Nutrients available in the soil regulate the changes of soil microbial community alongside degradation of alpine meadows in the northeast of the Qinghai-Tibet Plateau

Soil Microbial Adaptation and Biogeochemical Feedback in Degraded Alpine Meadows of the Qinghai-Tibetan Plateau

Alpine meadows on the Qinghai-Tibetan Plateau are experiencing rapid degradation due to climate change and anthropogenic disturbances, leading to severe ecological consequences. In this study, we investigated the response of soil microbial communities and their metabolic functions across a degradation gradient using metagenomic sequencing and comprehensive soil physicochemical analysis in the city of Lhasa, China. Results showed that soil pH increased with degradation, while most nutrients, including different forms of nitrogen, phosphorus, and potassium, declined. pH, ammonium nitrogen, and organic matter were identified as key factors driving degradation dynamics. Microbial community composition shifted markedly, with distinct biomarker taxa emerging at different degradation levels. Network analysis revealed a progressive loss of microbial connectivity, with Actinobacteria dominance increasing in heavily degraded soils, while cross-phylum interactions weakened. Functional analysis of biogeochemical cycling genes showed that carbon, nitrogen, and phosphorus cycling were all disrupted by degradation, but each exhibited unique response patterns. These findings will extend our understanding of microbial-mediated soil processes under degradation and provide a scientific foundation for ecosystem management, conservation, and targeted restoration strategies in alpine meadows.

Biodiversity in mountain soils above the treeline

Biological diversity in mountain ecosystems has been increasingly studied over the last decade. This is also the case for mountain soils, but no study to date has provided an overall synthesis of the current state of knowledge. Here we fill this gap with a first global analysis of published research on cryptogams, microorganisms, and fauna in mountain soils above the treeline, and a structured synthesis of current knowledge. Based on a corpus of almost 1400 publications and the expertise of 37 mountain soil scientists worldwide, we summarise what is known about the diversity and distribution patterns of each of these organismal groups, specifically along elevation, and provide an overview of available knowledge on the drivers explaining these patterns and their changes. In particular, we document an elevation-dependent decrease in faunal diversity above the treeline, while for cryptogams there is an initial increase above the treeline, followed by a decrease towards the nival belt. Thus, our data confirm the key role that elevation plays in shaping the biodiversity and distribution of these organisms in mountain soils. The response of prokaryote diversity to elevation, in turn, was more diverse, whereas fungal diversity appeared to be substantially influenced by plants. As far as available, we describe key characteristics, adaptations, and functions of mountain soil species, and despite a lack of ecological information about the uncultivated majority of prokaryotes, fungi, and protists, we illustrate the remarkable and unique diversity of life forms and life histories encountered in alpine mountain soils. By applying rule- as well as pattern-based literature-mining approaches and semi-quantitative analyses, we identified hotspots of mountain soil research in the European Alps and Central Asia and revealed significant gaps in taxonomic coverage, particularly among biocrusts, soil protists, and soil fauna. We further report thematic priorities for research on mountain soil biodiversity above the treeline and identify unanswered research questions. Building upon the outcomes of this synthesis, we conclude with a set of research opportunities for mountain soil biodiversity research worldwide. Soils in mountain ecosystems above the treeline fulfil critical functions and make essential contributions to life on land. Accordingly, seizing these opportunities and closing knowledge gaps appears crucial to enable science-based decision making in mountain regions and formulating laws and guidelines in support of mountain soil biodiversity conservation targets.

Differentiation and Interconnection of the Bacterial Community Associated with Silene nigrescens Along the Soil-To-Plant Continuum in the Sub-Nival Belt of the Qiangyong Glacier

Plant microbiomes provide significant fitness advantages to their plant hosts, especially in the sub-nival belt. Studies to date have primarily focused on belowground communities in this region. Here, we utilized high-throughput DNA sequencing to quantify bacterial communities in the rhizosphere soil as well as in the root and leaf endosphere compartments of Silene nigrescens to uncover the differentiation and interconnections of these bacterial communities along the soil-to-plant continuum. Our findings reveal that the bacterial communities exhibit notable variation across different plant compartment niches: the rhizosphere soil, root endosphere, and leaf endosphere. There was a progressive decline in diversity, network complexity, network modularity, and niche breadth from the rhizosphere soil to the root endosphere, and further to the leaf endosphere. Conversely, both the host plant selection effect and the stability of these communities showed an increasing trend. Total nitrogen and total potassium emerged as crucial factors accounting for the observed differences in diversity and composition, respectively. Additionally, 3.6% of the total amplicon sequence variants (ASVs) were shared across the rhizosphere soil, root endosphere, and leaf endosphere. Source-tracking analysis further revealed bacterial community migration among these compartments. The genera Pseudomonas, IMCC26256, Mycobacterium, Phyllobacterium, and Sphingomonas constituted the core of the bacterial microbiome. These taxa are shared across all three compartment niches and function as key connector species. Notably, Pseudomonas stands out as the predominant taxon among these bacteria, with nitrogen being the most significant factor influencing its relative abundance. These findings deepen our understanding of the assembly principles and ecological dynamics of the plant microbiome in the sub-nival belt, offering an integrated framework for its study.

Effects of organic fertilizer replacement on the microbial community structure in the rhizosphere soil of soybeans in albic soil

With the intensification of agricultural production, the significance of soil biological health and microbial network structure has grown increasingly critical. Replacing chemical fertilizers with organic ones has garnered widespread attention as an effective strategy for enhancing soil quality. This study explored the mechanisms of how partial substitution of chemical fertilizers with organic ones affects the microbial community structure in soybean rhizosphere soil of Albic soil. Potting trials and high-throughput sequencing analysis revealed that, compared with conventional fertilization, the soil ACE and Chao1 diversity indices in the treatment with 75% organic fertilizer substitution significantly increased by 19.49% and 21.02%, respectively. The soil pH, organic matter, total phosphorus (TP), effective phosphorus (AP), and hydrolyzed nitrogen (HN) levels exhibited a marked increase of 4.33%, 18.67%, 20.90%, 23.35%, and 32.97% with high levels of organic fertiliser replacement, as compared to NPK. Meanwhile, the dominant phyla of Proteobacteria and Basidiomycota significantly increased by 36.11% and 286.79%, respectively. LEfSe analysis revealed that the fungal community was more sensitive to the fertilizer application strategy than the bacterial communities. Furthermore, redundancy analysis (RDA) demonstrated that soil pH and organic matter were primary environmental factors influencing microbial community structure. The co-occurrence network analysis showed that the partial utilization of organic fertilizers could strengthen the interrelationships among species, leading to a more complex and dense bacterial network. The findings can offer a significant scientific foundation for refining the fertilization strategies for Albic soil and facilitating the shift from conventional to sustainable agricultural practices.

Compositional shifts and co-occurrence patterns of topsoil bacteria and micro-eukaryotes across a permafrost thaw gradient in alpine meadows of the Qilian Mountains, China

Soil microorganisms play a pivotal role in the biogeochemical cycles of alpine meadow ecosystems, especially in the context of permafrost thaw. However, the mechanisms driving microbial community responses to environmental changes, such as variations in active layer thickness (ALT) of permafrost, remain poorly understood. This study utilized next-generation sequencing to explore the composition and co-occurrence patterns of soil microbial communities, focusing on bacteria and micro-eukaryotes along a permafrost thaw gradient. The results showed a decline in bacterial alpha diversity with increasing permafrost thaw, whereas micro-eukaryotic diversity exhibited an opposite trend. Although changes in microbial community composition were observed in permafrost and seasonally frozen soils, these shifts were not statistically significant. Bacterial communities exhibited a greater differentiation between frozen and seasonally frozen soils, a pattern not mirrored in eukaryotic communities. Linear discriminant analysis effect size analysis revealed a higher number of potential biomarkers in bacterial communities compared with micro-eukaryotes. Bacterial co-occurrence networks were more complex, with more nodes, edges, and positive linkages than those of micro-eukaryotes. Key factors such as soil texture, ALT, and bulk density significantly influenced bacterial community structures, particularly affecting the relative abundances of the Acidobacteria, Proteobacteria, and Actinobacteria phyla. In contrast, fungal communities (e.g., Nucletmycea, Rhizaria, Chloroplastida, and Discosea groups) were more affected by electrical conductivity, vegetation coverage, and ALT. This study highlights the distinct responses of soil bacteria and micro-eukaryotes to permafrost thaw, offering insights into microbial community stability under global climate change.IMPORTANCEThis study sheds light on how permafrost thaw affects microbial life in the soil, with broader implications for understanding climate change impacts. As permafrost degrades, it alters the types and numbers of microbes in the soil. These microbes play essential roles in environmental processes, such as nutrient cycling and greenhouse gas emissions. By observing shifts from bacteria-dominated to fungi-dominated communities as permafrost thaws, the study highlights potential changes in these processes. Importantly, this research suggests that the stability of microbial networks decreases with permafrost degradation, potentially disrupting the delicate balance of these ecosystems. The findings not only deepen our understanding of microbial responses to changing climates but also support the development of strategies to monitor and potentially mitigate the effects of climate change on fragile high-altitude ecosystems.

