Shaping Soil Microbial Communities Research Articles

Earthworms promote crop growth by enhancing the connections among soil microbial communities

Abstract Earthworms benefit plant growth and play a vital role in shaping soil microbial communities. However, how earthworms modify the soil microorganisms and thus affect plant growth is still unclear. Although fertilizers alter the assembly of microbial communities, further investigations are required to test the effect of fertilizer type on the relationship between earthworms, soil microbial communities and plants. We evaluated the role of earthworms in soil microorganisms and maize plant growth characteristics under organic or chemical fertilizers in field and greenhouse experiments. We explored the relationships between earthworms, soil microbial community and plant growth under different fertilizer types. We found that the presence of earthworms promoted plant growth, increased the amount of plant root exudates, and enhanced the connections between rhizosphere bacterial, fungal and protist communities. Both earthworms and fertilizer application significantly changed the structure of soil bacterial, fungal and protist communities. The complexity of the soil microbial community network increased under organic, compared to chemical fertilizer application. The greenhouse experiment showed that the effect of earthworms on plant growth was weakened when maize plants were grown in sterilized soil under organic or chemical fertilizers. Synthesis and applications: Our study provides solid evidence that earthworms largely depend on soil microorganisms for their effects on plants under the application of different fertilizer conditions. This may provide new insights into reducing the amounts of fertilizer used by enhancing the role of earthworms and soil microorganisms.

Earthworms promote crop growth by enhancing the connections among soil microbial communities

Abstract Earthworms benefit plant growth and play a vital role in shaping soil microbial communities. However, how earthworms modify the soil microorganisms and thus affect plant growth is still unclear. Although fertilizers alter the assembly of microbial communities, further investigations are required to test the effect of fertilizer type on the relationship between earthworms, soil microbial communities and plants. We evaluated the role of earthworms in soil microorganisms and maize plant growth characteristics under organic or chemical fertilizers in field and greenhouse experiments. We explored the relationships between earthworms, soil microbial community and plant growth under different fertilizer types. We found that the presence of earthworms promoted plant growth, increased the amount of plant root exudates, and enhanced the connections between rhizosphere bacterial, fungal and protist communities. Both earthworms and fertilizer application significantly changed the structure of soil bacterial, fungal and protist communities. The complexity of the soil microbial community network increased under organic, compared to chemical fertilizer application. The greenhouse experiment showed that the effect of earthworms on plant growth was weakened when maize plants were grown in sterilized soil under organic or chemical fertilizers. Synthesis and applications: Our study provides solid evidence that earthworms largely depend on soil microorganisms for their effects on plants under the application of different fertilizer conditions. This may provide new insights into reducing the amounts of fertilizer used by enhancing the role of earthworms and soil microorganisms.

Effects of microtopography on soil microbial communities in alpine meadows on the Qinghai-Tibetan Plateau

Heterogeneous habitats generated by diverse microtopography are critical in shaping soil microbial communities and their ecological functions. In this study, a combination of high-throughput sequencing technology and functional prediction was used to assess the effects of three microtopographic types (the shady slope, ravine, and sunny slope) on community structure, diversity, functional guilds, and the co-occurrence networks of soil microbes in alpine meadows. The results showed that the microbial α-diversity varied significantly across the three microtopographies, and fungal community structure was more responsive to microtopography than that of bacteria. In contrast, the co-occurrence network pattern of bacteria was more sensitive to environmental changes induced by microtopography. Mantel tests revealed that bacterial community structure was mainly impacted by plant diversity, belowground biomass, soil total phosphorus content and soil pH, and variations in fungal community structure were correlated with plant diversity, soil pH, and soil NH4+–N content. Meanwhile, regression analyses indicated that nitrogen fixers, ectomycorrhizal fungi, and endophytes relative abundances were positively linked to plant diversity, and soil pH negatively affected nitrogen fixers, ectomycorrhizal fungi, and methane oxidizers. Furthermore, different functional guilds with similar functions (e.g., ectomycorrhizal fungi vs. arbuscular mycorrhizal fungi) responded inconsistently to the microtopography, suggesting ecological niche differentiation of microorganisms in microtopographies. These findings highlight the importance of microtopography for driving bacterial and fungal diversity, community structure, functional profiles and co-occurrence networks in alpine ecosystems.

