense. The wide diversity of bacteria associated to pioneer plants at El Chichón volcano with PGPB qualities represent an alternative for the recovery of eroded environments, and they can be used efficiently as biofertilizers for agricultural crops growing under adverse conditions.

Diversity and composition of soil bacteria between abandoned and selective-farming farmlands in an antimony mining area

Background and aims

Land abandonment and selective farming are two common management methods to restore the soil conditions of low-pollution farmland in mining areas. The soil bacterial community plays an important role in farmland soil restoration; however, few studies have compared the composition and diversity of soil bacteria between the abandoned farmlands (AFS) and selective-farming farmlands (FFS). Here, the effects of AFS and FFS on soil properties and bacterial diversity were evaluated in an antimony (Sb) mining area in southern China. This study aimed to identify effective land management methods in terms of positive or negative changes in soil environment and bacterial diversity.

Methods

16S rRNA high-throughput sequencing was used to compare the diversity and composition of soil bacteria between AFS and FFS in the Xikuangshan (the largest Sb mine in the world).

Results

Compared to AFS, FFS had higher Sb concentration and nutritional properties (e.g., available N, P, and K) and lower Zn concentration (p < 0.05). The bacterial alpha diversity including Chao1 index, Simpson index, Shannon index and Pielou₋e index in FFS was higher than AFS (p < 0.05). At the phylum level, FFS had higher relative abundances of Chloroflexi, Acidobacteria, Gemmatimonadetes, and Rokubacteria, and lower relative abundances of Firmicutes, Actinobacteria, and Bacteroidetes. At the genus level, FFS had higher relative abundances of Acidothermus, Haliangium, and Rokubacteriales, and lower relative abundances of Bacillus, Rhodococcus, Sphingomonas, and 67-14. Redundancy analysis indicated that soil heavy metal content and soil fertility were closely correlated with the soil bacterial community. Altogether, selective farming of low-pollution farmland in the mining area can improve soil properties and soil bacterial diversity.

Variations of Phyllosphere and Rhizosphere Microbial Communities of Pinus koraiensis Infected by Bursaphelenchus xylophilus

Pine wood nematode, Bursaphelenchus xylophilus, as one of the greatest threats to pine trees, is spreading all over the world. Plant microorganisms play an important role in the pathogenesis of nematodes. The phyllosphere and rhizosphere bacterial and fungal communities associated with healthy Pinus koraiensis (PKa) and P. koraiensis infected by B. xylophilus at the early (PKb) and last (PKc) stages were analyzed. Our results demonstrated that pine wood nematode (PWD) could increase the phyllosphere bacterial Pielou_e, Shannon, and Simpson index; phyllosphere fungal Chao 1 index, as well as rhizosphere bacterial Pielou_e, Shannon, and Simpson index; and rhizosphere fungal Pielou_e, Shannon, and Simpson index. What's more, slight shifts of the microbial diversity were observed at the early stage of infection, and the microbial diversity increased significantly as the symptoms of infection worsened. With the infection of B. xylophilus in P. koraiensis, Bradyrhizobium (rhizosphere bacteria), Massilia (phyllosphere bacteria), and Phaeosphaeriaceae (phyllosphere fungi) were the major contributors to the differences in community compositions among different treatments. With the infection of PWD, most of the bacterial groups tended to be co-excluding rather than co-occurring. These changes would correlate with microbial ability to suppress plant pathogen, enhancing the understanding of disease development and providing guidelines to pave the way for its possible management.

Multiple heavy metal distribution and microbial community characteristics of vanadium-titanium magnetite tailing profiles under different management modes

Vanadium-titanium (V-Ti) magnetite tailings have caused great concern due to their safety hazards and environmental risks. However, the microbial community structure and the key geochemical factors of V-Ti magnetite tailing profiles under different management modes remain unclear. Therefore, we investigated the heavy metal distribution and the microbial community structure of the soils and tailings at varied depths of V-Ti magnetite tailing profiles with and without soil coverage. The results indicated that the topsoil covering measures retarded the acidification of tailings during stockpiling. However, As, Mn, and V in tailings have the ability to migrate to the overlying soil. Based on 16S rRNA gene amplicon sequencing, Proteobacteria was the dominant genus in the topsoil-covered tailings, whereas the most abundant genus in the exposed tailings was Betaproteobacteria. Furthermore, Rhodobacter, Hydrogenophaga, Novosphingobium, and Geobacter enriched in tailings may potentially contribute to V(V) biotransformation and the development of mine bioreremediation technologies. RDA and Spearman correlation analysis showed that pH, EC, Cd, Mn, Pb, and V were the main influencing factors regulating microbial community composition. Overall, this study provides insights for evaluating the soil covering management mode and the engineering applications of microbial technologies to manage V-Ti magnetite tailings.

