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Soil salinity, poor soil structure and macronutrient deficiencies are three important limitations responsible for poor crop yields in coastal saline soil. Therefore, the objective was to investigate the integrated effects of humic acid fertilizer and vermicompost on maize growth and nutrient uptake in coastal saline soil. The experiment included three treatments: (1) control without humic acid fertilizer and vermicompost (CK); (2) treatment with humic acid fertilizer (H); (3) treatment with vermicompost (V). Soil salinity, aggregates, nutrient availability and uptake, the soil microbial community from next-generation high-throughput sequencing, maize biomass and yield were determined in this study. The results showed that humic acid fertilizer and vermicompost increased soil macroaggregates by 77.59–125.58% and 35.02–91.02%, respectively, which could efficiently decrease soil salinity. Proteobacteria , Actinobacteria and Acidobacteria were the dominant bacterial phyla, and Ascomycota was the dominant fungal phylum in this coastal saline soil. The humic acid fertilizer and vermicompost could affect the fungal community structure in the six-leaf stage (6S) and the bacterial community structure in the harvest stage (HS), which consequently improved soil nutrient availability and maize nutrient uptake. The humic acid fertilizer and vermicompost could enhance nitrogen (N) nutrient absorption of the maize plant in the vegetative growth period (6S) and the phosphorus (P) and potassium (K) nutrient absorption in the reproductive growth period (tasseling stage (TS) and harvest stage (HS)) of maize, which played an important role in increasing the maize yield in coastal saline soil. Therefore, the application of humic acid fertilizer and vermicompost can be integrated as a practice for improving coastal saline soil. • Vermicompost (V) and humic acid fertilizer (H) increased macroaggregates in saline soil. • Soil bacterial and fungal community were improved by V and H in coastal saline area. • Impact of V and H on soil nutrient availability by regulating microbial community. • Integrated amelioration of saline soil by V and H could improve maize nutrient uptake. [ABSTRACT FROM AUTHOR]

Biochar (BC) addition is widely used in agriculture to condition soils. However, the effects of BC addition on soil microbial community diversity and composition in karstic regions are unclear, especially after long-term application. To address this knowledge-gap, a field experiment was established to examine changes in soil physicochemical properties and microbial communities following six years of BC amendment. BC was applied to calcareous soils in a karstic region of southwestern China at four levels (w/w): 0%, 1.0%, 5.0%, and 10%. Bacterial community composition was then investigated in both the rhizosphere and bulk soils by 16S rRNA gene sequencing on the Illumina MiSeq Platform. BC addition increased soil pH, total carbon (TC), total nitrogen (TN), and total hydrogen (TH) contents in the rhizosphere and bulk soils. In addition, BC amendment was associated with changes in soil bacterial community compositions and diversities, especially at higher BC application levels. The relative abundances of Gemmatimonadetes increased in rhizosphere soils with increasing BC amendment, while those of the Bacteroidetes , Firmicutes , and Cyanobacteria decreased. The relative abundances of Proteobacteria and Chloroflexi increased in bulk soils with increasing BC application levels, while those of the Bacteroidetes and Verrucomicrobia decreased. Canonical correspondence analysis indicated that bacterial community composition was related to soil characteristics including pH, TC, TN, and TH contents in both rhizosphere and bulk soils. Importantly, variations in these soil parameters were closely associated with BC application rates. These results indicate that long-term BC application significantly impacts soil bacterial community characteristics in karstic regions via modulation of soil physiochemical properties. • Six years biochar addition altered rhizosphere and bulk soil properties. • Biochar changed the diversity and composition of soil bacterial communities. • Abundance of rhizosphere Gemmatimonadetes was increased by biochar addition. • Biochar increased the abundance of Proteobacteria and Chloroflexi in the bulk soil. • Long-term biochar application significantly affects the bacterial community. [ABSTRACT FROM AUTHOR]

Abstract Despite hostile climate in the Kuwait desert, perennial vegetation patches persist but are affected by anthropogenic pressures and need to be conserved or restored to their original state. Our goal was to assess the bacterial community composition and structure in both rhizospheric and bulk (non-rhizospheric) soil samples from protected and unprotected sites of four dominant terrestrial vegetation types in the Kuwaiti desert. The bacterial composition and structure was investigated by Illumina MiSeq sequencing of the 16S rRNA gene. Compared to other desert soils, a relatively high diversity of bacteria was detected in this study. Bacterial sequences were affiliated with 13 phyla, most abundant of which revealed were Actinobacteria, Proteobacteria, Planctomycetes, Acidobacteria, Bacteroidetes and Firmicutes. The bacterial structure also commonly identified as Chloroflexi, Gemmatimonadetes, Saccharibacteria, Chlamydiae, Armantimonadetes, Deinococcus-Thermus and Verrucomicrobia. The analyses revealed that bacterial communities that were dominated by members of the phyla Actinobacteria and Proteobacteria found with higher diversity indices in rhizospheric soils. In addition, samples with high diversity indices as measured by the Chao1 and invsimpson indices were from rhizospheric soils, with some exceptions. The beta diversity indices of samples/habitats assessed via cluster analysis indicated noticeable differences in the bacterial community compositions of the sites. This study demonstrates the effect of protected and unprotected areas with vegetation covers and anthropogenic disturbances on Kuwait desert soil bacterial communities. This study provides the first insights into bacterial communities associated with protected and unprotected areas across the Kuwait desert. This information is essential for evaluating how natural and anthropogenic drivers affect plant-bacteria-soil systems in the Kuwait desert. Highlights • The study provides the first glimpse of bacterial communities from Kuwait soils. • Bacterial communities affected by site vegetation community and soil protection types. • The study detected thirteen bacterial phyla and a group of unclassified bacteria. • The phyla Actinobacteria and Proteobacteria are the most dominated members observed. [ABSTRACT FROM AUTHOR]