Interaction effects of pH and land cover on soil microbial diversity are climate-dependent.

Factors regulating the diversity and composition of soil microbial communities include soil properties, land cover and climate. How these factors interact at large scale remains poorly investigated. Here, we used an extensive dataset including 715 locations from 24 European countries to investigate the interactive effects of climatic region, land cover and pH on soil bacteria and fungi. We found that differences in microbial diversity and community composition between land cover types depended on the climatic region. In Atlantic, Boreal and Continental regions, microbial richness was higher in croplands and grasslands than woodlands while richness in Mediterranean areas did not vary significantly among land cover types. These differences were further related to soil pH, as a driver of bacterial and fungal richness in most climatic regions, but the interaction of pH with land cover depended on the region. Microbial community composition differed the most between croplands and woodlands in all regions, mainly due to differences in pH. In the Mediterranean region, bacterial communities in woodlands and grasslands were the most similar, whereas in other regions, grassland and cropland-associated bacteria showed more similarity. Overall, we showed that key factors interact in shaping soil microbial communities in a climate-dependent way at large scale.

Carbon and Nutrients from Organic Residues Modulate the Dynamics of Prokaryotic and Fungal Communities.

Inputs of carbon (C) and nutrients from organic residues may select specific microbes and shape the soil microbial community. However, little is known about the abiotic filtering of the same residues with different nutrient concentrations applied to the soil. In our study, we explored how applying organic residue, vinasse, as fertilizer in its natural state (V) versus its concentrated form (CV) impacts soil microbiota. We conducted two field experiments, evaluating soil prokaryotic and fungal communities over 24 and 45 days with vinasse (V or CV) plus N fertilizer. We used 16S rRNA gene and ITS amplicon sequencing. Inorganic N had no significant impact on bacterial and fungal diversity compared to the control. However, the varying concentrations of organic C and nutrients in vinasse significantly influenced the soil microbiome structure, with smaller effects observed for V compared to CV. Prokaryotic and fungal communities were not correlated (co-inertia: RV coefficient = 0.1517, p = 0.9708). Vinasse did not change the total bacterial but increased the total fungal abundance. A higher C input enhanced the prokaryotic but reduced the fungal diversity. Our findings highlight vinasse's role as an abiotic filter shaping soil microbial communities, with distinct effects on prokaryotic and fungal communities. Vinasse primarily selects fast-growing microorganisms, shedding light on the intricate dynamics between organic residues, nutrient concentrations, and soil microbes.

The mechanism effects of root exudate on microbial community of rhizosphere soil of tree, shrub, and grass in forest ecosystem under N deposition

Forests are composed of various plant species, and rhizosphere soil microbes are driven by root exudates. However, the interplay between root exudates, microbial communities in the rhizosphere soil of canopy trees, understory shrubs, grasses, and their responses to nitrogen (N) deposition remains unclear. Pinus tabulaeformis, Rosa xanthina, and Carex lancifolia were used to investigate root exudates, rhizosphere soil microbial communities, and their responses to N application in forest ecosystem. Root exudate abundances of P. tabulaeformis were significantly higher than that of R. xanthina and C. lancifolia, with carbohydrates dominating P. tabulaeformis and R. xanthina root exudates, fatty acids prevailing in C. lancifolia root exudates. Following N application, root exudate abundances of P. tabulaeformis and R. xanthina initially increased before decreasing, whereas those of C. lancifolia decreased. Microbial number of rhizosphere soil of C. lancifolia was higher than that of P. tabulaeformis and R. xanthina, but there was insignificant variation of rhizosphere soil microbial diversity among plant species. N application exerted promotional and inhibitory impacts on bacterial and fungal numbers, respectively, while bacterial and fungal diversities were increased by N application. Overall, N application had negative effects on root exudates of P. tabulaeformis, inhibiting rhizosphere soil microbial populations. N application suppressed rhizosphere soil microbial populations by increasing root exudates of R. xanthina. Conversely, N application elevated nutrient content in the rhizosphere soil of C. lancifolia, reducing root exudates and minimally promoting microbial populations. This study highlights the importance of understory vegetation in shaping soil microbial communities within forests under N deposition.