Nutrient Availability Shapes the Resistance of Soil Bacterial Community and Functions to Disturbances in Desert Ecosystem

Climate change has exposed desert ecosystems to frequent extreme disturbances, including wet-dry cycles and freeze-thaw events, which accelerate desertification on a global scale. The limited nutrient availability characteristic of these ecosystems may constrain microbial survival and growth, making them more vulnerable to environmental perturbations and stressors. However, how nutrient availability modulates the stability of soil ecological communities and functions in desert ecosystems remains poorly understood. In this study, we examined how nutrient addition, applied either before or after disturbances, affects the resistance of bacterial communities and multifunctionality to drought and freeze events in desert ecosystems. Our findings revealed that freeze-thaw events, rather than drought, significantly reduced bacterial diversity, with all disturbances altering the community structure. Pre-disturbance nutrient addition notably improved the resistance of soil bacterial diversity and community composition to disturbances, which played a critical role in maintaining multifunctionality in desert ecosystems. This enhanced bacterial resistance was strongly associated with increased bacterial network complexity and the enrichment of disturbance-tolerant taxa. Our results highlight the pivotal role of nutrient availability in stabilising soil bacterial communities and multifunctionality under extreme climatic conditions in desert ecosystems. These findings offer valuable insights and practical strategies for the ecological protection and management of desertification.

Aboveground-belowground linkages across vegetation degradation gradients differ among native eucalypt communities

Native vegetation degradation impacts soil communities and their functions. However, these impacts are often studied by comparing soil biotic attributes across qualitatively defined, discrete degradation levels within a single plant community at a specific location. Direct quantification of the relationships between vegetation and soil attributes across continuous degradation gradients and at larger scales is rare but holds greater potential to reveal robust patterns in aboveground-belowground linkages that may apply across different plant communities. We investigated how native vegetation attributes relate to soil communities and their functions across a degradation gradient within three native temperate eucalypt woodland and forest communities that differed in soil nutrient availabilities. Across remnant patches of native vegetation in the Sydney Basin bioregion, we established plots representing different levels of decline in their vegetation quality (i.e., increased exotics and canopy changes) compared to relevant reference communities. In those plots, we assessed soil community groups (microbes and fauna), carbon (C) and nutrient cycling (litter decomposition, enzyme activity, and phosphate and nitrate accumulation rates), soil pH, texture and vegetation attributes (composition, structure, and function). Our unique study design revealed that the relationships between vegetation degradation and soil biota across the food web (i.e., AM fungi, Fungi:bacteria ratio, Gram-positive bacteria, total nematodes) were highly dependent on the plant community. However, the degradation impacts on soil functions (i.e., total enzyme activity, and phosphate availability) were mostly consistent, suggesting their potential as belowground indicators of ecosystem degradation, with a notable positive association observed in phosphate availability rates. Additionally, the effects of vegetation degradation on soil biota and their functions appeared stronger in the nutrient-poor plant communities, suggesting greater vulnerability of their belowground components. Our findings call for caution when generalizing belowground responses to degradation and for further research on how nutrient availability mediates the impacts of degradation on aboveground-belowground linkages.

Effects of rocky desertification on soil bacterial community in alpine grasslands of the Qinghai-Tibet Plateau

The makeup of soil microbial communities may serve as a crucial predictor of the alpine grassland ecosystem. Climate change and human disturbance have resulted in intensified ecosystem degradation, such as grassland rocky desertification, which may modify the structures and composition of the microorganisms. However, little is known about the effects of rocky desertification on soil microbial communities of soil. Here, we investigated five different layers of rocky desertification grassland in the Qinghai-Tibet Plateau, including nil rock desertification (NRD); potential rocky desertification (PRD); light rocky desertification (LRD); moderate rocky desertification (MRD); and severe rocky desertification (SRD), we compared soil bacterial community with soil physiochemical properties in different rocky desertification conditions. The result showed that rocky desertification significantly altered the physiochemical properties of the soil but did not significantly affect the bacterial community microbial abundance and diversity. At the same time as rocky desertification increased, soil organic carbon (SOC), total nitrogen (TN), alkali hydrolyzable nitrogen (AN), available phosphorus (AP), and available potassium (AK) decreased significantly, while soil pH, total phosphorus (TP); and total potassium (TK) increased. Redundancy analysis revealed that pH, AK, TP, and SOC are key factors influencing soil bacterial communities. Our finding provides basic information and scientific reference for the restoration of the rocky desertification of alpine grasslands.

Urbanized lands degrade surrounding grasslands by deteriorating the interactions between plants and soil microbiome

To mitigate overgrazing on grasslands, towns were constructed in some pastoral regions of China to relocate pastoralists. Nevertheless, whether and how the urbanized lands impact the surrounding grassland ecosystem remains unclear. We assessed the impacts of urbanized lands on the plant and soil interactions within the surrounding grasslands in order to ensure an eco-sustainable pastoralist relocation. The town with 1 km radius was selected as urbanization sample and a grassland with 1 km radius was selected as nature grassland sample. Plants and soil were investigated in nature grassland (NG), and areas 1 km (T-1 km), 2 km (T-2 km), and 3 km (T-3 km) from the center of the town. In T-1 km and T-2 km, compared to the NG, plant diversity, the abundance of dominant plant species, the abundance of soil wood saprotroph fungi, soil water content (SWC), and total organic carbon (TOC) decreased, while soil plant pathogen fungi, soil pH, and total phosphatase (TP) increased. Conversely, no such changes were observed in T-3 km. The results of Mantel test and Partial least squares path model suggest that the decrease in soil TOC and SWC, along with the increase in pH and TP in T-1 km and T-2 km, lead to a decline in wood saprotroph fungi and an increase in plant pathogen fungi, ultimately resulting in reductions in plant diversity and the abundance of dominant plant species. These results indicate that towns in pastoral areas can lead to surrounding grassland degradation by deteriorating the plant-soil interactions.

Characteristics of the Bacterial Community in Alpine Meadows in Response to Altitude and Aspect in the Qilian Mountains, Northwest China

As one of the most sensitive and fragile alpine ecosystems in the Qilian Mountains, the alpine meadow holds significant scientific importance in understanding the changes in the characteristics of soil bacterial community in response to altitude and aspect variations. In our study, we analyzed the composition, diversity, and function of soil bacterial communities in alpine meadows at different altitudes and aspects and their relationship with environmental factors. Our results indicate that altitude and aspect orientation significantly influences the diversity index and composition of soil bacterial communities. Specifically, the Shannon and Chao1 indices of soil bacteria initially increased and then decreased with increasing altitude, with the Shannon index being lower in shady aspects compared to sunny aspects, and the Chao1 index being lower in sunny aspects above an altitude of 3400 m compared to shady aspects at the exact altitudes. Using Linear Discriminant Analysis Effect Size analysis, we identified 77 bacterial species in the research area, with key ecological functions primarily associated with nitrification, aerobic ammonia oxidation, and chitinolysis. Furthermore, we found that soil water content and Urease were the main factors influencing bacterial community composition. Our findings underscore the significant impact of altitude orientation on bacterial communities in alpine grasslands, emphasizing the importance of considering bacterial differences in evaluating alpine grassland health.

Vegetation degradation and its progressive impact on soil nitrogen mineralization in the Qinghai-Tibet Plateau's alpine wetlands: Insights from a three-year study

The soil nitrogen (N) cycle in the alpine wetland of the Qinghai-Tibet Plateau (QTP) has been strongly affected by vegetation degradation caused by climate change and human activities, subsequently impacting ecosystem functions. However, previous studies have rarely addressed how varying degrees of vegetation degradation affect soil net nitrogen mineralization rates and their temporal dynamics in these sensitive ecosystems. Therefore, we conducted a three-year field-based soil core in situ incubation mineralization experiment on the northeastern margin of the Tibetan Plateau from 2019 to 2021 to assess the variations in soil net ammonification, nitrification, and mineralization rates during the growing season (June to October). The main aim was to determine the dynamic effects of different degrees of vegetation degradation (non-degraded, lightly degraded, moderately degraded, and severely degraded) on soil net nitrogen transformation processes, as well as the impact of seasonal fluctuations in soil temperature and moisture on net nitrogen mineralization. Results indicated that vegetation degradation significantly reduced the net ammonification rate by 22.09%-97.10%, significantly increased the net nitrification rate by 45.38%, and significantly decreased the net mineralization rate by 9.49%-16.25%. Redundancy analysis (RDA) and random forest models revealed the supportive role of soil water content in the soil nitrogen transformation processes, particularly in promoting nitrification, while soil temperature was identified as a positive regulator of N cycling enzyme activity, indirectly affecting net nitrogen mineralization rates.