Highlights • Farm manure can increase soil enzymatic activities. • Farm manure can enhance the rhizospheric bacterial abundance and Shannon index. • Bacterial communities correlated with environmental factors and enzymatic activities. • Incorporation of organic manure can improve saline-alkaline soils fertility. Abstract Soil salinization is one of the key factors that threatens plant existence worldwide and is a major challenge to sustain crop production and soil quality. However, there has been limited research on the responses of microbial communities and enzyme activities under soil amendments application in saline alkaline soils. Here, we explored the response of microbial communities and enzyme activities to soil amendments based on 7-year field experiment. The five treatments included FA, amended with farm manure; DE, amended with desulfurization gypsum; SA, amended with sandy soil; M, amended with a mixture of FA, DE and SA; and CK, non-amended control. Relative to the CK treatment, the four amendments, particularly FA, DE and M, significantly decreased the soil pH. Enzyme activities (catalase, urease, alkaline phosphatase and cellulase) were increased in the FA, DE and M treatments, while no difference was observed between SA and CK, except in cellulase. A total of 439,575 effective sequences after filtering out of 1,017,148 raw reads were obtained resulting in 9096 OTUs. Six bacterial phyla of the highest relative abundance were detected including Proteobacteria , Chloroflexi , Bacteroidetes , Actinobacteria , Acidobacteria and Firmicutes across all soil samples (accounting for >85% of the reads). The bacterial community richness was increased in the FA, DE and M treatments, whereas it showed a similar pattern between the CK and SA treatments. Bacterial community diversity was remarkably higher in the M, FA and DE treatments compared to that of CK, while it was reduced in SA. There was a higher similarity in the bacterial communities among DE, FA and M, as well as between CK and SA. Our findings showed that organic manure is a better application approach for the restoration of saline-alkaline soil based on improving the bacterial community and enzyme activities. [ABSTRACT FROM AUTHOR]

Soil microbial communities are important for ecological restoration and succession on mine tailings. In the present study, we performed Illumina sequencing to investigate the effects of long term Lespedeza bicolor revegetation on bacterial diversity and community structure in mine tailings under subtropical and moist climatic conditions. Microbial diversity indices (Shannon, OTU number and coverage estimator) of the revegetated soils were higher than that of the control, and increased over sampling period compared to the decreased pattern in the control. Species within known acid tolerant and nutrient regulated genera dominated both revegetated tailings and the control, and exhibited more abundant in the revegetated tailings. At the phylum level, percentage of the Proteobacteria and Actinobacteria were remarkedly higher in revegetated tailings than that in the control, while Chloroflexi performed reversely. Overall, this study found the positive role of L. bicolor revegetation in bacterial diversity development in the acidic mine tailings. Furthermore, the 30-year L. bicolor revegetation made the microbial community structure more homogenizable as a decrease of dissimilarity in tailings was identified over sampling times. Redundancy analysis at the OTU level indicated that Olsen-P and pH were the main regulators of microbial composition, suggesting that soil P and pH are determinant for ecological restoration and microbial community development in acidic mine tailings. [ABSTRACT FROM AUTHOR]

Soil bacteria play a vital role in terrestrial ecosystems and are very sensitive to changes in the environment. Land subsidence due to underground coal mining could affect soil properties, but the extent of this effect on the soil bacterial community remains unclear. Here, we investigated the effect of land subsidence on soil bacterial communities and their response to changes in the soil environment in a control area and a land subsidence area in the West China Aeolian Sand Area. The results showed that electrical conductivity (EC), total carbon, (TC), total nitrogen (TN), available potassium (AK) and soil organic matter (SOM) at a soil depth of 20 cm were significantly decreased in the land subsidence area compared to the unexploited area, and Illumina MiSeq sequencing data revealed that the bacterial community at a soil depth of 0–180 cm was dominated by Pseudomonas, Gp4, Gp6, Sphingomonas , Gemmatimonas, Arthrobacter , Aciditerrimonas and Gaiella . Land subsidence decreased soil microbial richness and diversity. In addition, there was a significant decrease in the relative abundance of some core genera in the topsoil, such as Sphingomonas, Nocardioides and Saccharibacteria_genera_incertae_sedis , indicating that the dominant bacteria had strong anti-interference abilities and played important roles in the nutrient-poor soils of the mining area. Redundancy analysis (RDA) showed that the main factors driving the changes in the bacterial community structure were EC, water content (WC) and soil depth. The vertical leakage of water and nutrients was caused by subsidence and cracks in the ground, leading to decreased soil microbial richness and diversity. These results suggested that the soil nutrients and soil microbial community has yet to recover by self-healing after two years of land subsidence; thus, artificial restoration might be required. [ABSTRACT FROM AUTHOR]

