Search Results (17)

Microbes and enzymes play essential roles in soil and plant rhizosphere ecosystem functioning. However, fungicides and plant root secretions may impact the diversity and abundance of microbiota structure and enzymatic activities in the plant rhizosphere. In this study, we analyzed soil samples from the rhizosphere of four cannabinoid-rich hemp (Cannabis sativa) cultivars (Otto II, BaOx, Cherry Citrus, and Wife) subjected to three different treatments (natural infection, fungal inoculation, and fungicide treatment). DNA was extracted from the soil samples, 16S rDNA was sequenced, and data were analyzed for diversity and abundance among different fungicide treatments and hemp cultivars. Fungicide treatment significantly impacted the diversity and abundance of the hemp rhizosphere microbiota structure, and it substantially increased the abundance of the phyla Archaea and Rokubacteria. However, the abundances of the phyla Pseudomonadota and Gemmatimonadetes were substantially decreased in treatments with fungicides compared to those without fungicides in the four hemp cultivars. In addition, the diversity and abundance of the rhizosphere microbiota structure were influenced by hemp cultivars. The influence of Cherry Citrus on the diversity and abundance of the hemp rhizosphere microbiota structure was less compared to the other three hemp cultivars (Otto II, BaOx, and Wife). Moreover, fungicide treatment affected enzymatic activities in the hemp rhizosphere. The application of fungicides significantly decreased enzyme abundance in the rhizosphere of all four hemp cultivars. Enzymes such as dehydrogenase, dioxygenase, hydrolase, transferase, oxidase, carboxylase, and peptidase significantly decreased in all the four hemp rhizosphere treated with fungicides compared to those not treated. These enzymes may be involved in the function of metabolizing organic matter and degrading xenobiotics. The ecological significance of these findings lies in the recognition that fungicides impact enzymes, microbiota structure, and the overall ecosystem within the hemp rhizosphere. Full article

Forests are affected by a wide range of disturbances globally, resulting in the decline or death of large areas of them. There is a lack of comparative studies on how soil properties change in forests that die under the influence of disturbances, especially considering different levels of disturbance. For this study, we took Larix olgensis—a major plantation forest species in northeast China—as the research object, one in which a large outbreak of bark beetle led to large-scale forest death, and set up fixed sample plots characterized by different disturbance intensities. We investigated the responses of soil physicochemical properties and microbial community compositions to different disturbance intensities through the determination of soil nutrient indices and high-throughput sequencing. The results show that there were significant differences (p < 0.05) in the effects of different disturbance intensities on soil physicochemical properties, where the soil moisture content, total nitrogen, total carbon, and total phosphorus in the control group were significantly higher than those in the disturbed groups. The soil pH was highest under low-intensity disturbance and the soil total potassium content was highest under high-intensity disturbance. At different disturbance intensities, the highest soil moisture content was found in the high-intensity group. Proteobacteria, Actinobacteria, Verrucomicrobia, Acidobacteria, Candidatus_Rokubacteria, Chloroflexi, Gemmatimonadetes, and Thaumarchaeota were the dominant populations with higher abundances; meanwhile, the relative abundance of Bacteroidetes, Tenericutes, and a tentatively unclassified fungus differed significantly (p < 0.05) across disturbance intensities. Among the dominant microbial populations, Acidobacteria showed a significant negative correlation with soil pH and a significant positive correlation with total potassium content, Thaumarchaeota showed significant positive correlations with soil moisture content and total nitrogen content, and Firmicutes and Gemmatimonadetes showed significant negative correlations with total carbon content in the soil. Furthermore, soil total nitrogen content was the key factor driving changes in microbial communities. The results of this study provide a scientific basis for the study of the long-term effects of tree mortality caused by insect pests on soil microbial communities and their response mechanisms, which is of great theoretical value for the establishment of scientific and effective methods for woodland restoration. Full article