Phosphorus pool distributions and adsorption-desorption characteristics of soil aggregates in cut slopes of a permafrost zone in the Qinghai-Tibetan Plateau

Soil phosphorus (P) has attracted considerable attention from researchers because of its role in the restoration and stabilization processes of cut slopes in permafrost regions. However, the soil P pool distributions and adsorption-desorption characteristics in alpine cut slopes remain unclear. In this context, we examined in this study the P pools in the aggregates of surface cut soil slopes (0-10 cm) in areas with three permafrost types, including perennially frozen soil (PF), seasonally frozen ground (SFG), and non-frozen soil (NFS) in the Qinghai-Tibet Plateau, China. In addition, we assessed the P adsorption-desorption characteristics and their correlations with the P pools. The results showed the significant effects of the permafrost types on the contents of total P (TP), available P (AP), labile P (LP), moderately labile P (MLP) and stable P (SP). The inorganic P (IP) contents were higher than those of organic P (OP) in the cut soil slopes of the three permafrost types. In addition, H2O-Pi and NaHCO3-Pi accounted for small proportions of IP, while NaHCO3-Po accounted for the smallest proportion of OP. On the other hand, the SP contents in the soil aggregates were generally higher than those of MLP and LP. In fact, the LP contents in the PF, SFG, and NFS were 72.55, 44.68, and 49.42 mg/kg, respectively. The AP contents in the cut soil slopes of the three permafrost types were significantly correlated with the MLP and LP contents. Moreover, the P adsorption-desorption characteristics of the SFG and NFS were closely related to AP and MLP. Compared with the PF and NFS, the SFG exhibited low and high P adsorption and desorption capacities, respectively. The findings of this study provided an important theoretical basis for the restoration of cut slopes in alpine permafrost regions.

Co-application of sheep manure and commercial organic fertilizer enhances plant productivity and soil quality in alpine mining areas

Background and aims

The addition of organic fertilizers and sheep slat manure have important effects on soil quality in alpine mining areas, but how they affect soil physicochemical properties and microorganisms is not yet known.

Methods

The current study employed field-controlled experiments and high-throughput sequencing technology to investigate differences in soil physicochemical properties, microbial community structures, and diversity under four treatments: no fertilization (CK), 100% sheep manure (SM), a combination of 50% sheep manure and 50% commercial organic fertilizer (MF), and 100% commercial organic fertilizer (OF).

Results

Aboveground biomass increased by 191.93, 253.22, and 133.32% under SM, MF and OF treatments, respectively, when compared to CK treatment. The MF treatment resulted in significantly higher soil total nitrogen, total phosphorus, organic matter, and available nitrogen content compared to other treatments. Soil total nitrogen content, total phosphorus content, organic matter, available nitrogen content and available phosphorus content were 211, 120, 380, 557, and 271% higher, respectively, under the MF treatment than the CK treatment. Different nutrient additions significantly influenced soil microbial community composition. The SM and MF treatments notably increased soil bacterial and fungal community Operational Taxonomic Units (OTUs) indices and Chao 1 indices, while nutrient addition had no meaningful effect on the Simpson indices for microbial communities. There was a highly significant positive correlation between aboveground biomass and observed soil nutrient content.

Conclusion

The combined application of sheep manure and commercial organic fertilizer is more conducive to improving soil quality and enhancing plant productivity in alpine mining areas.

Critical review on unveiling the toxic and recalcitrant effects of microplastics in aquatic ecosystems and their degradation by microbes

Production of synthetic plastic obtained from fossil fuels are considered as a constantly growing problem and lack in the management of plastic waste has led to severe microplastic pollution in the aquatic ecosystem. Plastic particles less than 5mm are termed as microplastics (MPs), these are pervasive in water and soil, it can also withstand longer period of time with high durability. It can be broken down into smaller particles and can be adsorbed by various life-forms. Most marine organisms tend to consume plastic debris that can be accumulated easily into the vertebrates, invertebrates and planktonic entities. Often these plastic particles surpass the food chain, resulting in the damage of various organs and inhibiting the uptake of food due to the accumulation of microplastics. In this review, the physical and chemical properties of microplastics, as well as their effects on the environment and toxicity of their chemical constituents are discussed. In addition, the paper also sheds light on the potential of microorganisms such as bacteria, fungi, and algae which play a pivotal role in the process of microplastics degradation. The mechanism of microbial degradation, the factors that affect degradation, and the current advancements in genetic and metabolic engineering of microbes to promote degradation are also summarized. The paper also provides information on the bacterial, algal and fungal degradation mechanism including the possible enzymes involved in microplastic degradation. It also investigates the difficulties, limitations, and potential developments that may occur in the field of microbial microplastic degradation.

Response of soil fungal communities and their co-occurrence patterns to grazing exclusion in different grassland types

Overgrazing and climate change are the main causes of grassland degradation, and grazing exclusion is one of the most common measures for restoring degraded grasslands worldwide. Soil fungi can respond rapidly to environmental stresses, but the response of different grassland types to grazing control has not been uniformly determined. Three grassland types (temperate desert, temperate steppe grassland, and mountain meadow) that were closed for grazing exclusion for 9 years were used to study the effects of grazing exclusion on soil nutrients as well as fungal community structure in the three grassland types. The results showed that (1) in the 0-5 cm soil layer, grazing exclusion significantly affected the soil water content of the three grassland types (P < 0.05), and the pH, total phosphorous (TP), and nitrogen-to-phosphorous ratio (N/P) changed significantly in all three grassland types (P < 0.05). Significant changes in soil nutrients in the 5-10 cm soil layer after grazing exclusion occurred in the mountain meadow grasslands (P < 0.05), but not in the temperate desert and temperate steppe grasslands. (2) For the different grassland types, Archaeorhizomycetes was most abundant in the montane meadows, and Dothideomycetes was most abundant in the temperate desert grasslands and was significantly more abundant than in the remaining two grassland types (P < 0.05). Grazing exclusion led to insignificant changes in the dominant soil fungal phyla and α diversity, but significant changes in the β diversity of soil fungi (P < 0.05). (3) Grazing exclusion areas have higher mean clustering coefficients and modularity classes than grazing areas. In particular, the highest modularity class is found in temperate steppe grassland grazing exclusion areas. (4) We also found that pH is the main driving factor affecting soil fungal community structure, that plant coverage is a key environmental factor affecting soil community composition, and that grazing exclusion indirectly affects soil fungal communities by affecting soil nutrients. The above results suggest that grazing exclusion may regulate microbial ecological processes by changing the soil fungal β diversity in the three grassland types. Grazing exclusion is not conducive to the recovery of soil nutrients in areas with mountain grassland but improves the stability of soil fungi in temperate steppe grassland. Therefore, the type of degraded grassland should be considered when formulating suitable restoration programmes when grazing exclusion measures are implemented. The results of this study provide new insights into the response of soil fungal communities to grazing exclusion, providing a theoretical basis for the management of degraded grassland restoration.

Changes in soil bacterial community characteristics in patches of different vegetation types under different stages of restoration in the desert of northern China

In desert areas, the process of mobile sandy land changing to semi-fixed sandy land and eventually to fixed sandy land after undergoing vegetation restoration is inevitable. The presence of shrub patches and herb patches is common in this restoration process. No relevant studies have reported the soil bacterial community characteristics of different vegetation-type patches (shrub patches and herb patches) under different stages of restoration. Therefore, we utilized long-established experimental plots to collect soil from 0-20 cm soil layer under shrub patches (dominated by Salix psammophila) and herb patches under different stages of restoration (i.e., mobile sand land, semi-fixed sand land, and fixed sand land), by determining soil physicochemical properties, enzyme activities, and soil bacterial communities. Our results found that soil bacterial α-diversity under different restoration stages showed higher shrub patches than herb patches. The dominant bacterial communities (phyla) in shrub patches and herb patches at different recovery stages were Actinobacteria, Proteobacteria, and Bacteroidota. When the mobile sandy land returned to fixed sandy land, the relative abundance of Actinobacteria and Bacteroidota gradually decreased under shrub patches and herb patches, while the relative abundance of Proteobacteria increased significantly. In addition, herb patches significantly increased the relative abundance of bacteria (genus) relative to shrub patches at different stages of recovery. Soil nutrients, soil fine particles, and soil enzyme activities were significantly higher under shrub patches than under herb patches when fixed sandy land due to differences in life form and architecture between shrub patches and herb patches. Based on this, soil bacterial community composition and diversity under shrub patches were driven by more soil properties during the restoration of sandy land. This study complements the dynamic recovery processes and driving mechanisms of soil bacterial community structure under different vegetation patches in sandy areas, especially in the context of global climate change.