Poplar plantations have been established around the world to provide timber or fuelwood and to control erosion in degraded areas. The objective of this study was to investigate the effects of converting croplands to long-term hybrid poplar ( Populus × euramericana cv. I-72) plantations for 10, 15 and 20 years on soil bacterial and fungal communities and on their relationships with soil organic carbon (SOC) mineralization. Overall, the results indicated that the long-term hybrid poplar plantations increased soil pH, SOC, total N and moisture contents and decreased dissolved organic carbon (DOC), NH 4 + and NO 3 − contents compared to that on the cropland. There were lower cumulative amounts of CO 2 respired and SOC mineralization rates in the hybrid poplar plantation soils compared to that of the cropland. The hybrid poplar plantation with 20 years caused a greater fungal internal transcribed spacer (ITS) gene copy number and a lower bacterial 16S rRNA gene copy number and dehydrogenase and β-glucosidase activities compared to that in the cropland soils. As indicated by Illumina MiSeq sequencing, the establishment of hybrid poplar plantations harbored distinct soil bacterial and fungal communities, which were strongly correlated with specific soil properties. We further found that the SOC mineralization rate was positively correlated to the bacterial abundance and the relative abundances of Actinobacteria and Bacteroidetes, whereas negatively correlated to the fungal abundance. This study suggested that the long-term hybrid poplar plantation reduced SOC mineralization, causing changes in habitats that favor fungal community growth and shifts in bacterial community composition to more facultative and/or obligate anaerobes and less microbes that are capable of decomposing recalcitrant carbon, which may help enhance SOC accumulation in soil and mitigate climate change. [ABSTRACT FROM AUTHOR]

Fusarium wilt in cucumber results from continuous cropping and is a serious soil-borne fungal disease that threatens cucumber production around the world. The application of a novel fumigation agent based on ammonium bicarbonate to the soil as a strategy for controlling Fusarium wilt and its effects on soil microflora was investigated in a field with serious disease incidence in this study. Overall, the results showed that fumigation effectively controlled cucumber Fusarium wilt disease and significantly increased the total and mean cucumber fruit weight. Real-Time PCR results showed that the total bacterial and fungal numbers in the treatment (LAB) significantly decreased after fumigation and that significantly fewer fungi were observed after harvest (LABOF). The next-generation sequencing of the 16S rRNA and internal transcribed spacer (ITS) genes using MiSeq platform showed that the soil bacterial and fungal community structures in the fumigation treatment were significantly different from the control without fumigation regardless after fumigation or harvest. Compared to the control, higher abundances of Gemmatimonadetes , Verrucomicrobia and Zygomycota , and lower abundance of Ascomycota were observed in the fumigated soils after fumigation and harvest. Furthermore, the abundances of Mortierella and Gp1 were significantly higher. Most importantly, the abundance of Fusarium , which includes the pathogen potentially responsible for cucumber Fusarium wilt disease, was significantly lower in the fumigated soils after harvest. Redundancy analysis showed that the fumigated soils were dominated by Ohtaekwangia , Gp6 , and Gp4 , which were related to the soil total nitrogen (TN), ammonium nitrogen (NH 4 –N) and nitrate nitrogen (NO 3 –N) contents. In addition, Penicillium and Pseudaleuria fungi were dominant in the treatment and control, and the control was dominated by Fusarium . In conclusion, the observed disease suppression due to the novel ecological soil fumigation strategy may be attributed to general suppression resulting from altered soil properties, such as higher soil NH 4 –N, NO 3 –N and TON contents, and the alteration of the disturbed soil microflora in a cucumber monoculture system. [ABSTRACT FROM AUTHOR]