Increasing soil organic carbon (SOC) contents and reducing carbon dioxide (CO₂) emissions in paddy soil fields can result in positive impacts on climate change mitigation and soil quality. However, SOC accumulation and its microbial driving factors under enhanced fertilization strategies (e.g., organic matter application) are still unclear. Therefore, we investigated the effects of organic matter addition on SOC variations, CO₂ fluxes, and their relationships with soil bacterial compositions and functions through a 6-year fertilizer experiment in rice fields involving two fertilization types, namely chemical fertilizer (NPK) and chemical fertilizer combined with organic matter (NPK+OM). The results showed significantly higher and lower SOC contents (p < 0.05) in the 10–20 cm soil layer under the NPK+OM treatment before rice transplanting and after rice harvest, respectively, than those under the NPK treatment. The lower SOC contents after rice harvest might be due to the great nutrient consumption, resulting in higher rice yields in the NPK+OM than those in the NPK treatment by 6.68 to 32.35%. Compared with NPK, NPK+OM reduced the in-situ CO₂ fluxes by 38.70–118.59%. However, the ex-situ SOC mineralization rates were not affected by NPK+OM in the 0–10 and 10–20 cm soil layers. The 16S rRNA sequence indicated a significant increase in the abundance of non-singleton amplicon sequence variants (ASVs) in the NPK+OM treatment scenario compared to those in the NPK treatment scenario. The top three most important soil bacterial phylum influenced by NPK+OM were LCP-89, BRC1, and Rokubacteria in April, as well as Firmicutes, Nitrospinae, and BRC1 in July. Soil Actinobacteria was negatively correlated with the SOC contents in April and July. The results of the present study demonstrate the economic and ecological benefits of the organic matter addition in rice production, as well as the contribution of soil bacteria to SOC accumulation and CO₂ emission reduction. Full article

Introducing cover crops into maize rotation systems is widely practiced to increase crop productivity and achieve sustainable agricultural development, yet the potential for crop rotational diversity to contribute to environmental benefits in soils remains uncertain. Here, we investigated the effects of different crop rotation patterns on the physicochemical properties, enzyme activities, microbial biomass and microbial communities in soils from field experiments. Crop rotation patterns included (i) pure maize monoculture (CC), (ii) maize–garlic (CG), (iii) maize–rape (CR) and (iv) maize–annual ryegrass for one year (Cir1), two years (Cir2) and three years (Cir3). Our results showed that soil physicochemical properties varied in all rotation patterns, with higher total and available phosphorus concentrations in CG and CR and lower soil organic carbon and total nitrogen concentrations in the maize–ryegrass rotations compared to CC. Specifically, soil fertility was ranked as CG > Cir2 > CR > Cir3 > CC > Cir1. CG decreased enzyme activities but enhanced microbial biomass. Cir2 decreased carbon (C) and nitrogen (N) acquiring enzyme activities and soil microbial C and N concentrations, but increased phosphorus (P) acquiring enzyme activities and microbial biomass P concentrations compared to CC. Soil bacterial and fungal diversity (Shannon index) were lower in CG and Cir2 compared to CC, while the richness (Chao1 index) was lower in CG, CR, Cir1 and Cir2. Most maize rotations notably augmented the relative abundance of soil bacteria, including Chloroflexi, Gemmatimonadetes and Rokubacteria, while not necessarily decreasing the abundance of soil fungi like Basidiomycota, Mortierellomycota and Anthophyta. Redundancy analysis indicated that nitrate-N, ammonium-N and microbial biomass N concentrations had a large impact on soil bacterial communities, whereas nitrate-N and ammonium-N, available P, soil organic C and microbial biomass C concentrations had a greater effect on soil fungal communities. In conclusion, maize rotations with garlic, rape and ryegrass distinctly modify soil properties and microbial compositions. Thus, we advocate for garlic and annual ryegrass as maize cover crops and recommend a two-year rotation for perennial ryegrass in Southwest China. Full article

Plant secondary succession is a very effective approach for the rejuvenation of degraded ecosystems. In order to comprehend alterations and driving mechanisms of soil bacterial communities under secondary succession of old-field and reveal their subsequent impacts on the decomposition and accumulation of soil organic carbon (SOC) and nitrogen (SON), we investigated changes in soil bacterial communities following ~160 years of old-field succession on the Loess Plateau of China through analyses of quantitative polymerase chain reaction (qPCR) and Illumina MiSeq DNA sequencing of 16S rRNA genes. Our results revealed that subsequent to secondary succession of old-field, soil bacterial abundance progressively increased, while bacterial richness and diversity significantly decreased. Principal component analysis and Bray–Curtis similarity index showed that bacterial community composition gradually shifted following old-field succession. Specifically, the relative abundances of Proteobacteria, Rokubacteria, and Verrucomicrobia progressively increased, while Actinobacteria and Firmicutes slightly decreased following old-field succession. The most enriched of Proteobacteria (e.g., Rhizobiales, Xanthobacteraceae, Gammaproteobacteria, Bradyrhizobium, Rhizobiaceae, and Mesorhizobiur) were found in a climax forest, while Chloroflexi and Gemmatimonadetes had the lowest relative abundances. Further, the most enriched members of Actinobacteria, including Geodermatophilaceae, Frankiales, Blastococcus, Micrococcales, Micrococcacea, Propionibacteriales, Nocardioidaceae, Nocardioide, and Streptomycetaceae, were exhibited in the farmland stage. Our results suggested that secondary succession of old-field greatly modified soil bacterial communities via the transformation of soil nutrients levels, altering plant biomass and soil physiochemical properties. Soil bacterial community composition was transformed from oligotrophic groups to copiotrophic Proteobacteria following old-field succession, which may promote SOC and SON accumulation through increasing the utilization of labile organic carbon (C) and nitrogen (N), while decreasing decomposition of recalcitrant organic C and N from the early- to late-successional stages. Full article