Consistent predictors of microbial community composition across spatial scales in grasslands reveal low context-dependency.

Environmental circumstances shaping soil microbial communities have been studied extensively. However, due to disparate study designs, it has been difficult to resolve whether a globally consistent set of predictors exists, or context-dependency prevails. Here, we used a network of 18 grassland sites (11 of those containing regional plant productivity gradients) to examine (i) if similar abiotic or biotic factors predict both large-scale (across sites) and regional-scale (within sites) patterns in bacterial and fungal community composition, and (ii) if microbial community composition differs consistently at two levels of regional plant productivity (low vs. high). Our results revealed that bacteria were associated with particular soil properties (such as base saturation) and both bacteria and fungi were associated with plant community composition across sites and within the majority of sites. Moreover, a discernible microbial community signal emerged, clearly distinguishing high and low-productivity soils across different grasslands independent of their location in the world. Hence, regional productivity differences may be typified by characteristic soil microbial communities across the grassland biome. These results could encourage future research aiming to predict the general effects of global changes on soil microbial community composition in grasslands and to discriminate fertile from infertile systems using generally applicable microbial indicators.

Facilitating New Chromium Reducing Microbes to Enhance Hexavalent Chromium Reduction by In Situ Sonoporation-Mediated Gene Transfer in Soils.

Chromium (Cr) is a heavy metal with a high toxicity and pathogenicity. Microbial reduction is an effective strategy to remove Cr(VI) at contaminated sites but suffers from the low populations and activities of Cr-reducing microorganisms in soils. This study proposed an in situ sonoporation-mediated gene transfer approach, which improved soil Cr(VI) reduction performance by delivering exogenous Cr-transporter chrA genes and Cr-reducing yieF genes into soil microorganisms with the aid of ultrasound. Besides the increasing populations of Cr-resistant bacteria and elevated copy numbers of chrA and yieF genes after sonoporation-mediated gene transfer, three new Cr-reducing strains were isolated, among which Comamonas aquatica was confirmed to obtain Cr-resistant capability. In addition, sonoporation-mediated gene transfer was the main driving force significantly shaping soil microbial communities owing to the predominance of Cr-resistant microbes. This study pioneered and evidenced that in situ soil sonoporation-mediated gene transfer could effectively deliver functional genes into soil indigenous microbes to facilitate microbial functions for enhanced bioremediation, e.g., Cr-reduction in this study, showing its feasibility as a chemically green and sustainable remediation strategy for heavy metal contaminated sites.

Unravelling the dynamics of soil microbial communities under the environmental selection and range shift process in afforestation ecosystems

The process of forest range shift not only affects the vegetation aboveground but also influences the dynamics of belowground microbial communities. To investigate the changes in soil under forest range shift, we examined the natural forest soil microbiome along with its corresponding physicochemical properties, as well as the afforestation of natural forest by seedlings and sowing. By utilizing natural forests and employing different afforestation methods, we simulated the three stages of forest range shift: the staging stage, regeneration, and colonization. We employed network analysis and phylogenetic assemblages to examine the structure of soil microbial communities during these three stages in a macro-environmental change context. Ordination and regression analyses were also used to explore the correlation between microorganisms, environmental factors, and changes in their niches. The findings revealed that different afforestation (range shift) types led to distinct microbial compositions. Seedling afforestation exhibited similarities to mature forests, suggesting a significant influence on below-ground microorganisms. In contrast, sowing-based afforestation resulted in small changes in soil microbes, indicating a legacy effect on grassland soils. The impact of the rhizosphere on microbial composition remained consistent across the three forest types. Overall, this study underscores the significance of forest range shift in shaping soil microbial communities and emphasizes the need to consider these dynamics in forest management and restoration endeavours.

Biocontrol Activity of Aromatic and Medicinal Plants and Their Bioactive Components against Soil-Borne Pathogens.