A better understanding of fungal community composition and diversity and their dynamic patterns driving forces under different successional forest will contribute to the maintenance and preservation of natural ecosystems. The aim of this study was to compare soil fungal communities and soil microbial activities among three successional temperature Quercus mongolica forest stands (20, 30 and 40 years old) in Northeast China to investigate the maintenance mechanism of fungal diversity and provide the basic theory basis for the functions of fungus in nutrient cycle. Based on the sequences of rRNA with Illumina Miseq, 508 different fungal phylotypes were identified and grouped into Ascomycota, Basidiomycota, Chytridiomycota, Glomeromycota and Zygomycota. Russula was the dominant genus in these three successional stages of Q. mongolica forests. Fungal communities differed across these three stands and the fungal diversity and richness was significantly lower in the 30 years stand than in the 20 years and 40 years stands. Meanwhile, a total of 93 ectomycorrhizal fungus (EMF) phylotypes were observed and the EMF diversity was similar across the three successional stands. The activity of soil urease increased with forest development ages and cellulase activity first decreased and then increased from 20 years stand to 40 years stand. Both nitrogen mineralization and nitrification were the lowest in September in the 30 years stand and reached the maximum value in August. Both soil net N mineralization and N nitrification were the lowest in 40 years forest stage in October. The Redundance analysis showed that fungal community was strongly affected by stand ages and environmental factors and the nine plots in the three successional forest stands were significantly clustered across successional forest stands. The dominant Lachnum in Ascomycota positively, while the dominant Russula in Basidiomycota negatively, correlated with total P, available P, Soil organic carbon (SOC), NO 3 − -N, soil moisture or pH. Our results could provide insights into relationships between taxonomic fungal diversity and soil chemical properties along different stages of forest. The findings also imply the functions of soil fungi in sustaining soil biogeochemical cycling were driven by the secondary succession in temperate ecosystems. [ABSTRACT FROM AUTHOR]

To protect the limited forest resources, forestry soils for Panax ginseng cultivation is gradually replaced by farmland, but the extent to which soil type and cultivation age affects soil microbiome in the ginseng rhizosphere is not well known. By using Illumina MiSeq sequencing of the 16S and ITS2 rRNA genes, we tested the effects of two soil types (forest, and farmland) and three cultivation ages (four, five, and six years) on soil microbiome in the ginseng rhizosphere from nine locations in Jilin Province, China. Relative abundance and diversity of rhizosphere microbes differed among soil samples, and Ascomycota, Acidobacteria, Proteobacteria, Actinobacteria and Chloroflexi were the dominant phyla. Soil type positively influenced fungal community, while cultivation age had more positive effect on bacterial than on fungal community. Richness and diversity of fungal community was greater in forest than in farmland soils, while these parameters for bacterial communities were lower in forest than in farmland soils. A deterioration of soil fertility and continuous cultivation increased the proportion of pathogens such as Fusarium , Cylindrocarpon , but reduced the proportion of beneficial and neutral fungi and bacteria. The observed changes in soil properties (pH, organic matter, total nitrogen, total phosphorus, and total potassium) caused by soil type and cultivation age could be explained by the variations in the microbiome. A network analysis indicated that farmland and increasing cultivation age augmented the proportion of pathogens but diminished the proportion of beneficial and neutral fungi and bacteria. The present study showed that the rhizosphere microbiome differed between forest and farmland soils. Cultivation age had a stronger influence on bacterial than on fungal community. These findings suggested that soil microbiome dynamics may be a bioindicator of soil quality, and defining the microbial players involved in various cultivation ages will promote the selection and adoption of favorable ginseng cultivation lands. [ABSTRACT FROM AUTHOR]

The forest quality of Casuarina equisetifolia has reduced dramatically due to soil sickness under continuous monoculture. The effect of microbes on the growth of C. equisetifolia plants has been extensively investigated. In this study, quantitative PCR assays and Illumina MiSeq sequencing of targeted nirK and nosZ genes were carried out to identify the variations in abundance in the soil and community structure of denitrifying bacteria under the long-term consecutive monoculture of C. equisetifolia. The principal component analysis illustrated that the denitrifying bacterial community structure was obviously different among the soils in the treatments of no C. equisetifolia cultivation (CK), the first continuous plantation (FCP), the second continuous plantation (SCP), and the third continuous plantation (TCP). Taxonomic analysis demonstrated that in both the nirK and nosZ gene-containing denitrifying bacterial communities, Proteobacteria increased significantly in C. equisetifolia monocultures. Furthermore, the genera Bosea , Sinorhizobium , Streptomyces , Azospirillum , Mesorhizobium , Thiobacillus , Ochrobactrum , and Rhodoferax were enriched, while Rhodopseudomonas , Pseudomonas , Chelativorans , and Chelatococcus decreased under continuous monoculture (SCP and TCP). Redundancy analysis showed that Streptomyces , Pseudomonas , and Rhodopseudomonas were positively correlated with soil physicochemical factors. In summary, C. equisetifolia monoculture led to dramatic shifts in the quantity and community structure of denitrifying bacteria, contributing greatly to soil sickness in this tree species. • The soil nitrogen content decreased following C. equisetifolia monoculture. • C. equisetifolia monoculture affected the diversity indices of denitrifying bacteria. • Proteobacteria was the dominant nirK- and nosZ-denitrifying bacterial phylum. • The denitrifying bacteria might respond differently to physicochemical parameters. • Replanting problems of C. equisetifolia was associated with soil denitrification. [ABSTRACT FROM AUTHOR]