Artemisia smithii patches form fertile islands and lead to heterogeneity of soil bacteria and fungi within and around the patches in alpine meadows of the Qinghai-Tibetan Plateau

Herbivore-avoided plant patches are one of the initial characteristics of natural grassland degradation. These vegetation patches can intensify the spatial heterogeneity of soil nutrients within these grasslands. However, the effects of non-edible plant patches patches on the spatial heterogeneity of microorganisms have not been sufficiently studied in alpine meadows of the Qinghai-Tibetan Plateau, especially patches formed by herbaceous plants. To answer this question, soil nutrients, plant assembly, and microbial communities were measured inside, around, and outside of Artemisia smithii patches. These were 0 m (within the patch), 0-1 m (one meter from the edge of the patch), 1-2 m (two meters from the edge of the patch), 2-3 m (three meters from the edge of the patch), and >30 m (non-patch grassland more than thirty meters from the edge of the patch). Our results showed that A. smithii patches accumulated more aboveground biomass (AGB) within the patches (0 m), and formed fertile islands with the soil around the patches. Additionally, A. smithii patches increased soil bacterial diversity within (0 m) and around (0-1 m) the patches by primarily enriching copiotrophic bacteria (Actinobacteria), while the diversity of fungal communities increased mainly in the 0-1 m area but not within the patches. Bacterial community diversity was driven by pH, urease, nitrate nitrogen (NO3 --N), and microbial biomass carbon (MBC). The contents of soil water (SWC), soil organic matter (SOM), urease, NO3 --N, and MBC were the main factors influencing the diversity of the fungal community. This study elucidates the vegetation, nutrients, and microbial heterogeneity and their interrelationships, which are observed in fertile islands of herbivore-avoided plant patches in alpine meadows, and provides further insights into the spatial pattern of nutrients in patchy degraded grasslands.

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.

Impact of grassland degradation on soil multifunctionality: Linking to protozoan network complexity and stability

Soil protozoa, as predators of microbial communities, profoundly influence multifunctionality of soils. Understanding the relationship between soil protozoa and soil multifunctionality (SMF) is crucial to unraveling the driving mechanisms of SMF. However, this relationship remains unclear, particularly in grassland ecosystems that are experiencing degradation. By employing 18S rRNA gene sequencing and network analysis, we examined the diversity, composition, and network patterns of the soil protozoan community along a well-characterized gradient of grassland degradation at four alpine sites, including two alpine meadows (Cuona and Jiuzhi) and two alpine steppes (Shuanghu and Gonghe) on the Qinghai-Tibetan Plateau. Our findings showed that grassland degradation decreased SMF for 1-2 times in all four sites but increased soil protozoan diversity (Shannon index) for 13.82-298.01 % in alpine steppes. Grassland degradation-induced changes in soil protozoan composition, particularly to the Intramacronucleata with a large body size, were consistently observed across all four sites. The enhancing network complexity (average degree), stability (robustness), and cooperative relationships (positive correlation) are the responses of protozoa to grassland degradation. Further analyses revealed that the increased network complexity and stability led to a decrease in SMF by affecting microbial biomass. Overall, protozoa increase their diversity and strengthen their cooperative relationships to resist grassland degradation, and emphasize the critical role of protozoan network complexity and stability in regulating SMF. Therefore, not only protozoan diversity and composition but also their interactions should be considered in evaluating SMF responses to grassland degradation, which has important implications for predicting changes in soil function under future scenarios of anthropogenic change.

Soil microbial diversity and composition response to degradation of the alpine meadow in the southeastern Qinghai-Tibet Plateau

With the interaction between global climate change and unreasonable human utilization, the alpine meadows on the Qinghai-Tibet Plateau have suffered various weathering degrees. Uncovering the degradation mechanism and restoration strategies can be facilitated by gaining insights into the diversity of soil microflora during meadow degradation. Therefore, we used Illumina sequencing technology to investigate the patterns of soil microbial diversity, microbial community composition, and the driving factors of microbial change in all non-degraded (ND), lightly degraded (LD), moderately degraded (MD), and severely degraded (SD) alpine meadows in the southeastern Qinghai-Tibet Plateau. Our results pointed out that with the intensification of degradation, vegetation characteristics were significantly reduced, and soil parameters significantly varied among all degraded meadows. The contents of soil organic carbon (SOC), total nitrogen (TN), available phosphorus (AN), and total phosphorous (AK) in soils decreased with the increase of degradation. The dominant bacterial phyla were the same regardless of the meadow degradation level with Actinobacteria (37.67%) and Proteobacteria (20.62%) having the highest relative abundance. Meanwhile, the dominant fungi were Ascomycota (49.9%). Based on the linear discriminant analysis (LDA) and effect size (LEfSe) method, 38 bacterial and 49 fungal species were found to be affected in the degraded alpine meadow, most of which belonged to Actinobacteria and Ascomycota, respectively. Mantel test analysis illustrated that the bacterial community was mainly significantly dependent on below-ground biomass, pH, soil organic carbon, and total nitrogen, while the fungal community was significantly dependent on soil organic carbon, total nitrogen, available nitrogen, and available potassium. These results suggest that the degeneration of alpine meadows contributes to the variability of the diversity and composition of microflora on the Tibetan plateau. Yet this effect is mainly dependent on soil factors.

Soil fungal communities varied across aspects of restored grassland in former mining areas of the Qinghai-Tibet Plateau

To determine whether different aspects lead to a heterogeneous distribution of soil fungi, we investigated artificially established alpine grasslands in the Muli mining area in the Qinghai-Tibet Plateau. Employing high-throughput sequencing techniques, we analyzed the composition, diversity, and function of soil fungal communities across various aspects (flat, East-facing, South-facing, West-facing, North-facing). We also examined their relationships with environmental factors. Soil fungal communities of restored alpine grasslands differed significantly across aspects in terms of the dominant phyla, classes and species level. Compared with No aspect, the Shannon index of fungi respectively decreased by 2.99%, 19.32%, 19.37% and 10.56% for East aspect, South aspect, West aspect and North aspect, respectively, and the Chao1 index of fungi respectively decreased by-2.44%, 35.50%, 42.15% and 3.21%, respectively. A total of 22 different types of fungi were identified in the study area. Predictive analysis, based on PICRUSt2, indicated that the primary functions of the fungal communities across different aspects were aerobic respiration I (cytochrome c) and aerobic respiration II (cytochrome c). Among the environmental variables, total phosphorus (P) and total nitrogen (N) were the principal factors influencing the fungal community composition.In conclusion, aspect plays a significant role in shaping the composition of fungal communities and also affects their overall diversity.

Uneven distributions of unique species promoting N niche complementarity explain the stability of degraded alpine meadow

Alpine meadow degradation, usually involving decreased soil nitrogen (N) and patchy landscapes, is a challenge for natural restoration. However, the mechanism underlying plant species coexistence under degradation is unclear. In this study, we evaluated plant N niche complementarity in degraded alpine meadows on the Qinghai-Tibet Plateau using a 15N-labeling (15NO3-, 15NH4+, and 15N-glycine) experiment. At the community level, the concentration of 15NO3- in the degraded alpine meadow was 1.5 times higher than that in the undegraded alpine meadow; both alpine meadows had a significant preference for NO3- (60.72 % and 66.84 % for the degraded and undegraded alpine meadows, respectively), and the degree of glycine preference was significantly higher in the degraded alpine meadow (30.77 %) relative to the undegraded alpine meadow (21.85 %). At the species level, dominant species in both alpine meadows consistently preferred NO3-; the generalist species that can be found in both meadows and unique species of the two alpine meadows generally showed NO3- preferences, while the other plant species that were unevenly distributed in the degraded alpine meadow tended to show increased utilization of glycine, which could reduce N competition. We observed that differentiation among N sources and the uneven distribution of unique species may explain the stability of degraded alpine meadows. Our results suggested that uneven distributions of plants could have strong impacts on community stability and highlighted the importance of considering fine-scale analysis in studies of niche theory. This study has important implications for the restoration of degraded alpine meadows.