Soil-borne phytopathogens can have detrimental effects on both cereal and horticultural crops resulting in serious losses worldwide. Due to their high efficiency and easy applicability, synthetic pesticides are still the primary choice in modern plant disease control systems, but stringent regulations and increasing environmental concerns make the search for sustainable alternatives more pressing than ever. In addition to the incorporation of botanicals into agricultural practices, the diversification of cropping systems with aromatic and medicinal plants is also an effective tool to control plant diseases through providing nutrients and shaping soil microbial communities. However, these techniques are not universally accepted and may negatively affect soil fertility if their application is not thoroughly controlled. Because the biocontrol potential of aromatic and medicinal plants has been extensively examined over the past decades, the present study aims to overview the recent literature concerning the biopesticide effect of secondary metabolites derived from aromatic and medicinal plants on important soil-borne plant pathogens including bacteria, fungi, and nematodes. Most of the investigated herbs belong to the family of Lamiaceae (e.g., Origanum spp., Salvia spp., Thymus spp., Mentha spp., etc.) and have been associated with potent antimicrobial activity, primarily due to their chemical constituents. The most frequently tested organisms include fungi, such as Rhizoctonia spp., Fusarium spp., and Phytophthora spp., which may be highly persistent in soil. Despite the intense research efforts dedicated to the development of plant-based pesticides, only a few species of aromatic herbs are utilized for the production of commercial formulations due to inconsistent efficiency, lack of field verification, costs, and prolonged authorization requirements. However, recycling the wastes from aromatic and medicinal plant-utilizing industries may offer an economically feasible way to improve soil health and reduce environmental burdens at the same time. Overall, this review provides comprehensive knowledge on the efficiency of aromatic herb-based plant protection techniques, and it also highlights the importance of exploiting the residues generated by aromatic plant-utilizing sectors as part of agro-industrial processes.

Microbial interactions play an important role in regulating the effects of plant species on soil bacterial diversity.

Plant species and microbial interactions have significant impacts on the diversity of bacterial communities. However, few studies have explored interactions among these factors, such the role of microbial interactions in regulating the effects of plant species on soil bacterial diversity. We assumed that plant species not only affect bacterial community diversity directly, but also influence bacterial community diversity indirectly through changing microbial interactions. Specifically, we collected soil samples associated with three different plant species, one evergreen shrub (Rhododendron simsii) and the other two deciduous shrubs (Dasiphora fruticosa and Salix oritrepha). Soil bacterial community composition and diversity were examined by high-throughput sequencing. Moreover, soil bacterial antagonistic interactions and soil edaphic characteristics were evaluated. We used structural equation modeling (SEM) to disentangle and compare the direct effect of different plant species on soil bacterial community diversity, and their indirect effects through influence on soil edaphic characteristics and microbial antagonistic interactions. The results showed that (1) Plant species effects on soil bacterial diversity were significant; (2) Plant species effects on soil microbial antagonistic interactions were significant; and (3) there was not only a significant direct plant species effect on bacterial diversity, but also a significant indirect effect on bacterial diversity through influence on microbial antagonistic interactions. Our study reveals the difference among plant species in their effects on soil microbial antagonistic interactions and highlights the vital role of microbial interactions on shaping soil microbial community diversity.

Changes in vegetation types affect soil microbial communities in tropical islands of southern China

Soil microbial communities are the key drivers of nutrient cycling in ecosystems. However, the functional response of soil microbial community composition to contrasting vegetation types in tropical coral islands is still unclear. Tropical coral islands provide a unique, extreme habitat characterized by higher soil pH and P, but lower N and soil water contents. To determine the responses of soil microbial communities to changes in vegetation types, soil microbial biomass and community composition were investigated by determination of phospholipid fatty acids (PLFAs) under three vegetation types (including tree, shrub, and herb-vine) on Dong Island and Yongxing Island of southern China. Redundancy analysis (RDA) has been used to determine the driving factors (soil properties) for shaping soil microbial community composition. The results showed that the total biomass of PLFAs, as well as the specific microbial taxa [such as bacteria, Gram-positive bacteria (G+), Gram-negative bacteria (G-), fungi, arbuscular mycorrhizal fungi (AMF), and actinomycetes] increased in the soils from herb-vine via shrub to tree. Furthermore, along the above vegetation types gradient, the ratios of Gram-positive to Gram-negative bacteria (G+:G-), total saturated to total monounsaturated fatty acids (sat:mono), and fungi to bacteria (F:B) ratio decreased, indicating a shift in soil microbial community towards lower stress and copiotrophic dominance. Our findings indicate that soil microbial groups have a sensitive response to shifting plant communities in tropical coral islands, and soil water content, the ratios of soil organic matter and N content to P content, and soil pH might be the critical drivers of microbial community composition and structure in the study region.