Mechanism underlying how a chitosan-based phosphorus adsorbent alleviates cadmium-induced oxidative stress in Bidens pilosa L. and its impact on soil microbial communities: A field study

In the present study, field experiments were conducted in Side village, Yangshuo, Guilin, Guangxi Province, China, using four C-BPA application levels (control (0 mg m^-2), T1 (100 mg m^-2), T2 (200 mg m^-2) and T3 (400 mg m^-2)) to clarify the mechanism by which a chitosan-based phosphorus adsorbent (C-BPA) applied as a passivator helps Bidens pilosa L. (B. pilosa L.) alleviate cadmium (Cd)-induced oxidative stress in Cd-contaminated soil. In the aqueous phase, C-BPA successfully adsorbed Cd²⁺ on the surface primarily via ion exchange, and C-BPA has potential Cd²⁺ adsorption capacity, enabling its use as a passivator in real Cd-contaminated environments. In Cd-contaminated soils, under C-BPA application at the T3 level, the pH value increased by 11.2%, and the acid-soluble form of Cd decreased by 26.5%. Additionally, the application of C-BPA improved the rhizosphere soil environment and impacted the soil microbial community diversity and structure. Among soil microbes, the soil fungal community was more sensitive than bacteria to C-BPA application. Dehydrogenase, acetic acid, soil pH and Eurotiomycetes or Dothideomycetes significantly impacted Cd accumulation in the leaves of B. pilosa L.; Cd accumulation in leaves was decreased by 68.1% under C-BPA application at the T3 level. Additionally, the variation of increased catalase (CAT) and peroxidase (POD) jointly promoted plant growth; the plant weight was increased by 112.7% under the C-BPA application at the T3 level. Notably, the production of CAT and POD by B. pilosa L. was more effective than the synthesis of glutathione (GSH) in helping B. pilosa L. eliminate excess reactive oxygen species (ROS). Therefore, our findings demonstrated that the application of C-BPA to Cd-contaminated soil can greatly improve the rhizosphere soil environment, help B. pilosa L. eliminate ROS and promote plant growth.

Heavy metals speciation and distribution of microbial communities in sediments from the abandoned Mo-Ni polymetallic mines, southwest of China

Chemical fractions of heavy metals (Mo, Ni, Cu, Zn, Fe, Mn, Pb, Cd, and Cr) and compositions of bacteria and fungi in surface sediments from the Mo-Ni polymetallic mine area were analyzed. The results indicated that the mean concentrations of Mo, Ni, Cu, Zn, and Cd were higher than their background values. The mean percentage of Cr in residual fraction was much higher than that of other heavy metals. Mo, Cu, Zn, Fe, and Pb were mainly associated with oxidizable fraction. The dominant proportions of Mn and Cd were found in exchangeable fraction with mean percentages of 93.46% and 54.50%, respectively. According to RAC classification and potential ecological risk index (PERI), the Cd with high bioavailability had a very high environmental risk. The MisSeq sequencing results of bacteria and fungi revealed that microbial communities discrepantly respond to different sampling sites. The most abundant phylum of bacteria and fungi were Proteobacteria and Ascomycota, respectively. The bioavailable heavy metals including Mo-B, Pb-B, and Cd-B were recognized to have important influences on both dominant bacterial and fungal communities. The present study manifested that the bioavailability of heavy metal is very important to assess the potential environmental risk and plays a key role in shaping microbial structure.

