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Background: The saline-alkali soil area accounts for over 1/4-1/5 of the land area in Gansu Province of China, which are mainly distributed in the north of Hexi corridor and Jingtai basin. The unique ecological environment contains unique and diverse microbial resources. The investigation of microbial diversity in saline environment is vital to comprehend the biological mechanisms of saline adaption, develop and utilize microbial resources., Results: The Illumina MiSeq sequencing method was practiced to investigate the bacterial diversity and composition in the 5 subtypes and 13 genera of saline-alkali soil in Gansu Province, China. The results from this study show that Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Gemmatimonadetes were the dominant bacterial groups in 13 saline soil. Proteobacteria had the greatest abundance in sulfate-type meadow solonchaks and orthic solonchaks, chloride-type orthic solonchaks and bog solonchaks, sulfate-chloride-type, chloride-sulfate-type, and sulfate-type dry solonchaks. Halobacteria was the dominant bacterial class in soil samples except for sulfate-type meadow solonchaks and orthic solonchaks, chloride-type orthic solonchaks and bog solonchaks. The richness estimators of Ace and Chao 1 and the diversity indices of Shannon and Simpson revealed the least diversity in bacterial community in sulfate-chloride-type orthic solonchaks., Conclusions: The sulfate anion was the most important driving force for bacterial composition (17.7%), and the second most influencing factor was pH value (11.7%)., (© 2022. The Author(s).)

Tomato-rice rotation is prevalent in subtropical and tropical regions in China. This practice enhances crop productivity and the disease suppression property of soils against soil-borne plant pathogens. To explore the variations and dynamics of bacterial and fungal communities, bulk soil samples were collected during two consecutive years under a rotation system between tomato and rice originated from the year of 2010 in Hainan Island, and 16S rDNA and ITS amplicons were sequenced by Illumina MiSeq. The results demonstrated that potentially beneficial bacterial phyla Acidobacteria, Chloroflexi and genus Paenibacillus, as well as the fungal genus Mortierella were significantly enriched, while the potentially pathogenic fungal genus Fusarium was significantly decreased during the crop rotation. Measurements of soil physicochemical properties indicated that the soil acidification was improved. Redundancy analysis (RDA) revealed the correlation of the microbial community with soil pH and identified soil total phosphorus (TP) level as the highest determinant factor for both bacterial and fungal communities. This work provides a preliminary description of changes of the bacterial and fungal communities related to tomato-rice rotation in China and offered experimental evidences for exploring the effects of this agricultural practice on soil ecology.

Efficient degradation of polycyclic aromatic hydrocarbons (PAHs) in a petroleum-contaminated soil was challenging which requires ample PAH-degrading flora and nutrients. In this study, we investigated the effects of 'natural attenuation', 'bioaugmentation', 'compost only (raw materials of compost included pig manure and rice husk mixed at a 1:2 proportion, supplemented with 2.5% charcoal)', and 'compost with bioaugmentation' treatments on degradation of polycyclic aromatic hydrocarbons (PAHs) and microbial community shifts during the remediation of petroleum-contaminated soil. After sixteen weeks of incubation, the removal efficiencies of PAHs were 0.52 ± 0.04%, 6.92 ± 0. 32%, 9.53 ± 0.29%, and 18.2 ± 0.64% in the four treatments, respectively. 'Compost with bioaugmentation' was the most effective for PAH removal among all the treatments. Illumina sequencing analysis suggested that both the 'compost only' and 'compost with bioaugmentation' treatments changed soil microbial community structures and enhanced microbial biodiversity. Some of the microorganisms affiliated with the compost including Azomonas, Luteimonas, Pseudosphingobacterium, and Parapedobacter were able to survive and become dominant in the contaminated soil. The 'bioaugmentation and 'natural attenuation' treatments had no significant effects on soil microbial community structure. Inoculation of the PAH degraders including Bacillus, Pseudomonas, and Acinetobacter directly into the contaminated soil led to lower biodiversity under natural conditions. This result suggested that compost addition increased the α-diversity of both the bacterial and fungal communities in petroleum-contaminated soil, leading to higher PAH degradation efficiency in petroleum-contaminated soil., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Paeonia ludlowii is indigenous to Tibet and has an important ecological and economic value in China. In Tibet, P. ludlowii has been used in folk medicine with relative success. Plant microbial endophytes play an important role in plant growth, health and ecological function. The diversity of endophytic bacteria associated with P. ludlowii remains poorly understood. In this study, the structure of the endophytic bacterial communities associated with different tissues, including fruits, flowers, leaves, stems, and roots, and rhizosphere soils was analyzed with Illumina MiSeq sequencing of bacterial 16S rDNA. A total of 426,240 sequences and 4847 operational taxonomic units (OTUs) were obtained. The OTUs abundance of roots was higher than that of other tissues; however, the OTUs abundance was similar among different deep soil samples. In the plant tissues, Cyanobacteria was the most abundant bacterial phylum, followed by Proteobacteria; however, the most abundant phyla were Proteobacteria and Acidobacteria in soil samples from three different layers. In addition, the diversity and richness of the microorganisms in the soil were very similar to those in roots but higher than those in other tissues of P. ludlowii. Predictive metagenome analysis revealed that endophytic bacteria play critical functional roles in P. ludlowii. This conclusion could facilitate the study of the ecological functions of endophytic bacteria and their interactions with P. ludlowii to analyze the reasons why this important medicinal plant is becoming endangered.