Grazing management can alter soil properties and microbial communities that are critical to maintaining grasslands' long-term productivity and function, but information relevant to such influences operating on the Qinghai-Tibetan Plateau (QTP) of China is scarce. The present study was undertaken to examine the impact of different grazing management approaches [ e.g. , seasonal grazing (SG), continuous grazing (CG), and exclosure grazing (EG)] on soil properties and microbial communities on the QTP. Soil properties from two depths (0 to 0.15 m and 0.15 to 0.30 m) and microbial communities from topsoil (0 to 0.15 m) were measured in plots representative of each grazing type. Several soil properties were of greater magnitude in SG vs. CG sites: aboveground biomass, 838 vs. 46 g/m2; soil organic carbon 20.73 vs. 8.07 g/kg; total soil nitrogen 1.74 vs. 1.07 g/kg; total soil phosphorus 0.20 vs. 0.16 g/kg. Soil property values at the EG site were intermediate to those at the SG and CG sites. While no significant difference in richness and the α-diversity of soil bacteria and soil fungi occurred among grazing types, the β-diversity of soil fungi differed significantly, and the β-diversity of soil bacteria under EG was significantly different from that under SG or CG. Results from the present study suggest that grazing management can alter soil conditions and microbial β-diversity, and EG might prove a useful long-term option for grassland recovery. • Soil condition under seasonal grazing was better than under continuous grazing • Soil condition under exclosure grazing was intermediate between above-mentioned two • No difference in the α-diversity of soil microbes among the three types of management • The fungal communities were significantly different among these management practices • Exclosure grazing may be a useful, but slow, tool for grassland recovery on the QTP [ABSTRACT FROM AUTHOR]

The long-term effects of different combined organic–chemical fertilizer regimes on denitrifying communities remain unclear. In this study, we performed quantitative PCR and sequencing analyses to examine the abundance, diversity, and structure of two nir (nirK and nirS) denitrifying communities in response to five fertilization treatments, namely, no nitrogen (N) fertilizer (NF), chemical fertilizer (CF), pig manure + chemical fertilizer (PM), biogas slurry + chemical fertilizer (BF), and milk vetch + chemical fertilizer (GM). All N fertilizer treatments received equal amounts of total N, phosphorus (P), and potassium (K). Compared with the NF treatment, combined organic–chemical fertilization significantly increased abundances of the nirK and nirS genes (particularly in the GM treatment) (P < 0.05). Chemical fertilizer application, with or without organic materials, shifted the nirK -type community relative to that under the NF treatment. In comparison, only a distinguished effect of combined organic-chemical fertilizations on nirS -type denitrifying communities was observed. Fertilizer-induced changes in soil pH and organic matter were identified as the factors contributing most to observed variations in the abundance and composition of the two nir denitrifying communities. Nitrite reductase (NIR) activity was mirrored by the changes in nirS gene abundance. Network analysis revealed that nirK - and nirS -type denitrifying communities formed ecological clusters that were closely associated with carbon addition, and indicated that nirS operational taxonomic units (OTUs) had more opportunities to interact with each other or with nirK OTUs. Overall, a high sensibility of nirK -type denitrifying communities to N fertilization was observed, whereas the nirS -type denitrifiers were more responsive to organic–chemical fertilization than chemical fertilizer application alone, and the addition of carbon was established to be the principal factor implicated in shaping the co-occurrence network patterns of nir denitrifying communities. • nirK - and nirS -type communities responded differently to fertilizer treatments. • Organic–chemical treatments increased nirS -OTU diversity. • Soil pH and SOM drove changes in nirK - and nirS -type denitrifying communities. • nirS -type denitrifiers were more responsive to organic–chemical fertilization. • The NIR activity was mirrored by the shift of nirS gene abundance. [ABSTRACT FROM AUTHOR]

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. • Licorice is a medicinal and edible plant, which can suited for water and soil conservation. • DSE had a positive effect on the growth of licorice plants depending on DSE strains and water treatments. • DSE had a stronger influence on the fungal than on the bacterial community in licorice rhizosphere under drought stress. • DSE enriched beneficial fungi and growth-promoting bacteria, decreased relative abundance of pathogens under drought stress. [ABSTRACT FROM AUTHOR]

Intensive management of Eucalyptus plantations has caused several social/environmental issues, including the concern over transformation of monoculture plantation cutover area. However, how different transformation patterns of Eucalyptus plantations affect soil microbial communities and their functions is unclear. In this study, the effects of different transformation patterns on structure and potential function of soil bacterial and fungal communities were evaluated. Soil chemical properties and acid phosphatase, urease, and catalase activities were also measured. In the third-generation monoculture Eucalyptus plantations, soil organic matter, nutrient contents, and microbial biomass decreased significantly and the relative abundance of oligotrophic bacteria (Chloroflexi) and symbiotic fungi (ectomycorrhizae) increased significantly compare with CK. However, in the Eucalyptus × Manglietia glauca Blume mixed plantation (E × M) and a Manglietia glauca Blume plantation (Manglietia), soil fertility (e.g., soil organic matter, total nitrogen, total phosphorus, and total potassium) improved, especially in E × M. In addition, soil acid phosphatase (0.30 mg∙g−1∙h−1) and catalase (0.66 mg∙g−1∙h−1) activities and the bacterial gene copies:fungal gene copies ratio (46.70) increased significantly in E × M compared with those in the monoculture plantations. The relative abundance of copiotrophic bacteria (Actinobacteria) and nitrogen cycle-associated bacteria (orders Rhizobiales and Frankiales) increased significantly in E × M. The abiotic factors soil available nitrogen and available zinc were the significant drivers of soil bacterial community structure, whereas the structure of fungal communities was most affected by tree species, in addition to soil pH and available copper. The results indicated that the E × M transformation pattern in the cutover area of Eucalyptus plantations had a significant beneficial effect on the soil fertility. The study also indicated that young plantations with Eucalyptus species have specific requirements for soil available phosphorus, available potassium, and available magnesium. Thus, increasing the supply of these nutrients during plantation development may have a positive effect on the sustainable management of plantations. • Successive monoculture planting mode of Eucalyptus decreased soil nutrient contents. • Eucalyptus × Manglietia glauca plantation improved soil fertility and microbial biomass. • Soil bacterial communities were significantly affected by soil nutrient supply. • Soil fungal communities were most affected by tree species. [ABSTRACT FROM AUTHOR]