Re-vegetation Improves Soil Quality by Decreasing Soil Conductivity and Altering Soil Microbial Communities: A Case Study of an Opencast Coal Mine in the Helan Mountains

Microbial communities constitute a diverse genetic resource pool in the soil and are key indicators of soil health and quality. How re-vegetation affects soil microbial diversity and community composition at the dump of an opencast coal mine is largely unknown. Using high-throughput sequencing, we performed a comparative study of the bacterial and fungal communities from non-vegetated (bare land) soil and from areas re-vegetated by Astragalus laxmannii, Halogeton arachnoideus, and Artemisia desertorum at an opencast coal mine in the Helan Mountains in western China. These results indicated that re-vegetation significantly reduced soil conductivity. The soils re-vegetated by all three plant species showed greater richness of bacterial species than the bare land, and soils re-vegetated with A. desertorum and A. laxmannii showed significantly greater richness of fungal species than bare land. The bacterial and fungal β-diversity values differed significantly between vegetated and non-vegetated soil, and these differences were more pronounced for bacterial communities than for fungal communities. Re-vegetation significantly increased the relative abundances of Proteobacteria and Bacteroidota and decreased the relative abundance of Chloroflexi. The decreasing soil conductivity that occurred with re-vegetation was found to be an important environmental determinant of the soil microbial community. This study provides evidence that re-vegetation may enhance soil quality via decreasing soil conductivity and altering the soil microbial community, and A. laxmannii was found to be a more effective species than H. arachnoideus or A. desertorum with respect to decreasing soil conductivity and altering the soil microbial communities in the Opencast Coal Mine arid region. This work may provide a helpful guideline for selection of plant species for re-vegetation projects.

Natural Recovery from Fire Disturbance is More Favorable than Assisted Recovery for the Restoration of Soil Nematode-trapping Fungi

Fire is usually considered a severe disturbance factor in environment. Globally, rising temperatures and increasing human activities have intensified the severity and frequency of fire incidents; research on postfire recovery has inevitably become an important focus for ecologists. In terms of the restoration of burned areas, there are usually two primary approaches: natural recovery and assisted recovery. However, there are very few relevant studies that systematically compared these recovery alternatives suggesting which one is more favorable to the overall restoration of an ecosystem, especially to the soil microbes that function as indispensable components of ecosystems. In this study, the restoration of soil nematode-trapping fungi (NTF) was compared between natural and assisted recovery environments. Results showed that although the NTF community structures differed among the sample sites, the counts and diversity of the NTF communities in the upper and lower soil layers in the natural recovery area were higher than those in the assisted recovery and the unburned control areas. These findings suggests that artificial efforts to help ecosystem recovery after fire produce negative effects on the speed and quality of soil NTF community recovery. Instead, natural recovery appears to be the more suitable land management choice after fire disturbance.

Phytoextraction of metal(loid)s from contaminated soils by six plant species: A field study

Phytoextraction is an in situ remediation technique that uses (hyper)accumulator plant species to extract metal(loid)s from contaminated soils. Field studies can help in selecting appropriate plants for phytoextraction and in better understanding their phytoextraction performance. Hence, a field study was conducted using six (hyper)accumulator species (Solanum nigrum L., Bidens pilosa L., Xanthium strumarium L., Helianthus annuus L., Lonicera japonica T. and Pennisetum sinese R.) over two years in Jiaoxi town, Liuyang city, Hunan Province, China, to determine the effect of the (hyper)accumulator rhizospheres on field soils contaminated with multiple metal(loid)s and to analyze the variations in rhizosphere soil microbial community diversity and composition. After two years of field experiments, compared to the other four (hyper)accumulators, Bidens pilosa L. and Xanthium strumarium L. exhibited not only better metal(loid) phytoextraction abilities but also higher shoot biomasses. The contents of diethylenetriaminepentaacetic acid (DTPA)-extractable Pb, Cd and Zn decreased in the rhizosphere soils of all six (hyper)accumulators after repeated phytoextraction. Moreover, our findings illustrated that hyperaccumulator planting helps improve and rebuild the soil bacterial community composition and structure in contaminated soils by shifting the soil physiochemical properties. After repeated planting, the soil bacterial communities were reconstructed and dominated by Proteobacteria, Actinobacteriota, Chloroflexi and Acidobacteriota at the phylum level. The soil fungal communities were dominated by Ascomycota, Basidiomycota and Mortierellomycota at the phylum level. The reconstruction of soil microbial communities may help (hyper)accumulators adapt to metal(loid)-contaminated environments and improve their phytoextraction abilities.