Patterns of bacterial communities in the rhizosphere and rhizoplane of alpine wet meadows

Wet meadows, a type of wetland, are vulnerable to climate change and human activity, impacting soil properties and microorganisms that are crucial to the ecosystem processes of wet meadows. To decipher the ecological mechanisms and processes involved in wet meadows, it is necessary to examine the bacterial communities associated with plant roots. To gain valuable insight into the microbial dynamics of alpine wet meadows, we used Illumina MiSeq sequencing to investigate how environmental factors shape the bacterial communities thriving in the rhizosphere and rhizoplane of three plant species: Cremanthodium ellisii, Caltha scaposa, and Cremanthodium lineare. The most abundant bacterial phyla in rhizosphere and rhizoplane were Proteobacteria > Firmicutes > Actinobacteria, while Macrococcus, Lactococcus, and Exiguobacterium were the most abundant bacterial genera between rhizosphere and rhizoplane. The mantel test, network, and structure equation models revealed that bacterial communities of rhizosphere were shaped by total nitrogen (TN), soil water content (SWC), soil organic carbon (SOC), microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), pH, however, rhizoplane bacterial communities exhibited varying results. The bacterial communities exhibited significant heterogeneity, with stochastic process predominating in both the rhizosphere and rhizoplane. PICRUSt2 and FAPROTAX analysis revealed substantial differences in key biogeochemical cycles and metabolic functional predictions. It was concluded that root compartments significantly influenced the bacterial communities, although plant species and elevation asserted varying effects. This study portrays how physicochemical properties, plant species, and elevations can shift the overall structure and functional repertoire of bacterial communities in alpine wet meadows.

Assessing the win-win situation of forage production and soil organic carbon through a short-term active restoration strategy in alpine grasslands

Introduction

Grassland degradation has seriously affected the ecological environment and human livelihood. To abate these, implementing effective management strategies to restore and improve the service functions and productivity of degraded grasslands is crucial.

Methods

To evaluate the influences of restoration measures combined with different grazing intensities on short-term (1 year) grassland restoration, the changes in soil physicochemical properties, as well as plant traits under restoration measures of different grazing intensities, reseeding, and fertilization, were analyzed.

Results

Soil organic carbon (SOC) increased to varying degrees, whereas available nutrients decreased under all combined restoration measures. Reseeding, alone and in combination with fertilization, substantially increased SOC, improved grassland vegetation status, and enhanced grassland productivity. The aboveground biomass of Gramineae and the total aboveground biomass increased under the combined restoration measures of transferring livestock out of the pasture 45 days in advance, reseeding, and fertilization (T4). Redundancy analysis revealed a strong correlation between grassland vegetation characteristics, SOC, and available potassium. Considering soil and vegetation factors, the short-term results suggested that the combination measures in T4had the most marked positive impact on grassland restoration.

Discussion

These findings offer valuable theoretical insights for the ecological restoration of degraded grasslands in alpine regions.

Chemical fertilizer reduction combined with organic fertilizer affects the soil microbial community and diversity and yield of cotton

Introduction

The soil microbial community plays an important role in modulating cotton soil fertility. However, the effects of chemical fertilizer combined with organic fertilizer on soil chemical properties, microbial community structure, and crop yield and quality in arid areas are still unclear. This study aimed to explore the effects of different organic fertilizers on soil microbial community structure and diversity and cotton growth and yield.

Methods

High-throughput sequencing was used to study the soil bacteria and fungi in different growth stages of cotton. The field fertilization experiment had five treatments.

Results

The results indicated that the treatments of chemical fertilizer reduction combined with organic fertilizer significantly increased soil available nitrogen and phosphorus in cotton field. There were significant differences in the abundance of the bacterial and fungal communities in the dominant phyla among the treatments. At the phyla level, there were not significantly different in the diversity of bacteria and fungi among treatments. There were significant differences in the composition and diversity of bacterial and fungal communities during the entire cotton growth period (p = 0.001). The rhizosphere bacterial and fungal community structure was significantly affected by soil TK, NH4+, AK, TP, AN, and NO3-. The different fertilization treatments strongly influenced the modular structure of the soil bacterial and fungal community co-occurrence network. A reduction in chemical fertilizer combined with organic fertilizer significantly improved cotton stem diameter and seed yield, and the effect of the biological organic fertilizer on plant growth and yield formation was greater than that of ordinary organic fertilizer.

Discussion

This study provide a scientific and technical basis for the establishment of environmentally friendly green fertilization technology for cotton in arid areas and the promotion of sustainable development of cotton industry.

Exploitation alters microbial community and its co-occurrence patterns in ionic rare earth mining sites

The exploitation of ion-adsorption rare earth elements (REEs) deposits results in serious ecological and environmental problems, which has attracted much attention. However, the influences of exploitation on the prokaryotic communities and their complex interactions remain poorly understood. In the present study, bacterial and archaeal communities, as well as ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), in and around REEs mining area were investigated through high throughput sequencing and quantitative polymerase chain reaction (qPCR). Our results indicated that mining soil was characterized by poor soil structure, nutrient deficiency, and high concentrations of residual REEs. Oligotrophic bacteria (e.g., Chloroflexi and Acidobacteriota) were dominant in unexploited soil and mining soil, while copiotrophic bacteria (Proteobacteria and Actinobacteriota) were more abundant in surrounding soil. Nutrient was the key factor affecting microbial variation and abundance in mining soil. The bacterial community was more sensitive to REEs, while the archaeal communities were relatively stable. As the key members for ammonia oxidation, AOA outnumbered AOB in all the soil types, and the former was significantly influenced by pH, nutrients, and TREEs in mining soil. The microbial co-occurrence network analysis demonstrated that exploitation significantly influenced topological properties, decreased the complexity, and resulted in a much unstable network, leading to a more fragile microbial ecosystem in mining areas. Notably, the abundance of keystone taxa decreased after exploitation, and oligotrophic groups (Chloroflexi) replaced copiotrophic groups (Proteobacteria and Actinobacteriota) as the key to rebuilt a co-occurrence network, suggesting potentially important roles in maintaining network stability. The current results are of great significance to the ecological risk assessment of REEs exploitation.

Revealing ecotype influences on Cistanche sinensis: from the perspective of endophytes to metabolites characteristics

Introduction

Plant microorganism is critical to plant health, adaptability, and productive forces. Intriguingly, the metabolites and microorganisms can act upon each other in a plant. The union of metabolomics and microbiome may uncover the crucial connections of the plant to its microbiome. It has important benefits for the agricultural industry and human being health, particularly for Chinese medical science investigation.

Methods

In this last 2 years study, on the strength of the UPLC-MS/MS detection platform, we accurately qualitatively, and quantitatively measured the Cistanche sinensis fleshy stems of two ecotypes. Thereafter, through high-throughput amplicon sequencing 16S/ITS sequences were procured.

Results

PhGs metabolites including echinacoside, isoacteoside, and cistanoside A were significantly downregulated at two ecotypes of C. sinensis. Add up to 876 metabolites were monitored and 231 differential metabolites were analyzed. Further analysis of 34 core differential metabolites showed that 15 compounds with up-regulated belonged to phenolic acids, flavonoids, and organic acids, while 19 compounds with down-regulated belonged to phenolic acids, flavonoids, alkaloids, amino acids, lipids, and nucleotides. There was no noteworthy discrepancy in the endophytic bacteria's α and β diversity between sandy and loam ecotypes. By comparison, the α and β diversity of endophytic fungi was notably distinct. The fungal community of the loam ecotype is more abundant than the sandy ecotype. However, there were few such differences in bacteria. Most abundant genera included typical endophytes such as Phyllobacterium, Mycobacterium, Cistanche, Geosmithia, and Fusarium. LEfSe results revealed there were 11 and 20 biomarkers of endophytic bacteria and fungi in C. sinensis at two ecotypes, respectively. The combination parsing of microflora and metabolites indicated noteworthy relativity between the endophytic fungal communities and metabolite output. Key correlation results that Anseongella was positive relation with Syringin, Arsenicitalea is negative relation with 7-methylxanthine and Pseudogymnoascus is completely positively correlated with nepetin-7-O-alloside.

Discussion

The aim of this research is: (1) to explore firstly the influence of ecotype on C. sinensis from the perspective of endophytes and metabolites; (2) to investigate the relationship between endophytes and metabolites. This discovery advances our understanding of the interaction between endophytes and plants and provides a theoretical basis for cultivation of C. sinensis in future.

Reduced soil multifunctionality and microbial network complexity in degraded and revegetated alpine meadows

Understanding how microbial processes develop and change in alpine meadow soils is key to global initiatives toward environmental sustainability and local land management. Yet, how microbial interactions mediate soil multifunctionality in disturbed and managed alpine meadows remains understudied. Here, we investigated multiple community metrics, particularly microbial network properties and assembly processes, of soil bacterial and fungal communities and their links to certain soil functions along a degradation-restoration sequence of alpine meadows in the Qinghai-Tibetan Plateau. Meadow degradation caused significant declines in soil hydraulic conductivity (e.g., higher bulk density, reduced soil porosity and water content) and nitrogen availability, leading to lowered soil multifunctionality. Meadow degradation only caused weak changes in microbial abundance, alpha diversity, and community composition, but remarkably reduced bacterial network complexity, to a less extent for fungal network properties. Short-term artificial restoration with productive grass monocultures did not restore soil multifunctionality, in turn even destabilized bacterial network and favored pathogenic over mutualistic fungi. Soil fungi community are more stable than bacteria in disturbed alpine meadows, and they evolved with distinct assembly strategies (stochastic-dominant versus deterministic-driven processes, respectively). Further, microbial network complexity, positively and better predicts soil multifunctionality than alpha diversity. Our work shows how microbial interaction complexity may enhance soil multifunctionality in degraded alpine meadow ecosystems, noting that meadow restoration with low plant species diversity may failed in restoring multiple ecosystem functions. These findings would help predict the outcomes of global environmental changes and inform management strategies in regional grassland conservation and restoration.