Subsidence caused by underground coal mining results in soil degradation. However, little is known about bacterial community structure and its response to a 1-year-old coal mining subsidence area in arid and semiarid areas northwest China. Soil samples from 5 unexplored areas (MC, RC, YC, LC and ZC) and a 1-year-old subsidence area above a coal working face were collected and soil biogeochemical properties and bacterial community structure were determined. Results showed electrical conductivity (EC), soil water content (SWC), soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), dissolved organic carbon (DOC), available nitrogen (AN), available phosphorus (AP) and available potassium (AK) decreased with depth. The microbial biomass carbon (MBC), microbial biomass nitrogen (MBN) and the activity of β-1,4-glucosidase (BG), β-1,4- N -acetylglucosaminidase (NAG), alkaline phosphatase (PP) and catalase (CAT) were also reduced. The nutrients, BG, PP and MBC in subsidence of marginal zone of a coal working face were significantly lower than those in control, suggesting subsidence led to a loss in nutrients and a reduction in microbial biomass. High-throughput sequencing revealed that the Sphingomonas , Gemmatimonas , Pseudomonas and Gp6 , involved in C and N nutrient cycles, were dominant in this region. The relative abundances of Sphingomonas , Pseudomonas and Arthrobacter were decreased in subsidence due to the nutrient leakage and microbial biomass reduction. The predicted abundances of genes for metabolisms of xenobiotics via cytochrome P450 pathways and nitrogen were low in marginal zone, while peroxidase was high, indicating low capacities of degrading for xenobiotics and polycyclic aromatic hydrocarbons (PAHs) occurred marginal zone, while resistance to hydrogen peroxide was strengthened. Redundancy analysis (RDA) revealed EC, SWC and soil depth governed bacterial community structure. Overall, subsidence caused losses in soil water, nutrients and microbial biomass, alteration of bacterial community structure, and ultimately reduced soil nutrient conversion. Therefore, the cracks in the subsidence area should be filled manually in time, especially in marginal zone. • Soil biogeochemical properties varied with types of subsidence in arid and semiarid area. • Coal mining subsidence disturbed the bacterial community structure. • Coal mining subsidence affected the characteristics of soil bacterial metabolism. [ABSTRACT FROM AUTHOR]

Arbuscular mycorrhizal (AM) fungi are an important determinant of plant performance. The temporal distribution patterns of AM fungal communities, important groups in forest soil, are affected by various environmental factors. However, the effect of seasonal variation on AM fungal communities in forest soil is still not fully understood. To improve knowledge regarding the seasonal dynamics of AM fungal communities in forest soil, the Juglans mandshurica rhizosphere soil in a 30-year-old natural J. mandshurica and Larix gmelinii mixed forest in northeastern China was sampled and studied during different seasons. AM fungal community composition and structure in the rhizosphere soil were determined by using the Illumina MiSeq sequencing platform. The results showed that forest type significantly affected soil pH and the microbial biomass carbon (C mic), microbial biomass nitrogen (N mic), C, N, P, NH 4 +-N and NO 3 −-N contents. Similarly, soil moisture significantly decreased with seasonal progression in all forest types. Glomus and Diversispora were the dominant genera. The Shannon, Sobs and Chao1 indices of the mixed forest were higher in July than in May and September. The NO 3 −-N and water-soluble phenol (WSPh) contents were the most important factors driving the shift in the soil AM fungal community across the seasonal gradient. Network analysis revealed that AM fungal network structure was significantly different between seasons, and the number of links between species significantly increased with time. We observed a clear tendency for mixed forest management to significantly affect AM fungal community structure and composition but not diversity. Furthermore, the co-occurrence network and keystone taxa among AM fungi can change in response to environmental filtering due to mixed management in different seasons. • Mixed management had a significant effect on AM fungal community structure. • There was obvious seasonal variation in the AM fungal community in the mixed plantation. • Changes in NO 3 −-N and water-soluble phenol altered the AM fungal community. • AM fungal network structure was dynamic throughout the growing season. • Most of the hub OTUs belonged to Glomeromycetes in all seasons. [ABSTRACT FROM AUTHOR]