Phylum Gemmatimonadota and Its Role in the Environment

Bacteria are an important part of every ecosystem that they inhabit on Earth. Environmental microbiologists usually focus on a few dominant bacterial groups, neglecting less abundant ones, which collectively make up most of the microbial diversity. One of such less-studied phyla is Gemmatimonadota. Currently, the phylum contains only six cultured species. However, data from culture-independent studies indicate that members of Gemmatimonadota are common in diverse habitats. They are abundant in soils, where they seem to be frequently associated with plants and the rhizosphere. Moreover, Gemmatimonadota were found in aquatic environments, such as freshwaters, wastewater treatment plants, biofilms, and sediments. An important discovery was the identification of purple bacterial reaction centers and anoxygenic photosynthesis in this phylum, genes for which were likely acquired via horizontal gene transfer. So far, the capacity for anoxygenic photosynthesis has been described for two cultured species: Gemmatimonas phototrophica and Gemmatimonas groenlandica. Moreover, analyses of metagenome-assembled genomes indicate that it is also common in uncultured lineages of Gemmatimonadota. This review summarizes the current knowledge about this understudied bacterial phylum with an emphasis on its environmental distribution.

Effects of environmental factors on soil bacterial community structure and diversity in different contaminated districts of Southwest China mine tailings

A mass of tailings left by mineral exploitation have caused serious environmental pollution. Although many studies have shown that soil microorganisms have the potential to remediate environmental pollution, the interaction mechanism between microorganisms and the surrounding environment of tailings is still unclear. In this study, 15 samples around pyrite mine tailing were collected to explore the ecological effects of environmental factors on bacterial community. The results showed that most of the samples were acidic and contaminated by multiple metals. Cadmium (Cd), copper (Cu), nickel (Ni) migrated and accumulated to into downstream farmlands while chromium (Cr) was the opposite. Proteobacteria, Chloroflex and Actinobacteria were the dominant phyla. Soil pH, total phosphorus (TP), total nitrogen (TN), available potassium (AK), available phosphorus (AP), the bacteria abundance and diversity all gradually increased with the increase of the distance from the tailing. Invertase, acid phosphatase, total organic carbon (TOC), pH, TP and Cr were the main influencing factors to cause the variation of bacterial community. This work could help us to further understand the changes in soil microbial communities around pollution sources.

Soil Rehabilitation Promotes Resilient Microbiome with Enriched Keystone Taxa than Agricultural Infestation in Barren Soils on the Loess Plateau

Drylands provide crucial ecosystem and economic services across the globe. In barren drylands, keystone taxa drive microbial structure and functioning in soil environments. In the current study, the Chinese Loess plateau’s agricultural (AL) and twenty-year-old rehabilitated lands (RL) provided a unique opportunity to investigate land-use-mediated effects on barren soil keystone bacterial and fungal taxa. Therefore, soils from eighteen sites were collected for metagenomic sequencing of bacteria specific 16S rRNA and fungi specific ITS2 regions, respectively, and to conduct molecular ecological networks and construct microbial OTU-based correlation matrices. In RL soils we found a more complex bacterial network represented by a higher number of nodes and links, with a link percentage of 77%, and a lower number of nodes and links for OTU-based fungal networks compared to the AL soils. A higher number of keystone taxa was observed in the RL (66) than in the AL (49) soils, and microbial network connectivity was positively influenced by soil total nitrogen and microbial biomass carbon contents. Our results indicate that plant restoration and the reduced human interventions in RL soils could guide the development of a better-connected microbial network and ensure sufficient nutrient circulation in barren soils on the Loess plateau.

Changes in diversity and composition of rhizosphere bacterial community during natural restoration stages in antimony mine

Background

Open pit antimony (Sb) mining causes serious soil pollution, and phytoremediation is a low-cost approach to remediate heavy metal contaminated soil. Rhizosphere bacteria play an important role in ecological restoration in mining areas. There is a knowledge gap on how to find suitable rhizosphere microorganisms to improve the phytoremediation effect. Understanding the differences of rhizosphere bacterial diversity in different restoration stages is helpful to find suitable bacteria for ecological restoration.