Effects of phthalate esters on soil microbial community under different planting patterns in Northern China: Case study of Hebei Province

Soil microorganisms are biological factors involved in the farmland environment. The factors that shape soil microbial communities and how these are influenced by geographic location, planting pattern (open-field or greenhouse), and soil organic pollutants (phthalate esters, PAEs) remain poorly understood at large scales. Using 16 S rRNA gene and ITS sequencing, we characterized the soil microbiota in open-field and greenhouse soils in Hebei Province, China, and correlated their structure and composition to geographic location, planting pattern and PAEs. Compared with geographic location, planting pattern is more decisive for shaping soil microbes and has more significant effects on bacteria, and the effects are shaped by the number and types of core OTUs. PAEs participated in the shaping of soil microbial communities by altering the relative abundances of dominant microorganisms in the two planting patterns, and the effects of PAEs with high Kow were more significant. PAEs have a greater impact on bacteria than fungi in both planting patterns. Bacteria in the greenhouse soil were sensitive to the 9 kinds of PAEs detected, however in the open-field samples, mainly responded to PAEs with high Kow and rarely respond to PAEs with low Kow. DEHP and DBP, as two monomers with the highest concentration, have significant effects on dominant genera of microorganisms under both planting patterns, with inhibiting effect on bacteria and significantly promotion on fungi. Our study clarified the factors that have a substantial impact on soil microorganisms at the provincial scale and the mechanisms involved in shaping soil microbial community structure, as well as the significant impact of PAEs on soil microbial dominant microorganisms.

Shifts in rhizosphere microbial communities in Oplopanax elatus Nakai are related to soil chemical properties under different growth conditions

Plant growth environment plays an important role in shaping soil microbial communities. To understand the response of soil rhizosphere microbial communities in Oplopanax elatus Nakai plant to a changed growth conditions from natural habitation to cultivation after transplant. Here, a comparative study of soil chemical properties and microbial community using high-throughput sequencing was conducted under cultivated conditions (CT) and natural conditions (WT), in Changbai Mountain, Northeast of China. The results showed that rhizosphere soil in CT had higher pH and lower content of soil organic matter (SOM) and available nitrogen compared to WT. These changes influenced rhizosphere soil microbial communities, resulting in higher soil bacterial and fungi richness and diversity in CT soil, and increased the relative abundance of bacterial phyla Acidobacteria, Chloroflexi, Gemmatimonadetes, Firmicutes and Patescibacteria, and the fungi phyla Mortierellomycota and Zoopagomycota, while decreased bacterial phyla Actinobacteria, WPS-2, Gemmatimonadetes, and Verrucomicrobia, and the fungi phyla Ascomycota, and Basidiomycota. Redundancy analysis analysis indicated soil pH and SOM were the primarily environmental drivers in shaping the rhizosphere soil microbial community in O. elatus under varied growth conditions. Therefore, more attention on soil nutrition management especially organic fertilizer inputs should be paid in O. elatus cultivation.

Tillage Practices and Residue Management Manipulate Soil Bacterial and Fungal Communities and Networks in Maize Agroecosystems.

Tillage practices and residue management are highly important agricultural practices. However, very few studies have examined the influence of tillage practices and residue management on both bacterial and fungal communities and network patterns in consecutive years. We examined the effects of different tillage practices, including no tillage, rotary tillage, and deep tillage, on soil bacterial and fungal communities and co-occurrence networks following residue removal and residue retention in 2017 and 2018. This study showed that both bacterial and fungal communities were unaffected by tillage practices in 2017, but they were significantly impacted in 2018. Soil fungal operational taxonomic unit (OTU) richness was significantly enhanced by deep tillage compared with no tillage in 2018, while bacterial OTU richness was unaffected in either year. Tillage practices had differing effects on soil microbial co-occurrence networks, with rotary and deep tillage increasing the complexity of bacterial networks but simplifying fungal networks. However, residue retention only induced a shift in the fungal community and simplified soil bacterial and fungal networks in 2018. This study highlights the dissimilar responses of bacterial and fungal networks to tillage practices and emphasizes that tillage practice is more important than residue management in shaping soil microbial communities.