Enantioselective biodegradation of racemic dichlorprop in two soils was investigated in the laboratory. Chiral separation of racemic dichlorprop was achieved by using HPLC with Phenomenex Lux Amylose-2. The first-order kinetic model fitted well the dissipation data of racemic dichlorprop and its pure R- and S-enantiomers. S-dichlorprop was preferentially degraded in both soils and enantioselectivity was affected by soil pH. The half-lives (DT 50 ) of S-dichlorprop were 8.22 days in soil A and 8.06 days in soil D, while R-dichlorprop was more persistent with DT 50 of 12.93 days in soil A and 12.38 days in soil D, respectively. Dichlorprop dissipated faster in soil D with lower organic matter content. In sterilized soils, neglected dissipation was observed and enantiomer fraction values remained constant, indicating that the enantioselective degradation was mainly controlled by soil microorganisms. Soil microbial community structure and diversity was assessed by Illumina MiSeq sequencing of 16S rRNA genes from dichlorprop and no dichlorprop contaminated microcosms. Compared with controls, dichlorprop application had no significant effect on microbial community structures at phylum level, but increased bacterial diversity and dichlorprop degradation related taxa in both soils. S-dichlorprop preferential degradation might be attributed to the S-enantiomer preferred degraders in the family of Sphingomonadaceae .

Biochar amendment of soil is well known to improve soil fertility and microbial function. However, little is known about the effect of biochar addition to reclaimed soil in coal mining subsidence area on microbial community. A plant soil cultivation experiment was conducted with wheat grown and four treatments were included: P and K fertilizer (CK); NPK inorganic fertilizer (NPK); NPK inorganic fertilizer and straw (NPKS); and NPK inorganic fertilizer and biochar (NPKB). The results indicated that biochar amendment significantly increased the concentrations of NH 4 -N, total N, and available P and K compared with the NPK. Biochar addition also significantly increased the grain yield and total biomass of wheat. Furthermore, biochar amendment treatment increased the absolute abundance and altered the community structure of soil bacteria and fungi in the reclaimed soil. Illumina MiSeq sequencing showed that the addition of biochar increased α-diversity of bacteria and relative abundances of Proteobacteria, Actinobacteria, and Bacteroidetes, whereas the relative abundance of Firmicutes were decreased by 61%. However, biochar addition did not change the relative abundance of dominant fungal phyla. Redundancy analysis (RDA) suggested that total N, available P, and K contents were the key factors correlated with changes in microbial community structure. Overall, our results suggest that biochar amendment in reclaimed soil in coal mine subsidence area could increase wheat yield and abundance and alter microbial community compositions.+ -N, total N, and available P and K compared with the NPK. Biochar addition also significantly increased the grain yield and total biomass of wheat. Furthermore, biochar amendment treatment increased the absolute abundance and altered the community structure of soil bacteria and fungi in the reclaimed soil. Illumina MiSeq sequencing showed that the addition of biochar increased α-diversity of bacteria and relative abundances of Proteobacteria, Actinobacteria, and Bacteroidetes, whereas the relative abundance of Firmicutes were decreased by 61%. However, biochar addition did not change the relative abundance of dominant fungal phyla. Redundancy analysis (RDA) suggested that total N, available P, and K contents were the key factors correlated with changes in microbial community structure. Overall, our results suggest that biochar amendment in reclaimed soil in coal mine subsidence area could increase wheat yield and abundance and alter microbial community compositions.