Methods

A method of the substitution of "space" for "time" was used to study the effect of natural restoration on rhizosphere bacterial community. According to the dominant vegetation types (herb, shrub, and tree) in the natural restoration area of Sb mining, the early restoration (ER), middle restoration (MR), and later restoration (LR) from the largest Sb mine (Xikuangshan mine) in the world were selected to evaluate the differences in the composition and diversity of rhizosphere bacteria during three natural restoration stages. Each restoration stage had five samples. To determine the relationship between restoration stages and bacterial diversity in the rhizosphere, high throughput sequencing of PCR amplified were used.

Results

Alpha diversity, as assessed by Chao indices, appeared lowest in ER but this trend was not seen with other diversity metrics, including the Simpson and Shannon. Beta diversity analysis suggested there were differences in rhizobacterial community structure associate with restoration stage. At the phylum level, natural restoration led to a significant increase in the relative abundance of Actinobacteria in the MR, and a significant decrease in the relative abundance of Patescibacteria in the LR. Additionally, Calditrichaeota, Deferribacteres and Epsilonbacteraeota were only found in ER. At the genus level, the relative abundance of RB41 and Haliangium were highest in LR plots, while that of Bacillus and Gaiella were highest in ER plots. Additionally, the Azorhizobium genus was only detected in the ER phase. Overall, our findings suggested that several rhizosphere microbial communities had significant differences among three natural restoration stages (ER, MR, and LR) and the rhizosphere bacterial communities mainly appeared in the early restoration stage can be preferred for remediation of pollution soil in Xikuangshan.

Near-natural transformation of Pinus tabuliformis better improve soil nutrients and soil microbial community

Pinus tabulaeformis plantations have been established around northern China to restore degraded land and provide timber or fuelwood. In recent years, widely distributed monoculture P. tabulaeformis forests have been transformed into mixed forests due to various ecological problems. However, the current research on the influence of near-natural transformation of P. tabulaeformis on soil microbial diversity and community composition remains limited. Therefore, we examined the effect of forest conversion from monoculture Pinus tabuliformis (PT) to P. tabuliformis-Armeniaca vulgaris (PTAU), P. tabuliformis - Robinia pseudoacacia (PTRP), P. tabuliformis - Vitex negundo L. var. heterophylla (PTVN) forests on soil microbial community diversity and composition. The results indicated that compared to PT, PTAU, PTVN, and PTRP could enhance the soil pH, TC, TN, AN, and AK in different degrees, the most obvious in PTAU. Near-natural transformation of P. tabuliformis could improve soil bacterial Pielou_e index, and Simpson index, as well as soil fungal Chao1 index. Proteobacteria and Ascomycota were the dominant soil microbial community at the phylum level. What’s more, both soil bacterial and fungal community among PT, PTAU, PTRP and PTVN showed clear different, and PTAU obviously altered the soil microbial community structure. Proteobacteria was the predominant group in PT, while, Gemmatimonadetes enriched in PTVN. Ascomycota was the predominant group in PTAU, while, Basidiomycota was the predominant group in PTRP. Near-natural transformation of P. tabuliformis could change soil microbial community via altering soil characteristics. In brief, our research results revealed the influence of tree composition and soil nutrient availability on soil microbial diversity and composition, and provided management guidance for introduction soil microbial community in forest protection and management.

Soil characteristics and microbial community response in rare earth mining areas in southern Jiangxi Province, China

The microbial community and functional flora in rare earth mining areas are correlated, but the characteristics and metabolic pathways of pollutant in such mining areas are still poorly known. The heavy metals, rare earth elements, and microorganisms present after mining of rare earth mine sites were analyzed. After mining, all sampling sites exhibited low pH and low total organic carbon levels, accompanied by high iron and aluminum concentrations. The development of vegetation is closely related to the development of microorganisms. In the complex environment of rare earth mining areas, Proteobacteria exhibit an absolute competitive advantage. During mine environmental recovery, the relative abundances of Acidobacteria and Chloroflexi will increase markedly, and with further restoration the relative abundance of Firmicutes will gradually decrease. Many genera of bacteria related to the N cycle and heavy metal metabolism were detected in the study area, indicating the important metabolic pathways for ammonia nitrogen and heavy metals in rare earth mining areas. Bacterial genera that promote plant nitrogen fixation also occur in the area, further revealing the nitrogen cycle. This research is important for health assessment and recovery of rare earth mines.