Long-Term Application of Bio-Compost Increased Soil Microbial Community Diversity and Altered Its Composition and Network.

The influence of bio-compost on the diversity, composition and structure of soil microbial communities is less understood. Here, Illumina MiSeq sequencing and a network analysis were used to comprehensively characterize the effects of 25 years of bio-compost application on the microbial diversity of soil and community composition. High dosages of bio-compost significantly increased the bacterial and fungal richness. The compositions of bacterial and fungal communities were significantly altered by bio-compost addition. Bio-compost addition enriched the relative abundance of beneficial microorganisms (such as Sphingomonas, Acidibacter, Nocardioides, etc.) and reduced the relative abundance of harmful microorganisms (such as Stachybotrys and Aspergillus). Electrical conductivity, soil organic matter and total phosphorus were the key factors in shaping soil microbial community composition. The bacterial network was more complex than fungal network, and bacteria were more sensitive to changes in environmental factors than fungi. Positive interactions dominated both the bacterial and fungal networks, with stronger positive interactions found in the bacterial network. Functional prediction suggested that bio-composts altered the soil bacterial-community metabolic function with respect to carbon, nitrogen and phosphorus cycles and fungal community trophic modes. In conclusion, suitable bio-compost addition is beneficial to the improvement of soil health and crop quality and therefore the sustainability of agriculture.

The discovery of pivotal fungus and major determinant factor shaping soil microbial community composition associated with rot root of American ginseng

ABSTRACT American ginseng, a valuable medicinal and food plant, is threatened by rot root, which affects its yield and quality. However, limited studies have investigated the changes in soil microbial community and physiochemical properties between healthy and rot root American ginseng. Here, high-throughput sequencing and soil physiochemical properties were used to characterize these changes. The soil physiochemical properties showed significance differences between the soil of healthy and rot root, in which the pH, available potassium, available phosphorus, soil organic carbon and soil organic matter were significantly higher in healthy root soil. Besides, fungal α-diversity was also higher in healthy root soil than that in rot root. Importantly, the dominant fungal genera differed between soils of healthy and rot root of American ginseng, and LEfSe further indicated that six fungal genera (Devriesia, Chrysosporium, Dichotomopilus, Pseudeurotium, Acaulium and Scedosporium) were significantly enriched in the soil of healthy plants, whereas six fungal genera (Gibellulopsis, Fusarium, Plectosphaerella, Tetracladium, Gibberella and Ilyonectri) were significantly enriched in the soil of rot root, suggesting that an increase in the relative abundance of these pathogenic fungi (Fusarium, Plectosphaerella, and Ilyonectri) may be associated with ginseng rot root. Notably, this study is the first to report that an increase in the relative abundances of Gibellulopsis and Gibberella in the rot root soil of American ginseng may be associated with the onset of rot root symptoms in this plant. The functional profile prediction showed that the there was a significantly Pathotrophs increase in the rot root soil compared with healthy root soil and Saprotrophs were more abundant in the healthy root soil. Finally, correlation analyses revealed that soil cation exchange capacity was an important factors affecting the composition of rot root of American ginseng soil microbial communities. This study not only used a new approach to explore the new fungal associated with rot root in American ginseng but also excavated the major soil physiochemical properties affecting the microbiome diversity, providing foundation for developing biocontrol strategies against rot root.