Balanced fertilization strategies that combine the use of organic and inorganic fertilizers have been adopted to increase soil fertility and crop yield and to safeguard environment. However, knowledge on the influence of these fertilization strategies on microbe-mediated nitrogen cycling in the agricultural ecosystems remains limited. We analyzed the denitrifiers with nitrite reductase genes (nirK and nirS) in three soil aggregate classes (large macroaggregates, >2 mm; small macroaggregates, 0.25–2 mm; and microaggregates, <0.25 mm) in response to long-term application of inorganic fertilizers (NPK), NPK plus straw (NPKS), and NPK plus manure (NPKM) in the fluvo-aquic soil of North China Plain. Both fertilization and aggregate size had significant effects on the nirK and nirS gene abundances and soil potential denitrification activity (PDA). PDA in the combined fertilizer-treated soils (NPKS and NPKM treatments) was two times more than that in inorganic NPK-treated soil. PDA dramatically increased in small macroaggregates and microaggregates of NPKS treatment. The nirS gene abundance was significantly higher than that of the nirK gene abundance, and NPKS and NPKM treatments increased the nirS to nirK ratio in bulk soils and in microaggregates compared with NPK treatment and control. Correlation analysis and automatic linear modeling revealed a primary correlation between PDA and abundance of nirS -type denitrifiers. Soil properties, such as SOC, pH and TN, significantly affected the community structure of nirK - and nirS -type denitrifiers while only aggregate size significantly influenced the composition of nirK -type denitrifiers. Taken together, our results suggest that long-term combined fertilization increased the denitrification potential in small macroaggregate and microaggregate classes, and the increased gene abundance and the shift community structures of nirS - and nirK -type denitrifiers were potentially responsible for an increase in the promoted denitrification. • Higher PDA was detected in combined fertilization than inorganic fertilization. • PDA and denitrifying gene abundances were significantly increased in NPKS, particularly in its microaggregates. • nirS - and nirK -type denitrifiers influenced by soil properties were responsible for the promoted denitrification. • Aggregate size significantly influenced community structure of nirK -type denitrifiers [ABSTRACT FROM AUTHOR]

Boreal forests in permafrost zone store significant quantities of carbon that are readily threatened by increases in fire frequency and temperature due to climate change. Soil carbon is primarily released by microbial decomposition that is sensitive to environmental conditions. Under increasing disturbances of wildfire, there is a pressing need to understand interactions between wildfires and microbial communities, thereby to predict soil carbon dynamics. Using Illumina MiSeq sequencing of bacterial 16S rDNA and GeoChip 5.0K, we compared bacterial communities and their potential functions at surface and near-surface permafrost layers across a chronosequence (>100 years) of burned forests in a continuous permafrost zone. Postfire soils in the Yukon and the Northwest Territories, Canada, showed a marked increase in active layer thickness. Our results showed that soil bacterial community compositions and potential functions altered in 3-year postfire forest (Fire 3) comparing to the unburned forests. The relative abundance of Ktedonobacteria (Chloroflexi) was higher in Fire 3 surface soils, while Alphaproteobacteria and Betaproteobacteria (Proteobacteria) were more abundant in unburned ones. Approximately 37% of the variation in community composition can be explained by abiotic variables, whereas only 2% by biotic variables. Potential functional genes, particularly for carbon degradation and anammox, appeared more frequent in Fire 3 than in unburned soils. Variations in functional gene pools were mainly driven by environmental factors (39%) and bacterial communities (20%; at phylum level). Unexpectedly, wildfire solely altered bacterial communities and their functional potentials of the surface layers, not the near-permafrost layers. Overall, the response of bacterial community compositions and functions to wildfire and the environment provides insights to re-evaluate the role of bacteria in decomposition. [ABSTRACT FROM AUTHOR]

High salinity, poor soil structure and nutrient deficiencies are the main limitations in saline-alkali soils. We investigated the effects on the microstructure, and the aerobic and anaerobic bacterial communities in the macroaggregates following addition of vermicompost and humic acid fertilizer to saline-alkali soil. These effects could enhance salt leaching and inhibit nitrogen losses in the topsoil. Vermicompost and humic acid fertilizer improved soil aggregate stability and the microstructure of macroaggregates (porosity, path tortuosity and effective porosity), which in turn increased soil permeability and salt leaching in saline-alkali topsoil. The improvement in aggregate microstructure affected the soil bacterial community of the macroaggregates by increasing the relative abundances of aerobic heterotrophs, such as Chloroflexi and Bacteroidetes. Additionally, vermicompost and humic acid fertilizer influenced nitrogen cycling by the macroaggregate microbial community, and stimulated nitrification by increasing archaeal and bacterial amoA gene copy numbers in the topsoil, but inhibited nitrite-reducing bacteria by decreasing nirS and nirK gene copy numbers. Furthermore, these amendments increased microbial N 2 O reduction by increasing nosZ gene copy numbers, suggesting that vermicompost and humic acid fertilizer have the potential to reduce N 2 O emissions in saline-alkali soil. In summary, vermicompost and humic acid fertilizer can ameliorate saline-alkali soils by replenishing organic matter, improving aggregate microstructure, and regulating the microbial community, which could increase salt leaching and inhibit nitrogen losses. • Vermicompost (V) and humic acid fertilizer (H) improved aggregate microstructure in saline soil. • Improvement in aggregate microstructure affected soil bacterial community in macroaggregates. • Improvement in aggregate microstructure increased salt leaching and inhibited nitrogen loss. • V and H ameliorated saline soil by increasing SOM and improving aggregate microstructure. [ABSTRACT FROM AUTHOR]