Transgenic soybean of GsMYB10 shapes rhizosphere microbes to promote resistance to aluminum (Al) toxicity

Plant resistance genes could affect rhizosphere microbiota, which in turn enhanced plant resistance to stresses. Our previous study found that overexpression of the GsMYB10 gene led to enhanced tolerance of soybean plants to aluminum (Al) toxicity. However, whether GsMYB10 gene could regulate rhizosphere microbiota to mitigate Al toxicity remains unclear. Here, we analyzed the rhizosphere microbiomes of HC6 soybean (WT) and transgenic soybean (trans-GsMYB10) at three Al concentrations, and constructed three different synthetic microbial communities (SynComs), including bacterial, fungal and cross-kingdom (bacteria and fungi) SynComs to verify their role in improving Al tolerance of soybean. Trans-GsMYB10 shaped the rhizosphere microbial communities and harbored some beneficial microbes, such as Bacillus, Aspergillus and Talaromyces under Al toxicity. Fungal and cross-kingdom SynComs showed a more effective role than the bacterial one in resistance to Al stress, and these SynComs helped soybean resist Al toxicity via affecting some functional genes that involved cell wall biosynthesis and organic acid transport etc. Overall, this study reveals the mechanism of soybean functional genes regulating the synergistic resistance of rhizosphere microbiota and plants to Al toxicity, and also highlights the possibility of focusing on the rhizobial microbial community as a potential molecular breeding target to produce crops.

A functional metagenomics study of soil carbon and nitrogen degradation networks and limiting factors on the Tibetan plateau

Introduction

The Three-River Source Nature Reserve is located in the core area of the Qinghai-Tibetan Plateau, with the alpine swamp, meadow and steppe as the main ecosystem types. However, the microbial communities in these alpine ecosystems, and their carbon and nitrogen degrading metabolic networks and limiting factors remain unclear.

Methods

We sequenced the diversity of bacteria and fungi in alpine swamps, meadows, steppes, and their degraded and artificially restored ecosystems and analyzed soil environmental conditions.

Results

The results indicated that moisture content had a greater influence on soil microbial community structure compared to degradation and restoration. Proteobacteria dominated in high moisture alpine swamps and alpine meadows, while Actinobacteria dominated in low moisture alpine steppes and artificial grasslands. A metabolic network analysis of carbon and nitrogen degradation and transformation using metagenomic sequencing revealed that plateau microorganisms lacked comprehensive and efficient enzyme systems to degrade organic carbon, nitrogen, and other biological macromolecules, so that the short-term degradation of alpine vegetation had no effect on the basic composition of soil microbial community. Correlation analysis found that nitrogen fixation was strong in meadows with high moisture content, and their key nitrogen-fixing enzymes were significantly related to Sphingomonas. Denitrification metabolism was enhanced in water-deficient habitats, and the key enzyme, nitrous oxide reductase, was significantly related to Phycicoccus and accelerated the loss of nitrogen. Furthermore, Bacillus contained a large number of amylases (GH13 and GH15) and proteases (S8, S11, S26, and M24) which may promote the efficient degradation of organic carbon and nitrogen in artificially restored grasslands.

Discussion

This study illustrated the irrecoverability of meadow degradation and offered fundamental information for altering microbial communities to restore alpine ecosystems.

Vis-NIR Spectroscopy Combined with GAN Data Augmentation for Predicting Soil Nutrients in Degraded Alpine Meadows on the Qinghai-Tibet Plateau

Soil nutrients play vital roles in vegetation growth and are a key indicator of land degradation. Accurate, rapid, and non-destructive measurement of the soil nutrient content is important for ecological conservation, degradation monitoring, and precision farming. Currently, visible and near-infrared (Vis-NIR) spectroscopy allows for rapid and non-destructive monitoring of soil nutrients. However, the performance of Vis-NIR inversion models is extremely dependent on the number of samples. Limited samples may lead to low prediction accuracy of the models. Therefore, modeling and prediction based on a small sample size remain a challenge. This study proposes a method for the simultaneous augmentation of soil spectral and nutrient data (total nitrogen (TN), soil organic matter (SOM), total potassium oxide (TK₂O), and total phosphorus pentoxide (TP₂O₅)) using a generative adversarial network (GAN). The sample augmentation range and the level of accuracy improvement were also analyzed. First, 42 soil samples were collected from the pika disturbance area on the QTP. The collected soils were measured in the laboratory for Vis-NIR and TN, SOM, TK₂O, and TP₂O₅ data. A GAN was then used to augment the soil spectral and nutrient data simultaneously. Finally, the effect of adding different numbers of generative samples to the training set on the predictive performance of a convolutional neural network (CNN) was analyzed and compared with another data augmentation method (extended multiplicative signal augmentation, EMSA). The results showed that a GAN can generate data very similar to real data and with better diversity. A total of 15, 30, 60, 120, and 240 generative samples (GAN and EMSA) were randomly selected from 300 generative samples to be included in the real data to train the CNN model. The model performance first improved and then deteriorated, and the GAN was more effective than EMSA. Further shortening the interval for adding GAN data revealed that the optimal ranges were 30-40, 50-60, 30-35, and 25-35 for TK₂O, TN, TP₂O₅, and SOM, respectively, and the validation set accuracy was maximized in these ranges. Therefore, the above method can compensate to some extent for insufficient samples in the hyperspectral prediction of soil nutrients, and can quickly and accurately estimate the content of soil TK₂O, TN, TP₂O₅, and SOM.

Rare Bacteria Can Be Used as Ecological Indicators of Grassland Degradation

Grassland degradation is a major ecological problem at present, leading to changes in the grassland environment and the soil microbial community. Here, based on full-length 16S rRNA gene sequencing, we highlight the importance of small-scale environmental changes on the Qinghai-Tibet Plateau grassland for the composition and assembly processes of abundant and rare bacterial taxa. The results showed that grassland vegetation coverage affected the taxonomic and phylogenetic composition of rare bacterial taxa more than abundant bacterial taxa. The taxonomic composition and phylogenetic composition of rare bacterial taxa were also affected by soil nutrients. The relative contribution of deterministic processes (variable selection and homogeneous selection) to rare bacterial taxa was higher than that of the abundant bacterial taxa. The competitive potential within rare bacterial taxa was lower than that of the competitive potential between rare and non-rare bacterial taxa or within non-rare bacterial taxa. The assembly of rare bacterial taxa was more susceptible to environmental changes caused by grassland degradation than the abundant bacterial taxa. Furthermore, the distribution of rare bacterial taxa in the different degraded grassland soil was more local than that of abundant bacterial taxa. Thus, rare bacterial taxa could be considered an ecological indicator of grassland degradation. These findings help to improve our understanding of the composition and assembly mechanism of the bacterial communities in degraded grassland and provide a basis for the establishment of the grassland degradation management strategy.

Populus root exudates are associated with rhizosphere microbial communities and symbiotic patterns

Introduction

Microbial communities in the plant rhizosphere are critical for nutrient cycling and ecosystem stability. However, how root exudates and soil physicochemical characteristics affect microbial community composition in Populus rhizosphere is not well understood.

Methods

This study measured soil physiochemistry properties and root exudates in a representative forest consists of four Populus species. The composition of rhizosphere bacterial and fungal communities was determined by metabolomics and high-throughput sequencing.

Results

Luvangetin, salicylic acid, gentisic acid, oleuropein, strigol, chrysin, and linoleic acid were the differential root exudates extracted in the rhizosphere of four Populus species, which explained 48.40, 82.80, 48.73, and 59.64% of the variance for the dominant and key bacterial or fungal communities, respectively. Data showed that differential root exudates were the main drivers of the changes in the rhizosphere microbial communities. Nitrosospira, Microvirga, Trichoderma, Cortinarius, and Beauveria were the keystone taxa in the rhizosphere microbial communities, and are thus important for maintaining a stable Populus microbial rhizosphere. The differential root exudates had strong impact on key bacteria than dominant bacteria, key fungi, and dominant fungi. Moreover, strigol had positively effects with bacteria, whereas phenolic compounds and chrysin were negatively correlated with rhizosphere microorganisms. The assembly process of the community structure (keystone taxa and bacterial dominant taxa) was mostly determined by stochastic processes.