Benzoic acid plays a part in rhizosphere microbial composition of peach seedlings grown in replanted soil

Soil micro-ecological imbalance is one of the critical factors associated with peach replanting issues. In an effort to understand the primary driving force in shaping soil microbial community, we analyzed soil nutrient, pH value, and autotoxin benzoic acid (BA) content, as well as rhizosphere microbial structure of peach seedlings grown in replanted soil (RS) and non-replanted soil (NS), both of which were collected from a same orchard. The results showed that depletion of soil nutrients, decreased soil pH, the accumulation of BA, and the deterioration of the soil microbial community were consistently detected in RS compared with NS, and led to the poor growth performance of peach seedlings. High-throughput sequencing analysis indicated that the soil microbial composition differed significantly between the NS and RS samples. Over time, the rhizosphere microbes of peach seedlings in RS and NS exhibited a similar trend of increasing bacterial richness and decreasing fungal richness. Interestingly, the NS had a high level of Bacillus and Ascobolus, whereas the RS enriched with Burkholderia and pathogenic Fusarium. Furthermore, canonical correspondence analysis revealed that soil nutrient and pH predominated the microbial composition of NS, whereas high level of soil BA played a crucial role in forming the microbial composition of RS. Altogether, this study provides a novel insight into better understanding of soil bacterial and fungal community structure in the RS, and aid in developing more effective means to alleviate the peach replant problem.

Colonization by dark septate endophytes improves the growth and rhizosphere soil microbiome of licorice plants under different water treatments

Dark septate endophytes (DSE) are facultative biotrophic ascomycetes that colonize plant roots. DSE may provide nutrients to their plant hosts and help them adapt to various abiotic and biotic stresses. However, their effects on the microbiome composition in plant rhizosphere need further clarification. Here, we conducted a pot experiment to establish whether the responses of licorice (Glycyrrhiza uralensis) to DSE (Acrocalymma vagum, Paraboeremia putaminum) inoculation under different water treatments are caused by changes in the rhizosphere microbiome. Rhizosphere microbiome compositions were measured by Illumina MiSeq sequencing of the 16S and ITS2 rRNA genes. The inoculation with DSE strains had a positive effect on plant growth of licorice depending on DSE species and water treatments. Subsequently, a total of 1278 fungal and 1583 bacterial operational taxonomic units (OUTs) were obtained at a 97% sequence similarity level. Ascomycota were the predominant fungi and Proteobacteria, Actinobacteria, Chloroflexi and Firmicutes were the predominant bacteria. DSE inoculation and water regime significantly influenced the microbiome composition. However, the effects of DSE on the fungal community were greater than those on the bacterial community. P. putaminum exerted a stronger impact on the licorice rhizosphere microbiome than A. vagum under drought stress. The observed changes in edaphic factors (water condition, soil organic matter, available nitrogen, available phosphorus, and available potassium) caused by DSE inoculation could be explained by the variations in microbiome composition. A network analysis indicated that DSE inoculation augmented the relative abundance of beneficial symbiotrophic fungi and growth-promoting bacteria but diminished the relative abundance of pathogens in the licorice rhizosphere. The present study showed that the licorice rhizosphere microbial community differed between the DSE-inoculated and uninoculated plants. DSE had a stronger influence on the fungal than on the bacterial rhizosphere community under drought stress. These give us the guidance to develop biofertilizers with DSE consortia to enhance the cultivation of medicinal plants by shaping soil microbial community structure and soil nutrient status in dryland agriculture.

Effects of vegetation type and soil horizon on soil bacterial and fungal communities in a dry–hot valley

Soil horizon and vegetation cover significantly impact the spatial patterns of soil fungal and bacterial communities. However, such impacts and their interactions are poorly characterized in dry–hot environments. Soil samples were collected from two soil horizons (humus and mineral) along a vegetation gradient (shrubland, grassland, and shrub–grass ecotone) in a dry-hot valley of Southwestern China to assess the effects of vegetation versus soil horizons on shaping soil microbial communities. We used denaturing gradient gel electrophoresis to estimate the microbial spatial pattern change across the vegetation gradients and clone libraries targeting small subunit rRNA genes to characterize the microbial community structures between distinct vegetation types and soil horizons. Bacterial DNA profile patterns were not significantly different across vegetation types but strongly correlated with soil horizons, with significant interaction effects. By contrast, fungi were remarkably different across vegetation types and soil horizons, without significant interactions effect. Distinct vegetation types did not necessarily harbor distinct bacterial or fungal community compositions. Rather, both community compositions were most strongly affected by the soil horizons. Together with these results, the soil vertical heterogeneity rather than vegetation changes is suggested to best predict shifts in soil microbial communities in this dry-hot valley area.