The seasonal flooding and drainage process affect the paddy soils, the existence of the iron state either Fe(III) or Fe(II) is the main redox system of paddy soil. Its morphological transformation affects the redox nature of paddy soils, which also affects the distribution of bacterial community diversity. This study based on molecular biological methods (qPCR, Illumina MiSeq sequencing technique) to investigate the effect of Fe(II) and environmental factors on cbbM genes containing carbon fixing microbes. Both Eh5 and pH were reduced with Fe(II) concentrations. The Fe(II) addition significantly affects the cbbM gene copy number in both texture soils. In loamy soil, cbbM gene copy number increased with high addition of Fe(II), while both low and high concentrations significantly reduced the cbbM gene copy number in sandy soil. Chemotrophic bacterial abundance significantly increased by 79.7% and 54.8% with high and low Fe(II) addition in loamy soil while in sandy soil its abundance decreased by 53% and 54% with the low and high Fe(II) accumulation. The phototrophic microbial community increased by 37.8% with low Fe(II) concentration and decreased by 16.2% with a high concentration in loamy soil, while in sandy soil increased by 21% and 14.3% in sandy soil with low and high Fe(II) addition. Chemoheterotrophic carbon fixing bacterial abundance decreased with the Fe(II) accumulation in both soil textures in loamy soil its abundance decreased by 5.8% and 24.8%, while in sand soil 15.7% and 12.8% with low and high Fe(II) concentrations. The Fe(II) concentration and soil textures maybe two of the major factors to shape the bacterial community structure in paddy soils. These results provide a scientific basis for management of paddy soil fertility and it can be beneficial to take measures to ease the greenhouse gases effect., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Fungi play a critical role in farmland ecosystems, especially in improving soil fertility; however, little is known about the changes in fungal communities caused by mudflat reclamation under rice cultivation. In this study, mudflats located in Yancheng, China, which were divided into nine plots with 0, 11, and 20 years of successive rice cultivation histories, were sampled to determine the fungal community composition by using Illumina MiSeq sequencing. Results show that the Shannon diversity of the fungal communities did not change significantly but the species richness increased under mudflat reclamation with long-term rice cultivation. Ascomycota was the dominant phylum throughout the reclaimed mudflats samples, while Sordariomycetes was the dominant class. Fungal functional prediction found that the relative abundance of saprotrophs gradually increased with mudflat reclamation and mainly belonged to Ascomycota after 20 years of successive reclamation. Redundancy analysis showed that electrical conductivity, organic matter, and total nitrogen were the main factors affecting the composition and ecological function of the fungal community during mudflat reclamation. In short, a fungal community dominated by Ascomycota was established during mudflat reclamation under rice cultivation, which is more conducive to promoting soil fertility because of the higher proportion of saprotrophic fungi in Ascomycota.

Microbial communities drive geochemical cycles in soils. Relatively few studies have assessed the long-term impacts of different types of soil amendments under field conditions in long-term experiments. The response of soil microbial organisms in a Mollisol cultivated with maize for 35 years was examined. Treatments involved the use of N, P, and K fertilizers and two doses of straw residue in isolation or combined. Real-time PCR and Illumina MiSeq sequencing methods were used to characterize the microbial community. The results showed that addition of nitrogen fertilizers decreased soil pH, but this was mitigated when a high dose of straw was also incorporated. Long-term application of inorganic fertilizers was able to alter the abundance of functional soil microbial population. Application of inorganic N fertilizer resulted in distinctive changes on N-cycle microorganisms. Phosphate-solubilizing functional genes abundance was lower in plots with no phosphate fertilizer. Sequencing analysis showed that the presence or absence of N in the fertilizer mix is a key factor affecting bacterial community diversity of agricultural soil, and pH, total organic C, and total N show a high correlation with bacterial community composition. Nitrogen addition increased the N concentration in the soil, which could cause changes in the soil pH and change the soil bacterial community. Our findings proved that interaction of N fertilizer with other fertilizers can affect microbial communities.