Soil microorganisms play an important role in determining nutrient cycling. The integration of fish into rice fields can influence the diversity and structural composition of soil microbial communities. However, regarding the rice–fish co-culture (RF) farming system in Thailand, the study of the diversity and composition of soil microbes is still limited. Here, we aim to compare the microbial diversity, community composition, and functional structure of the bacterial communities between RF and rice monoculture (MC) farming systems and identify the environmental factors shaping bacterial community composition. Bacterial taxonomy was observed using 16s rRNA gene amplicon sequencing, and the functional structures of the bacterial communities were predicted based on their taxonomy and sequences. The results showed that soil organic carbon, total nitrogen (TN), organic matter, available phosphorous, and clay content were significantly higher in RF than in MC. The most dominant taxa across both paddy rice fields belonged to Actinobacteria, Chloroflexi, Proteobacteria, Acidobacteria, and Planctomycetes. The taxa Nitrosporae, Rokubacteria, GAL15, and Elusimicrobia were significantly different between both rice fields. At the genus level, Bacillus, Anaeromyxobacter, and HSB OF53-F07 were the predominant genera in both rice fields. The most abundant genus in MC was Anaeromyxobacter, whereas RF belonged to Bacillus. The community composition in MC was positively correlated with magnesium and sand content, while in RF was positively correlated with pH, TN, and clay content. Nitrogen fixation, aromatic compound degradation, and hydrocarbon degradation were more abundant in RF, while cellulolysis, nitrification, ureolysis, and phototrophy functional groups were more abundant in MC. The enzymes involved in paddy soil ecosystems included phosphatase, β-glucosidase, cellulase, and urease. These results provide novel insights into integrated fish in the paddy field as an efficient agricultural development strategy for enhancing soil microorganisms that increase soil fertility. Full article

This research aimed to reveal the response characteristics of soil microbial community structure to different degrees of tourism disturbance. To explore the soil microbial community structure’s response mechanism, we set up continuous plots with different interference intensities: high disturbance, middle disturbance, and the control area. We collected 0–10 cm topsoil in all plots and used Illumina MiSeq high-throughput sequencing method to obtain and analyze the response characteristics of soil microbial community composition and structure under different tourism disturbances. These results were then combined with alpha diversity and environmental factors to explore the microbial response mechanism. In the tested soil, Acidobacteria, Chlorocurve, and Proteobacteria were the main bacterial phyla, while Basidiomycota and Ascomycota were the main fungal phyla. Based on the phylum, the relative abundance of the microbial community between the interference groups was compared using a significance test, with significant differences found between the interference groups in the phyla Chloroflexus, GAL15, Rokubacteria, and Blastomonas (p < 0.05). The relative abundance of the dominant phyla in the fungal community was significantly different among the groups (p < 0.05). A principal component analysis of the soil microbial community structure suggested that the soil microbial community structure was significantly different for different interference levels. Full article