Biological nitrogen fixed by diazotrophs is important because it is the largest natural source of nitrogen to support primary productivity and maintain ecosystem sustainability when anthropogenic nitrogen inputs are lacking, especially in mining areas. The present study selected six different land use types (a corn field, a vegetable field, an area of shrubs, a mine tailing, a forest and a citrus orchard) as variables related to the mining activities around the Siding mining area, Liuzhou, Guangxi Province, China. A 0–10 cm soil layer was sampled, and the heavy metal concentrations and soil physicochemical properties were measured. Illumina MiSeq sequencing technology was used to analyze the abundance and structural diversity of the diazotroph community. The distribution of diazotroph assemblages among the different land use types and the main soil environmental properties that drive diazotroph community compositions were determined. The results indicated that the phylum Cyanobacteria (85.89%) was the most dominant taxon in the diazotrophic community in the citrus orchard. However, in the soils of the five other land use types, Proteobacteria was the most dominant taxon in the diazotrophic community, with a high abundance that ranged from 60.08% to 99.96%. Spearman's correlation analysis and redundancy analysis results indicated that the soil organic matter (OM) content in the citrus orchard was significantly higher than that in other areas, and the difference in soil OM content might be the main reason for the difference in the diazotrophic communities. The diazotrophic communities and their associated diversity under different land use types were driven by soil heavy metal and soil N (including NH 4 +-N, NO 3 −-N and total N (TN)) contents. Specifically, TN was highly correlated with the NMDS1 score of the soil diazotrophic community, which indicated that the soil TN content was the main reason for the high similarity among the diazotrophic communities in the corn field, vegetable field and shrub soils. Overall, our study offers a detailed description of the characteristics of the diazotroph community structure under different land use types around a mining area. • Soil diazotrophs were studied in six different land use types around mining area. • Diazotrophic communities were strongly associated with the different land use patterns. • Proteobacteria and Cyanobacteria were the most dominant diazotroph communities. • Diazotrophic communities were driven by soil heavy metal concentrations and soil N contents. [ABSTRACT FROM AUTHOR]

• Fungal alpha diversity values were not different between Heterodera avenae females and cysts. • H. avenae females had a distinct fungal community structure compared to that of cysts. • Mortierellomycota and Ascomycota was more abundant in females and cysts, respectively. • Majority of fungal taxa maintain a steady-state composition from the females to cysts. Cysts of plant-parasitic nematodes containing eggs with secondary-stage juveniles represent entities for long-term survival in soils and serve as an inoculum source for the next cropping season. Fungi are considered to be one of the major factors regulating population densities of cyst nematodes in natural and agricultural ecosystems. However, our understanding regarding the structure of fungal communities colonizing white females and cysts of the cereal cyst nematode (CCN, Heterodera avenae) and information on microbial succession from female to cyst is still limited. Herein, CCN white females attached to wheat roots and mature brown cysts in soil were collected from wheat grown fields at four different locations in central China, and their associated fungal communities were investigated using high-throughput sequencing. The results showed that there were no significant differences in the observed OTUs and Shannon diversity of fungal communities in the white females and cysts across the four locations. However, the mycobiota composition was different between white females and cysts. The phylum Mortierellomycota was more abundant in the white females than in cysts, while Ascomycota had higher relative abundance in the cysts than in white females. An operational taxonomic unit (OTU) enrichment analysis using combined samples for the white females as well as for the cysts from four locations revealed that only a small subset of OTUs were significantly enriched in white females (15 OTUs) and cysts (12 OTUs). These OTUs belonged to genera such as Mortierella , Fusarium , Alternaria , Aphroditeola , Cladosporium , Cryptococcus , Olpidium , Penicillium , Periconia , Volvariella , Phaeosphaeria and Moleospora , and most of them were assigned to functional traits such as endophyte, plant pathogen, animal pathogen, fungal parasite and saprophyte. However, the relative abundances of previously well-documented nematode egg-parasites such as Pochonia chlamydosporia , Purpureocillium lilacinum and other potent taxa were not significantly different between white females and cysts. Our results indicated that white females and cysts harbor diverse mycobiota, and the majority of fungal taxa maintain a steady-state composition from the white females to mature brown cysts. [ABSTRACT FROM AUTHOR]