Overexploitation of rare earth elements (REEs) has caused serious desertification and environmental pollution. The ecological restoration of mining areas has attracted increasing attention in China. Soil microbiota is important for successful ecological remediation of abandoned mine land. In this study, soil samples were collected from a restored REE mine site, and the bacterial community composition and diversity were assessed by Illumina high-throughput sequencing targeting the V3-V4 region of the 16S rRNA gene. Microbiota significantly developed in the remediated land. A total of 663,781 effective 16S rRNA gene sequences were obtained, which were classified into 28 bacterial phyla and 3 archaeal phyla. The dominant phyla across all samples (>5% of total effective sequences) were Proteobacteria, Acidobacteria and Firmicutes. Bacterial diversity indices (OTU number, Shannon index and Chao1 index) of the restored soils were higher than those of the tailings and even surpassed those in the unmined site. Redundancy analysis indicated that soil nutrients (soil organic carbon, available phosphorus and total nitrogen) were the dominant factors, followed by soil pH, affecting bacterial community structure. In general, these results suggested that soil amendment and phytoremediation effectively improved the soil environment of the abandoned mine site, which also increased our understanding of the correlation between microbial variation and soil properties in restored REE mine soils., (Copyright © 2019 Elsevier B.V. All rights reserved.)

The fungicides used to control diseases in cereal production can have adverse effects on non-target microbial communities, with possible consequences for plant health and productivity. Although we know that fungicides affect microbial community structure and soil activities, it is unclear how crop cultivars have altered the impact of fungicides on rhizomicrobiomes. In this study, the rhizosphere bacterial and fungal communities and structures of cultivated crops and their wild relatives were studied by Illumina MiSeq sequencing analysis. The results indicated that the rhizomicrobiome communities of wild crops reacted more strongly to fungicides than that of their cultivated relatives. Furthermore, fungal community composition was more affected by fungicides than bacterial community composition. Remarkably, the same trend was observed in both soybean and rice with regard to the influence of crop cultivar on the response of the rhizomicrobiome to fungicide application, although the level of the response was not similar. We report for the first time that the rhizomicrobiomes of wild crops reacted more strongly to fungicides than the rhizomicrobiomes of cultivated crops.

This study investigated the effects of 35 years of application of inorganic fertilizers containing nitrogen (N), phosphate (P), or potassium (K) alone or in combination on the abundance and composition of diazotrophic community in a black soil (Mollisol) in northeast China. The abundance and composition of diazotrophic community were analyzed using qPCR and Illumina MiSeq sequencing targeting nifH genes. Nitrogen fertilization decreased the abundance and Shannon diversity of nifH genes. The diazotrophic community was dominated by Alphaproteobacteria (Bradyrhizobium at the genus level), with relatively higher abundance in the N fertilization treatments than in the non-N fertilization treatments. All diazotrophic communities were clustered into two groups with and without N fertilization history, and the soil pH, total C, total N, and NO 3 - -N significantly influenced the structure of the whole diazotrophic community. Moreover, random matrix theory analysis elucidated a clear difference in network structures between the N and non-N fertilization treatments, with N fertilization causing a less stable network structure. These results highlighted that it was N fertilizer, but not P and K fertilizers, contributed to great changes in the diazotrophic community in this black agricultural soil., (Copyright © 2019 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.)