Rokubacteria is a phylogenetic clade of as-yet-uncultivated prokaryotes, which are detected in diverse terrestrial habitats and are commonly addressed as members of the rare biosphere. This clade was originally described as a candidate phylum; however, based on the results of comparative genome analysis, was later defined as the order-level lineage, Rokubacteriales, within the phylum Methylomirabilota. The physiology and lifestyles of these bacteria are poorly understood. A dataset of 16S rRNA gene reads retrieved from four boreal raised bogs and six eutrophic fens was examined for the presence of the Rokubacteriales; the latter were detected exclusively in fens. Their relative abundance varied between 0.2 and 4% of all bacteria and was positively correlated with pH, total nitrogen content, and availability of Ca and Mg. To test an earlier published hypothesis regarding the presence of methanotrophic capabilities in Rokubacteria, peat samples were incubated with 10% methane for four weeks. No response to methane availability was detected for the Rokubacteriales, while clear a increase in relative abundance was observed for the conventional Methylococcales methanotrophs. The search for methane monooxygenase encoding genes in 60 currently available Rokubacteriales metagenomes yielded negative results, although copper-containing monooxygenases were encoded by some members of this order. This study suggests that peat-inhabiting Rokubacteriales are neutrophilic non-methanotrophic bacteria that colonize nitrogen-rich wetlands. Full article

The present study investigated the potential changes in the structure of bacterial communities and their functional profiles in the rhizospheres of Panax notoginseng cultivated under field (CK) and pine forest conditions (T). The rhizospheres of two-year-old P. notoginseng plants were used to extract DNA for metagenomic sequencing and metabolites for metabolomic profiling. The results revealed a higher root weight (p < 0.05) in plants grown under the forest than CK. The rhizospheric bacterial community comprised mainly three dominant phyla including Acidobacteria, Proteobacteria, and Candidatus rokubacteria which accounted for 75% of the total microbial population. Among them, Acidobacteria was the most abundant bacterial taxa, accounting for 42.4% and 40.4% of the total populations in CK and T, respectively. Relative abundances of bacterial genera revealed that Bradyrhizobium, Candidatus koribacter and Edaphobacter, were the dominant genera in both groups. Comparatively, a higher Proteobacteria to Acidobacteria ratio was observed in forest rhizospheres than in field conditions. Candidatus Rokubacteria and Candidatus nitrostelea were identified as biomarker taxa in forest rhizospheres, while the same could be said for taxa belonging to betaproteobacteria and gammaproteobacteria, Burkholderiales and Verrucomicrobia for field rhizospheres. No differential metabolite contents were observed between the two rhizosphere groups, indicating no adverse effects of P. notoginseng cultivation on the soil quality under forest plantation. Full article

The rapidly emerging fertilizer rapeseed used as green manure has wide applications for use. However, there have been few studies on its decomposition and effects on soil nutrients and microorganisms after its decay. In this study, 12 rapeseed lines to be screened were decomposed through a randomized block field design with two green-manure-specific varieties as the controls. The contents of nitrogen, phosphorus, and potassium from the plants, soil nutrients, and microbial changes after degradation were measured. There were substantial differences in the rates of decomposition and cumulative release of nutrients among the different lines after 30 days of rolling. The contents of phosphorus and potassium in the soil were 1.23–2.03 and 3.93–6.32 times those before decomposition, respectively. In addition, there was a significant difference in the relative content of soil microorganisms at the phylum level after the decomposition of different species of rapeseeds. Most of the top 20 bacterial groups significantly correlated with the characteristics of plant decomposition and soil nutrient content, including Proteobacteria, Actinomycetes, Armatimonadetes, Rokubacteria, and Planctomycetes. A principal component analysis showed that the soil microorganisms and nutrients are the leading factors that enable the evaluation of the decomposing characteristics of green manure rapeseed. Numbers 5 (purple leaf mustard) and 8 (Xiafang self-seeding) were more effective than two controls, which can be used as excellent types of germplasm to promote the breeding of green manure rapeseed. Full article

Soil microbial communities play an important role in maintaining the ecosystem during forest secondary succession. However, the underlying mechanisms that drive change in soil microbial community structures during secondary succession remain poorly defined in species-rich subtropical coniferous forests. In this study, Illumina high-throughput sequencing was used to analyze the variations in soil microbial community structures during forest secondary succession in subtropical coniferous forests in China. The role of soil properties and plant diversity in affecting soil bacterial and fungal communities was determined using random forest and structural equation models. Highly variable soil microbial diversity was observed in different stages of secondary succession. Bacterial community diversity rose from early to middle and late successional stages, whereas fungal community diversity increased from early to middle successional stages and then declined in the late stage. The relative abundance of Acidobacteria, Gemmatimonadetes, Eremiobacterota(WPS-2), Rokubacteria, and Mortierellomycota increased during succession, whereas the relative abundance of Ascomycota and Mucoromycota decreased. The community composition and diversity of the soil microbial community were remarkably influenced by plant diversity and soil properties. Notably, tree species richness (TSR) displayed a significant and direct correlation to the composition and diversity of both bacterial and fungal communities. The carbon-to-nitrogen (C:N) ratio had a direct impact on the bacterial community composition and diversity, and pH had a marked impact on the fungal community composition and diversity. Furthermore, succession stage and plant diversity indirectly impacted the composition and diversity of soil bacterial and fungal communities via soil properties. Overall, it can be concluded that soil intrinsic properties and plant diversity might jointly drive the changes in soil microbial community composition and diversity during secondary succession of subtropical coniferous forests. Full article