Vegetation richness, species identity and soil nutrients drive the shifts in soil bacterial communities during restoration process

Soil bacteria play an essential role in functioning of ecosystems and maintaining of biogeochemical cycles. However, little is known about changes in the compositions and functional groups of soil bacterial communities during different restoration stages. The influences of aboveground vegetation and belowground soil properties on soil bacterial communities were also unclear during this process. Here we sequenced the soil bacterial communities in different stages of sand fixation. Sand fixation increased the diversity of the bacterial communities, among which the populations of Actinobacteria, Acidobacteria and Gemmatimonadetes changed significantly. The function prediction showed sand fixation increased Gram-positive and aerobic bacteria. Bacterial structure is significantly correlated with plant richness, coverage and biomass. In particular, we found species identity was an important determinant in structuring bacterial composition. Soil properties were all significantly correlated with soil bacterial community richness and diversity. Fusobacteria was strongly positively correlated with sand, Chloroflexi with total N and Gemmatimonadetes with SOM and total C. It suggested that soil nutrients (TC, TN and SOM) have large consequences for soil bacterial community dissimilarities. These results indicated that vegetation richness, especially species identity, together with improvement in soil nutrients, play key roles in driving the shifts in soil microbial community structure and function during restoration process.

Analysis of microbial community structure and diversity in surrounding rock soil of different waste dump sites in fushun western opencast mine

It is importance to understand the correlation between the physicochemical properties of different surrounding rock soil and microbial communities in Fushun western opencast mining for the ecological restoration of land after mine closure. In this study, two layers of soil samples were collected from four different areas in Fushun western opencast mining: coal gangue area (CGA), green mudstone area (GMA), oil shale area (OSA) and mixed area (MA). Then, the effects of different surrounding rock soil physicochemical properties on the microbial communities were explored using the High-throughput sequencing technique. A wide diversity of taxonomical groups were present in four soil cores, and many were correlated with soil physicochemical properties. The obvious differences in microbial communities between different areas showed the influence of different surrounding rock soil on the microbial communities were significant. Redundancy analysis and the network diagram confirmed that soil physicochemical properties pH (Pondus Hydrogenii)-AN (Available Nitrogen)-EC (Electronic Conductivity)-WC (Water Content)-TK (Total Nitrogen), Cd (Cadmium)-Ni (Nickel) had great influence on the microbial communities. Therefore, this study can provide scientific judgments for the different surrounding rock soil physicochemical properties in coal mining, microbial-mediated rock mineralization and biogeochemical cycles.

Appropriate human intervention stimulates the development of microbial communities and soil formation at a long-term weathered bauxite residue disposal area

Bauxite residue discharged to disposal areas, which could generate environmental pollution issues. Long-term natural restoration may improve the physicochemical properties of the residues, in turn supporting vegetation establishment, and effectively managing pollution. Nevertheless, the effects of short-term human intervention on soil formation in the weathered disposal areas are still relatively unknown. Thus, residue samples with different depths from different regions including no vegetation, sparse vegetation, complete vegetation coverage, and complete vegetation coverage following sewage sludge treatment were selected to analyze microbial community using Illumina high-throughput sequencing technology and evaluate soil formation process. Long-term weathering changed pH, the fraction of water-stable aggregates and nutrient concentrations, whilst promoting Proteobacteria, Chloroflexi, Acidobacteria and Planctomycete populations. Sewage sludge addition enhanced aggregate stability and significantly changed microbial community diversity. Sewage sludge application enriched the relative abundances of Proteobacteria and Bacteroidetes, whilst decreasing the relative abundance of Acidobacteria, which may be due to variation in environmental factors. Canonical correspondence analysis revealed that pH and EC were the main factors affecting microbial structure, followed by organic carbon content and aggregate stability. The results enhance the understanding of soil formation in bauxite residue and reveal the potential benefit of human intervention in ecological reconstruction at disposal areas.