The alpine steppe at Qinghai-Tibetan Plateau is an important area for conserving water source and grassland productivity; however, knowledge about the microbial community structure and function and the risk to human health due to alpine plant-soil ecosystems is limited. Thus, we used prediction methods, such as Tax4Fun, and performed a metagenome pre-study using 16S rRNA sequencing reads for a small scale survey of the microbial communities at degraded alpine steppes (i.e., non-degraded (ND), lightly degraded (LD), moderately degraded (MD), heavily degraded (HD), and extremely degraded (ED) steppes) by Illumina high-throughput sequencing technology. Although there were no significant differences in the microbial alpha diversity among the different degraded alpine steppes and the dominant phyla at the different degraded alpine steppes, including Actinobacteria, Proteobacterial, Acidobacteria and Chloroflexi, were similar, the beta-diversity significantly differed, indicating that alpine steppe degradation might result in variation in microbial community compositions. The linear discriminate analysis (LDA) effect size (LEfSe) analysis found twenty-one biomarkers, most of which belonged to Actinobacteria, suggesting that microbes with a special function (such as the decomposition soil organic matter) might survive in alpine steppes. In addition, the functional profiles of the bacterial populations revealed an association with many human diseases, including infectious diseases. In addition, the microbial communities were mainly correlated with the populations of Gramineae and soil total phosphorous. These results suggested that alpine steppe degradation could result in variations in the microbial community composition, structure and function at Qinghai-Tibetan Plateau. Further studies investigating the degraded alpine steppe environment are needed to isolate these potential pathogenic microbes and help protect livestock using these alpine steppes., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Although effects of biochar application on soil microorganism have been increasingly reported, the direct evidences for demonstrating the contributions of biochar chemical and physical properties to soil microorganisms are still lacking. Herein, we partitioned corn-straw biochar (BC) into three fractions, including aqueous extractable substances (AE), organic extractable substances (OE) and the remaining solid (EBC) after these two extractions. These fractions and BC were added to purple soil for a 30-day incubation. Soil properties, microbial α-diversity indices and microbial community compositions were analysed after the incubation. The results showed the obvious changes in soil properties, along with higher available P, available K and total organic C, as well as, lower pH and available N than those of soil without biochar, were observed in the BC-treated soil. Illumina Miseq sequencing displayed a distinct difference between responses of bacteria and fungi to biochar application, in which fungal richness and diversity were increased, and no significant changes happened in bacterial richness. Furthermore, biochar had apparent effects on bacterial and fungal community compositions at phylum level, which were most close to the influences of AE and EBC, respectively. These results suggested that AE, improving soil nutrients (e.g., total N), played a pivotal role in changing bacterial phylum community composition. The EBC, regarded as physical structure and relatively recalcitrant compounds of BC, had a dominant contribution to the influence of biochar on the fungal community composition., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Mixed soil microbiomes were established by introducing aliquots of a paddy soil into a red soil. The new mixed microbiomes effectively metabolized high-molecular-weight polycyclic aromatic hydrocarbons (PAHs, pyrene) in the soil mixtures. The pyrene removal efficiencies were 19% and 98%, respectively, in the original red soil and the paddy soil. The pyrene removal effectiveness by the mixed microbial community was enhanced by increasing the amount of paddy soil inoculant and the pyrene removal rates were 93%, 58% and 27% in paddy soil/red soil mixtures of 1:1, 3:7 and 1:9 (w/w), respectively. Supplementation with sterile paddy soil and nutrients changed the soil environment but the pyrene removal efficiency was not enhanced, indicating that the microbial composition largely determined the extent of pyrene removal. Moreover, the pyrene removal rate was positively related to the pyrene dioxygenase gene (nidA) abundance. The greater the percentage of the paddy soil in the soil mixture the greater the similarity of the mixed microbiome to that of the original paddy soil itself. The community of the inoculated sterile paddy soil was similar to that of the red soil and the community diverged from those of the red soil and the paddy soil with increasing culture time. After culture for 42 days, some enriched genera were responsible for PAH degradation, notably Nevskia, Ralstonia, Gemmatimonas and Lysobacter, while some genera have no clear classification information or category name at the genus level, such as f__Acidobacteriaceae and o__JG30-KF-AS9. This study is very important in recognizing the role of natural soil in the formation of a mixed microbiome to stimulate the degradation of PAHs in a soil with low intrinsic PAH degradation capability., (Copyright © 2018 Elsevier B.V. All rights reserved.)