In the present study 12 water samples of five sampling sites (Tatabánya, Dandár, Szentendre, Szent Flórián and Ciprián groundwaters) known as nutrient-depleted aquatic environments were studied using amplicon sequencing (NGS) and cultivation techniques. Diversity indices and cell counts were determined to assess the species richness in relation to the cell counts within the samples, and the oligocarbophile growth capability of the isolated bacteria was tested in microtiter plates. Altogether, 55 bacterial phyla were identified from the samples by amplicon sequencing. The microbial communities of the different sampling times of the same sites did not differ significantly. Patescibacteria and Proteobacteria were present in all samples. Ciprián sample was dominated by Bacteroidetes, while in Dandár sample a high ratio of Chloroflexi was detected. Rokubacteria and WOR-1 dominated Szent Flórián sample and Tatabánya had a high number of Epsilonbacteraeota. Nine archaeal phyla were also detected; the samples were characterized by the presence of unclassified archaea and Nanoarchaeota, among them Woesearchaeia, as the most dominant. Crenarchaeota and Altiarchaeota were detected in high ratios in Dandár water samples. Among Thaumarchaeota the family Nitrosopumilaceae, and orders of Nitrosotaleales and Nitrososphaerales appeared in Szent Flórián and Tatabánya samples. Key organisms of the different biogeochemical cycles were discovered in these nutrient-depleted environments: methanogenic archaea, methanotrophic bacteria, ammonia oxidizer, nitrate reducers, diazotrophs, sulfate reducers, and sulfur oxidizer. Diversity indices and cell counts of the samples show negative correlation in case of bacteria and positive in case of archaea in Ciprián sample. The high diversity indices in Szentendre samples are connected to low cell counts, most probably due to the vulnerability of the groundwaters to the external environment factors which lead to the infiltration of soil microbes and contaminants to the water. The isolated bacteria were affiliated into four phyla, most of them belonging to Proteobacteria (59%) followed by Actinobacteria (21%), Firmicutes (17%) and Verrucomicrobia (1%). The members of the facultative chemolithotrophic genera of Sphingobium, Sphingomonas, Sphingopyxis were characterizing only Szentendre, Szent Flórián and Tatabánya samples. Only 10% of the isolated species showed an obligate oligocarbophile character. From the samples, a high number of novel bacterial taxa were cultivated. As a conclusion, our results confirmed the predominance of unclassified and unknown taxa in subsurface water, pointing to the importance and necessity of further studies to characterize these microbial populations. Full article

In order to explore the relationship between microbial diversity and metabolites in the litter layer of northern temperate forests, the microbial community structure and metabolite species in the litter layer of an original Korean pine forest and Korean pine plantation of northern temperate climate were determined on the basis of high-throughput sequencing and metabonomic techniques. The results showed that there were 698 bacterial genera and 363 fungal genera in the litter samples in the original Korean pine forest. Linear discriminant effect size (LEfSe) analysis showed that there were 35 indicator bacterial species and 19 indicator fungal species. In the litter samples of the Korean pine plantation, there were 622 bacterial genera and 343 fungal genera. Additionally, LEfSe analysis showed that there were 18 indicator bacterial species and 5 indicator fungal species. The litter of the two forest types contained 285 kinds of organic compounds, among which 16 different metabolites were screened, including 6 kinds of organic acids, 5 kinds of amino acids, 2 kinds of sugars, 2 kinds of sugar alcohols, and 1 kind of lipid. Latescibacteria, Rokubacteria, and Olpidiomycota are unique to the original Korean pine forest. They can catalyze the degradation rate of litter and decompose cellulose and chitin, respectively. Subgroup 6 was abundant in the lower litter layer. Subgroup 6 can grow with carbon compounds as substrate. It was clear that the microbial diversity of the litter layer in the original Korean pine forest was higher than that of the Korean pine plantation. Moreover, whether original forest or plantation forest, the lower-litter layer microbial diversity was higher than that in the middle-litter layer. CCA showed that the main metabolites were related to Chitinophagaceae_uncultured were saccharopine. The main metabolites associated with Mortierella and Polyscytalum were myo-inositol. At the same time, analysis of the difference between the litter layer of the original Korean pine forest and the Korean pine plantation also provides a theoretical basis for their participation in the element cycles of forest ecosystems. Full article