Use of Piptatherum miliaceum to enable the establishment success of Salvia rosmarinus in Technosols developed from pyritic tailings

With this study we aimed to assess the effect of the prior development of Piptatherum miliaceum (Pm) in a Technosol on the establishment of Salvia rosmarinus (Sr) as a cash crop. An experimental pot was performed with two biochar (BCh) doses (BCh1 and BCh2) mixed with marble waste and pyritic tailings, with and without Pm. After 12 months of Pm growth, the pots with this species were divided into two sets: Sr alone and Sr + Pm. An agricultural soil (AGR) was used as an external control. The results showed that the growth of Sr led to similar shoot biomass to AGR. Sr + Pm reduced shoot biomass by 50%. Total soil organic and recalcitrant C, and total and recalcitrant N showed the highest values in vegetated pots, with no effect of the BCh rate. The decrease in the soil metals availability was related with increases in soil pH. BCh1Sr + Pm treatment showed a microbial community structure more similar to AGR, related to higher fungal and bacterial abundance, enzyme activities and soluble carbon. Thus, growing Sr + Pm seems a suitable strategy to improve soil properties, including microbial abundance, with low translocation of metals. Although the BCh rate did not affect plant growth or soil physicochemical properties, the lowest rate contributed to the growth of soil microorganisms better. The simultaneous growth of Sr + Pm reduced biomass production, and a source of available nutrients is also recommended. Further studies are needed to test this strategy in the field, and to ensure its suitability and a constant biomass production.

Profiling multiple heavy metal contamination and bacterial communities surrounding an iron tailing pond in Northwest China

Northwest China is abundant in iron ore reserves and has become one of the important iron ore mining bases in China. However, the contamination and microbial community structure of iron tailing ponds in Northwest China have not been extensively investigated. In the present study, we characterized the main physicochemical properties, the multiple heavy metal contamination, and the bacterial community structure of the soils surrounding an iron tailing pond in Linze County, Zhangye city, Gansu Province. The tailing-associated soils were barren, exhibiting alkaline pH and low organic matter (OM), total nitrogen (TN) and total potassium (TK) compared with the control areas. There was considerable multiple heavy metal pollution in the iron tailing pond, mainly including lead (Pb), manganese (Mn), arsenic (As), cadmium (Cd), zinc (Zn), iron (Fe) and copper (Cu). Among the 303 identified core operational taxonomic units (OTUs), Actinobacteria, Proteobacteria and Deinococcus-Thermus were predominant at the phylum level, and Blastococcus, Arthrobacter, Marmoricola, Kocuria, Truepera, and Sphingomonadaceae were prevalent at a finer taxonomic level. The bacterial richness and diversity of the tailing samples were significantly lower than those of the reference samples. RDA, VPA and Spearman correlation analyses showed that the soil pH, CEC, OM, TP, TK, Cd, Pb, Ni, Zn, As and Mn had significant effects on the bacterial community composition and distribution. This work profiles the basic features of the soil physicochemical properties, the multiple heavy metal contamination and the bacterial community structure in an iron tailing pond in Northwest China, thereby providing a foundation for the future ecological remediation of the iron tailing environment in the area.

Development of a Soil Quality Index for Soils under Different Agricultural Management Conditions in the Central Lowlands of Mexico: Physicochemical, Biological and Ecophysiological Indicators

The Bajío—Mexico’s central lowlands—is a region of economic importance because of its agricultural industry. Over time, agricultural practices have led to soil deterioration, loss of fertility, and abandonment. In this study, six agricultural soils were analyzed: AGQ, CTH, CTJ, JRM, CRC, and CYI, and used to develop a soil quality index (SQI) that includes the use of physicochemical, biological, and ecophysiological indicators to differentiate soil quality. Principal component analysis (PCA) was used, reducing the indicators from 46 to 4, which represents 80.4% of data variability. It was implemented the equation of additive weights using the variance of the principal components as a weight factor for the SQI. The developed SQI was according to the indicators WHC, SLT, N-NO3−, and qCO2, differentiating the quality of soils from the agricultural management in low quality (JRM < CYI < AGQ) and moderate quality (CTJ < CRC < CTH). The use of biological and ecophysiological indicators added to the PCA and the equation of additive weights allowed establishing an SQI with a minimum of indicators, sensitive to agricultural management, facilitating its interpretation and implementation for the Mexican Bajío region and soils in similar conditions around the world.