Discussion

This study showed the association of rhizosphere microorganisms (dominant and keystone taxa) with differential root exudates in the rhizosphere of Populus plants, and revealed the assembly process of the dominant and keystone taxa. It provides a theoretical basis for the identification and utilization of beneficial microorganisms in Populus rhizosphere.

Grassland Degradation Has Stronger Effects on Soil Fungal Community Than Bacterial Community across the Semi-Arid Region of Northern China

Soil microbes play crucial roles in grassland ecosystem functions, such as soil carbon (C) pool and nutrient cycle. Soil microbes in grasslands are susceptible to the degradation mediated by climate change and anthropogenic disturbance. However, research on how the degradation influences the diversity and community structure of different soil microbial taxa is relatively scarce. We conducted a large-scale field survey to describe the effects of four degradation levels (PD: potential degradation, LD: light degradation, MD: moderate degradation, and SD: severe degradation) on soil bacterial and fungal community in the semi-arid grasslands of northern China. We found that soil moisture, nutrients, and clay content decreased, but soil sand content increased along the increasing degradation gradient. However, the degradation had no effects on soil pH and the C:N ratio. Grassland degradation had non-significant effect on soil bacterial diversity, but it significantly affected soil bacterial community structure. The degradation decreased soil fungal diversity and had a relatively larger influence on the community structure of soil fungi than that of bacteria. The community composition and structure of soil fungi were mainly affected by soil nutrients and texture, while those of soil bacteria were mainly affected by soil pH. These results indicate that changes in soil properties induced by grassland degradation mainly drive the variation in the soil fungal community and have less effect on the soil bacterial community. This study reveals the sensitivity of soil fungal community to grassland degradation, highlighting the priority of soil fungal community for the management and restoration of degraded grasslands.

Microecosystem of yak rumen on the Qinghai-Tibetan Plateau is stable and is unaffected by soil or grass microbiota

The rumen of livestock grazing on the Qinghai-Tibetan Plateau (QTP) acts as a transfer station for the circulation of soil, grass, faecal mineral elements and nutrients. Whether the microorganisms from the soil and grass could circulate through livestock rumen and excreted faeces. We studied the structural composition and interactive networks of microbiomes (bacteria and fungi) in soil, grass, and grazing yaks (rumen and faeces) on the QTP by using 16S rRNA gene and internally transcribed spacer (ITS) sequencing technology and to calculate the contribution rate of microorganisms from one habitat to another habitat using SourceTracker analysis. The meta-co-occurrence network revealed that soil, grass, rumen, and faeces comprise four independent habitats. The bacterial and fungal composition was significantly different in these four habitats. Soil microbiota showed the highest alpha diversity and microbial network complexity. Rumen microbiota demonstrated the highest microbial network stability and synergy, while grass endophytes showed the lowest microbial network complexity, stability, and synergy. According to the SourceTracker model, grass contributes 0.02% to the rumen microbes of yaks, while soil microorganisms do not circulate in the rumen. The soil and grass microbiota originating from faeces were 4.5% and 1.2%, respectively. The contribution of soil to grass was found to be 1.1%. Overall, the rumen microbiota of yaks is relatively stable and is only minimally influenced by the microbiota inhabiting the environment under natural grazing conditions. However, the contribution of yaks to soil and grass microbiota is relatively high when compared with the contribution of soil and grass to yaks microbiota.

Responses and comprehensive evaluation of growth characteristics of ephemeral plants in the desert-oasis ecotone to soil types

The ecological environment of the Gurbantünggüt desert-oasis ecotone is extremely fragile. Ephemeral plants are an important part of the ecosystem and play an essential role in maintaining the ecological stability of the ecotone. However, few studies have focused on the growth, soil quality and system sustainability of ephemeral plants in different soils. This study was based on two typical soil types (grey desert soil, GS; aeolian soil, AS) in the aforementioned ecotone, considered four ephemeral plants (Tetracme recurvata, TR; Tetracme contorta, TC; Malcolmia scorpioides, MS; Isatis violascens, IV) as the research object, analysed plant characteristics and soil properties, and comprehensively evaluated the ephemeral plant system by analysing the soil quality index (SQI) and sustainability index (SI). The results showed that there were significant differences in biomass and nutrient accumulation between different ephemeral plants, which were significantly affected by soil types. In the two examined soils (GS and AS), the contents of nutrients and microbial carbon (MBC) and nitrogen (MBN) in the rhizosphere soil were higher than those in the bare soil (BS), and there were significant differences among different species. The key soil factors related to total biomass in GS and AS were also different. The SQI of ephemeral plants was significantly higher than that of the BS, and varied with soil types and plant species. The species with the highest SQI of the key factor data set in GS and AS were IV and TR, respectively. The SI analysis indicated that IV in GS and MS and IV in AS were sustainable, and the plant properties can be better used to assess the sustainability of ephemeral plant systems. In conclusion, ephemeral plants improved the soil quality and system sustainability of the study ecotone. Further, the growth of ephemeral plant and rhizosphere soil properties vary with plant species and soil types; thus, selecting suitable species for large-scale planting in different soil types is of great significance for improving the ecological stability of the ecotone.

Response of microbial community structure to chromium contamination in Panax ginseng-growing soil

Chromium (Cr) contamination in soil poses a serious security risk for the development of medicine and food with ginseng as the raw material. Microbiome are critical players in the functioning and service of soil ecosystems, but their feedback to Cr-contaminated ginseng growth is still poorly understood. To study this hypothesis, we evaluated the effects of microbiome and different Cr exposure on the soil microbial community using Illumina HiSeq high-throughput sequencing. Our results indicated that 2467 OTUs and 1785 OTUs were obtained in 16S and ITS1 based on 97% sequence similarity, respectively. Bacterial and fungal diversity were affected significantly in Cr-contaminated soil. Besides, Cr contamination significantly changed the composition of the soil bacterial and fungal communities, and some biomarkers were identified in the different classification level of the different Cr-contaminated treatments using LEfSe. Finally, a heatmap of Spearman's rank correlation coefficients and canonical discriminant analysis (CDA) indicated that Chloroflexi, Gemmatimonadetes, Acidobacteria, Verrucomicobia, and Parcubacteria in phylum level and Acidimicrobiia, Gemmatimonadetes, and Deltaproteobacteria in class level were positively correlated with AK, AP, and NO₃^--N (p < 0.05 or p < 0.01), but negatively correlated with total Cr and available Cr (p < 0.05 or p < 0.01). Similarly, in the fungal community, Tubaria, Mortierellaceae, and Rhizophagus in the phylum level and Glomeromycetes, Agaricomycetes, and Exobasidiomycetes in the class level were positively correlated with AK, AP, and NO₃^--N (p < 0.05 or p < 0.01), but negatively correlated with total Cr and available Cr (p < 0.05 or p < 0.01). Our findings provide new insight into the effects of Cr contamination on the microbial communities in ginseng-growing soil.

Synergetic effects of microbial-phytoremediation reshape microbial communities and improve degradation of petroleum contaminants

Microbial-phytoremediation is an effective bioremediation technology that introduces petroleum-degrading bacteria and oil-tolerant plants into oil-contaminated soils in order to achieve effective degradation of total petroleum hydrocarbons (TPH). In this work, natural attenuation (NA), microbial remediation (MR, using Acinetobacter sp. Tust-DM21), phytoremediation (PR, using Suaeda glauca), and microbial-phytoremediation (MPR, using both species) were utilized to degrade petroleum hydrocarbons. We evaluated four different biological treatments, assessing TPH degradation rates, soil enzyme activities, and the structure of microbial community in the petroleum-contaminated soil. This finding revealed that the roots of Suaeda glauca adsorbed small amounts of polycyclic aromatic hydrocarbons, causing the structure of soil microbiota community to reshape. The abundance of petroleum-degrading bacteria and plant growth-promoting rhizobacteria (PGPR) has increased, as has microbial diversity. According to correlation research, these genera increased soil enzyme activity, boosted the number of degradation-functional genes in the petroleum hydrocarbon degradation pathway, and accelerated the dissipation and degradation of TPH in petroleum-contaminated soil. This evidence contributes to a better understanding of the mechanisms involved in the combined microbial-phytoremediation strategies for contaminated soil, specifically the interaction between microflora and plants in co-remediation and the effects on the structural reshaping of rhizosphere microbial communities.