Basal stem rot (BSR), caused by Ganoderma boninense, is the most devastating oil palm disease in South East Asia, costing US$500 million annually. Various soil physicochemical parameters have been associated with an increase in BSR incidences. However, very little attention has been directed to understanding the relationship between soil microbiome and BSR incidence in oil palm fields. The prokaryotic and eukaryotic microbial diversities of two coastal soils, Blenheim soil (Typic Quartzipsamment—calcareous shell deposits, light texture) with low disease incidence (1.9%) and Bernam soil (Typic Endoaquept—non-acid sulfate) with high disease incidence (33.1%), were determined using the 16S (V3–V4 region) and 18S (V9 region) rRNA amplicon sequencing. Soil physicochemical properties (pH, electrical conductivity, soil organic matter, nitrogen, phosphorus, cation exchange capacity, exchangeable cations, micronutrients, and soil physical parameters) were also analyzed for the two coastal soils. Results revealed that Blenheim soil comprises higher prokaryotic and eukaryotic diversities, accompanied by higher pH and calcium content. Blenheim soil was observed to have a higher relative abundance of bacterial taxa associated with disease suppression such as Calditrichaeota, Zixibacteria, GAL15, Omnitrophicaeota, Rokubacteria, AKYG587 (Planctomycetes), JdFR-76 (Calditrichaeota), and Rubrobacter (Actinobacteria). In contrast, Bernam soil had a higher proportion of other bacterial taxa, Chloroflexi and Acidothermus (Actinobacteria). Cercomonas (Cercozoa) and Calcarisporiella (Ascomycota) were eukaryotes that are abundant in Blenheim soil, while Uronema (Ciliophora) and mammals were present in higher abundance in Bernam soil. Some of the bacterial taxa have been reported previously in disease-suppressive and -conducive soils as potential disease-suppressive or disease-inducible bacteria. Furthermore, Cercomonas was reported previously as potential bacterivorous flagellates involved in the selection of highly toxic biocontrol bacteria, which might contribute to disease suppression indirectly. The results from this study may provide valuable information related to soil microbial community structures and their association with soil characteristics and soil susceptibility to Ganoderma. Full article

Fertilizer application to arable soils could be effective for soil nutrients. However, there are many negative effects in croplands with long-term chemical fertilizer application. Whether eco-friendly fertilizer addition could enhance soil quality and soil microbial activity has been investigated before; however, how top- and rhizosphere soil bacterial communities respond to their short-term effects is not well known. Here, we used Illumina MiSeq sequencing to determine the changes of bacterial community structure in both topsoil and rhizoshpere after one month of the addition of three different eco-friendly fertilizers—biochar (B), microbial fertilizer (MF), fertilizer synergist (FS) and selected soil base fertilizer (CK) as a control, in an irrigated agroecosystem of cabbage crop (Brassica oleracea L. var. capitata L.). The results show that three different eco-friendly fertilizers significantly enhanced cabbage growth. The Shannon and Ace indexes of the bacterial community significantly decreased under the FS treatment in both soils, but the total abundance of bacteria was maximal under the FS treatment in the topsoil and the MF treatment in the rhizosphere. The addition of the three fertilizers led to significant differences in the relative abundance of bacteria community at the phylum level, such as Proteobacteria, Acidobacteria, Rokubacteria and Planctomycetes in the topsoil, and Chloroflexi, Actinobacteria, Firmicutes and Rokubacteria in the rhizosphere. The same phylum showed the inconsistent changes under different fertilizer treatments in both topsoil and rhizosphere. The dominant genera, i.e., Nitrosospira and Massilia in the topsoil, and Flavobacterium, Nitrosospira and Pseudomonas in the rhizosphere, were much higher under the FS treatment than others. Redundancy analysis showed that total nitrogen and available phosphorus were the key factors that shaped the bacterial community in this ecosystem. These results highlighted that the short-term addition of eco-friendly fertilizer had an improvement effect on the quality of both topsoil and rhizosphere in croplands with long-term chemical fertilizer application. Full article