Keystone Microbiomes Revealed by 14 Years of Field Restoration of the Degraded Agricultural Soil Under Distinct Vegetation Scenarios

Agricultural intensification accelerates the degradation of cropland, and restoration has been managed by changing its vegetation. However, the keystone microbiome that drives the decomposition of plant-associated organic matter in the restoration is poorly understood. In this study, we established a 14-year field restoration experiment on a degraded cropland with four treatments: (1) bare land soil without biomass input (BL), (2) maize cropland (CL) without fertilization and biomass input, (3) natural grassland (GL), and (4) alfalfa cropland (AL) with biomass left in the fields. The activity of total soil microbiome was assessed by community-level physiological profiling (CLPP) with Biolog EcoPlates analysis, and keystone microbiome was identified as phylotypes showing statistically significant increase in the restored soils (GL and AL) relative to the degraded BL soil. The results showed that GL and AL treatments improved soil fertility as indicated by significant increase in soil organic carbon, total nitrogen, and available phosphorus when compared to BL treatment. The significant difference was not observed between CL and BL treatments except for pH and available phosphorus, indicating that the input and microbial decomposition of plant-associated organic matter were the key for restoration of soil fertility. Similar results were obtained for soil microbial activities of carbon utilization efficiency via CLPP analysis, and real-time quantitative polymerase chain reaction of 16S rRNA genes further revealed significantly higher abundance of total soil microbial community in GL and AL soils than in BL and CL. High-throughput sequencing of total 16S rRNA genes revealed the Bacteroidetes as the only keystone taxa at phylum level, and 106 and 120 genera were keystone phylotypes. Compared with BL and CL, the genera that increase significantly in GL and AL are called keystone genera of ecological restoration. The dominant keystone genera included Reyranella, Mesorhizobium, Devosia, Haliangium, Nocardioides, and Pseudonocardia. Significantly higher abundance of Bacillus genus in BL soil implied it might serve as an indicator of agricultural land degradation. Statistical analysis showed that soil organic carbon and pH were significantly correlated with the input of plant-associated organic matters and dynamic changes of keystone taxa. These results suggest that the vegetation of natural grass (GL) and alfalfa plant (AL) and subsequent decomposition of plant-associated materials could serve as effective strategies for restoration of the degraded cropland by stimulating the keystone microbiomes and improving their physiological metabolisms of carbon utilization efficiency.

Effects of afforestation with Pinus sylvestris var. mongolica plantations combined with enclosure management on soil microbial community

Grazing and litter removal can alter understory structure and composition after afforestation, posing a serious threat to sustainable forest development. Enclosure is considered to be an effective measure to restore degraded forest restoration. However, little is known about the dynamics of soil nutrients and microbial communities during the forest restoration process. In the present study, the effects of Arachis hypogaea (AH), Pinus sylvestris var. mongolica (PSM) and Pinus sylvestris var. mongolica with enclosure (PSME) on soil chemical properties and soil microbial communities were studied in Zhanggutai, Liaoning Province, China. The results showed that PSME could remarkably contribute to improve soil total C, total N and total P compared to PSM and AH. Additionally, PSM could clearly increase the soil bacterial community diversity and fungal Chao1 index and ACE index. Additionally, PSME could further increase soil Chao1 index and ACE index of soil bacteria. Soil total C, total N and available N were the main factors related to soil microbial diversity. Actinobacteria and Ascomycota were the predominant bacterial and fungal phyla, respectively. Specifically, PSME could increase the relative abundances of Actinobacteria, Gemmatimonadetes, Ascomycota and Mortierellomycota and decreased the relative abundances of Acidobacteria, Chloroflexi and Basidiomycota than PSM. PSM and PSME could clearly change soil microbial communities compared with AH and PSME could remarkably shift soil fungal communities than PSM. What's more, the soil microbial community structure were affected by multiple edaphic chemical parameters. It can be seen that afforestation combined with enclosed management potentially regulate microbial properties through shifting the soil properties. This study can provide new ideas for further understanding the impact of enclosure on PSM and provide theoretical support for the management of PSM.