Effects of cadmium contamination on bacterial and fungal communities in Panax ginseng-growing soil

Background

Cadmium (Cd) contamination in soil poses a serious safety risk for the development of medicine and food with ginseng as the raw material. Microorganisms are key players in the functioning and service of soil ecosystems, but the effects of Cd-contaminated ginseng growth on these microorganisms is still poorly understood. To study this hypothesis, we evaluated the effects of microorganisms and Cd (0, 0.25, 0.5, 1.0, 2.0, 5.0, and 10.0 mg kg^-1 of Cd) exposure on the soil microbial community using Illumina HiSeq high-throughput sequencing.

Results

Our results indicated that Cd-contaminated soil affected the soil microbial diversity and composition, and bacterial diversity was affected more than fungal diversity in Cd-contaminated soil, especially according to Shannon indices. The abundance of the soil microbial community decreased and the composition changed according to the relative abundances at the phylum level, including those of Saccharibacteria and Gemmatimonadetes in bacteria and Mortierellomycota in fungi. The LEfSe algorithm was used to identify active biomarkers, and 45 differentially abundant bacterial taxonomic clades and 16 differentially abundant fungal taxonomic clades were identified with LDA scores higher than 4.0. Finally, a heatmap of Spearman's rank correlation coefficients and canonical discriminant analysis (CDA) indicated that some key biomarkers, Arenimonas, Xanthomonadales, Nitrosomonadaceae, Methylophilales, Caulobacterales, Aeromicrobium, Chitinophagaceae, Acidimicrobiales, Nocardioidaceae, Propionibacteriales, Frankiales, and Gemmatimonadaceae, were positively correlated with the total and available Cd (p<0.05) but negatively correlated with AK, AP, and pH (p<0.05) in the bacterial community. Similarly, in the fungal community, Tubaria, Mortierellaceae, and Rhizophagus were positively correlated with the total and available Cd but negatively correlated with AK, AP, TK, and pH.

Conclusion

Cd contamination significantly affected microbial diversity and composition in ginseng-growing soil. Our findings provide new insight into the effects of Cd contamination on the microbial communities in ginseng-growing soil.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02488-z.

Variations and Mutual Relations of Vegetation–Soil–Microbes of Alpine Meadow in the Qinghai-Tibet Plateau under Degradation and Cultivation

Artificial cultivation had been applied to recover the meadow suffering from serious degradation in the Qinghai–Tibet Plateau. Studies focusing only on the changes in vegetation, soil and microbes along the meadow degradation were insufficient, and artificial cultivation as an important part of succession was always neglected. Here, the variables of vegetation, soil, and soil bacteria are surveyed in four types of alpine meadow in the protected lands of the Qinghai–Tibet Plateau: intact alpine meadow (IAM), moderate degradation alpine meadow (MDAM), extreme degradation alpine meadow (black soil beach (BSB)), and artificial alpine grassland (AAG). The results indicated that degradation and cultivation significantly changed the characteristics of the vegetation community, physicochemical features of the soil, and soil bacterial community diversity. Soil bacteria took a considerably longer time to adapt to degradation and cultivation than vegetation and soil. Compared to IAM and BSB, ADAM and AAG had more specific bacteria identified by ANOVA and LEfSe analysis, implying an unstable state. Combined with vegetation and soil variables, it was speculated that the unstable AAG was not significantly improved from the degraded meadow, and also lagged significantly compared to IAM. Correlation analysis revealed that aboveground biomass, species richness, vegetation coverage, SOC, C/N, BD, WC, and pH were significantly associated with bacterial diversity under community level. Aboveground biomass was an effective indicator for soil bacterial gene copies. Redundancy analysis demonstrated that the soil bacterial community is mainly regulated by the vegetation coverage, Gleason index, Simpson index, TN, TP, and pH under phylum and genus level. Partial mantel test analysis indicated that the physicochemical features of the soil were the most important factor correlating with the soil bacterial community along the degradation and cultivation, compared to other environmental factors.

Soil Bacterial Community Shifts Are Driven by Soil Nutrient Availability along a Teak Plantation Chronosequence in Tropical Forests in China

Simple Summary

Tropical forests play an important role in the global carbon cycle, especially in the context of global climate change. Soil microorganisms are essential to the functions, services, and productivity of terrestrial ecosystems as a link to maintain the connections and interactions between the aboveground and belowground ecosystems. The interactions between plants and the soil microbiome are crucial for plant growth, health, and resistance to stressors. However, information on the response of soil microbial communities to a chronosequence of woody plants is lacking, especially in tropical forests. This study compares the soil properties, diversity, composition, and co-occurrence patterns of bacterial communities in the rhizosphere and bulk soils along a teak plantation chronosequence. The results show that the composition and co-occurrence patterns of the bacterial communities are statistically different among the plantations, while stand age has no significant impact on soil bacterial alpha diversity. The results further show that soil nutrients play a key role in shaping the soil bacterial community. The study also provides information about the dynamics and characteristics of these soil bacterial communities and adds valuable information that may underpin new strategies for the management of teak plantations.

Abstract

Soil bacterial communities play crucial roles in ecosystem functions and biogeochemical cycles of fundamental elements and are sensitive to environmental changes. However, the response of soil bacterial communities to chronosequence in tropical ecosystems is still poorly understood. This study characterized the structures and co-occurrence patterns of soil bacterial communities in rhizosphere and bulk soils along a chronosequence of teak plantations and adjacent native grassland as control. Stand ages significantly shifted the structure of soil bacterial communities but had no significant impact on bacterial community diversity. Bacterial community diversity in bulk soils was significantly higher than that in rhizosphere soils. The number of nodes and edges in the bacterial co-occurrence network first increased and then decreased with the chronosequence. The number of strongly positive correlations per network was much higher than negative correlations. Available potassium, total potassium, and available phosphorus were significant factors influencing the structure of the bacterial community in bulk soils. In contrast, urease, total potassium, pH, and total phosphorus were significant factors affecting the structure of the bacterial community in the rhizosphere soils. These results indicate that available nutrients in the soil are the main drivers regulating soil bacterial community variation along a teak plantation chronosequence.

Alterations in Arbuscular Mycorrhizal Community Along a Chronosequence of Teak (Tectona grandis) Plantations in Tropical Forests of China

Arbuscular mycorrhizal (AM) fungi play a crucial role in promoting plant growth, enhancing plant stress resistance, and sustaining a healthy ecosystem. However, little is known about the mycorrhizal status of teak plantations. Here, we evaluated how the AM fungal communities of rhizosphere soils and roots respond to different stand ages of teak: 22, 35, 45, and 55-year-old from the adjacent native grassland (CK). A high-throughput sequencing method was used to compare the differences in soil and root AM fungal community structures. In combination with soil parameters, mechanisms driving the AM fungal community were revealed by redundancy analysis and the Mantel test. Additionally, spore density and colonization rates were analyzed. With increasing stand age, the AM fungal colonization rates and spore density increased linearly. Catalase activity and ammonium nitrogen content also increased, and soil organic carbon, total phosphorous, acid phosphatase activity, available potassium, and available phosphorus first increased and then decreased. Stand age significantly changed the structure of the AM fungal community but had no significant impact on the diversity of the AM fungal community. However, the diversity of the AM fungal community in soils was statistically higher than that in the roots. In total, nine and seven AM fungal genera were detected in the soil and root samples, respectively. The majority of sequences in soils and roots belonged to Glomus. Age-induced changes in soil properties could largely explain the alterations in the structure of the AM fungal community along a chronosequence, which included total potassium, carbon-nitrogen ratio, ammonium nitrogen, catalase, and acid phosphatase levels in soils and catalase, acid phosphatase, pH, and total potassium levels in roots. Soil nutrient availability and enzyme activity were the main driving factors regulating the shift in the AM fungal community structure along a chronosequence of the teak plantations.

The Influence of Climate Warming and Humidity on Plant Diversity and Soil Bacteria and Fungi Diversity in Desert Grassland

Our study, which was conducted in the desert grassland of Ningxia in China (E 107.285, N 37.763), involved an experiment with five levels of annual precipitation 33% (R33), 66% (R66), 100% (CK), 133% (R133), 166% (R166) and two temperature levels (inside Open-Top Chamber (OTC) and outside OTC). Our objective was to determine how plant, soil bacteria, and fungi diversity respond to climate change. Our study suggested that plant α-diversity in CK and TCK were significantly higher than that of other treatments. Increased precipitation promoted root biomass (RB) growth more than aboveground living biomass (ALB). R166 promoted the biomass of Agropyron mongolicum the most. In the fungi communities, temperature and precipitation interaction promoted α-diversity. In the fungi communities, the combination of increased temperature and natural precipitation (TCK) promoted β-diversity the most, whose distance was determined to be 25,124 according to PCA. In the bacteria communities, β-diversity in CK was significantly higher than in other treatments, and the distance was determined to be 3010 according to PCA. Soil bacteria and fungi α- and β-diversity, and ALB promoted plant diversity the most. The interactive effects of temperature and precipitation on C, N, and P contents of plants were larger than their independent effects.