The objective of this study was to characterize the diversity and dynamics of rhizosphere bacterial community, especially the response of dominant and rare bacterial taxa to the cultivation of Bt cotton for different root environments at different growth stages. qPCR analyses indicated that bacterial abundances of the taproots and lateral root rhizospheres of the Bt cotton SGK321 were significantly different at seedling and bolling stages. But no significant differences were detected between the same root zones from Bt and the conventional cotton varieties. Total bacterial genera had similar pattern with dominant genera in abundance, and with rare genera in richness to the changes of bacterial community, respectively. Although the rhizosphere bacterial diversity of the three cotton varieties changed in taproot and lateral root, no significant differences were detected in the same root environments between Bt and conventional cotton. Moreover, Soil pH was more correlated with variations in the bacterial community composition than Bt proteins. In conclusion, these results revealed no indication that rhizosphere bacterial community of Bt cotton had different response to increased Bt protein regarding the same root environment. In particular, dominant and rare bacterial taxa showed the variation in diversity and community composition in different root microhabitats., (Copyright © 2018 Elsevier B.V. All rights reserved.)

How fungi respond to long-term fertilization in Chinese Mollisols as sensitive indicators of soil fertility has received limited attention. To broaden our knowledge, we used high-throughput pyrosequencing and quantitative PCR to explore the response of soil fungal community to long-term chemical and organic fertilization strategies. Soils were collected in a 35-year field experiment with four treatments: no fertilizer, chemical phosphorus, and potassium fertilizer (PK), chemical phosphorus, potassium, and nitrogen fertilizer (NPK), and chemical phosphorus and potassium fertilizer plus manure (MPK). All fertilization differently changed soil properties and fungal community. The MPK application benefited soil acidification alleviation and organic matter accumulation, as well as soybean yield. Moreover, the community richness indices (Chao1 and ACE) were higher under the MPK regimes, indicating the resilience of microbial diversity and stability. With regards to fungal community composition, the phylum Ascomycota was dominant in all samples, followed by Zygomycota, Basidiomycota, Chytridiomycota, and Glomeromycota. At each taxonomic level, the community composition dramatically differed under different fertilization strategies, leading to different soil quality. The NPK application caused a loss of Leotiomycetes but an increase in Eurotiomycetes, which might reduce the plant-fungal symbioses and increase nitrogen losses and greenhouse gas emissions. According to the linear discriminant analysis (LDA) coupled with effect size (LDA score > 3.0), the NPK application significantly increased the abundances of fungal taxa with known pathogenic traits, such as order Chaetothyriales, family Chaetothyriaceae and Pleosporaceae, and genera Corynespora, Bipolaris, and Cyphellophora. In contrast, these fungi were detected at low levels under the MPK regime. Soil organic matter and pH were the two most important contributors to fungal community composition., (© 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

Heavy metal pollution has become a widespread environmental problem due to rapid economic development. The phylogenetic diversity and structure of microbial communities in lead (Pb)-contaminated Lou soils were investigated using Illumina MiSeq sequencing of 16S rRNA genes. The presence of Pb 2+ in soil showed weak impact on the diversity of soil bacteria community, but it influenced the abundance of some genera of bacteria, as well as soil physicochemical properties. We found significant differences in the relative abundances of heavy-metal-resistant bacteria such as Bacillus, Streptococcus, and Arthrobacter at the genus level. Available Pb and total Pb negatively correlated with soil organic matter but positively affected available phosphorus. The abundance of main bacteria phyla was highly correlated with total Pb. The relative abundance of Gemmatimonadetes, Nitrospirae, and Planctomycetes was negatively correlated with total Pb. Collectively, Pb influences both the microbial community composition and physicochemical properties of soil.

Denitrification causes nitrogen loss from agricultural soils and emission of nitrous oxide (N 2 O). Water addition leads to an increase in soil moisture which greatly influenced soil denitrification. However, it is unclear how irrigation management affected the denitrifying bacterial communities in agricultural systems. In the present study, we investigated the abundance, diversity, and composition of the nirS-, nirK-, and nosZ-denitrifying bacterial communities in the soil under different long-term irrigation regimes by using real-time PCR (qPCR) and Illumina MiSeq sequencing approaches. Results showed that the abundance of nosZ gene was 3.94-6.01 and 35.09-60.21 times more than that of nirS and nirK genes, and the abundance of nirS gene was 5.84-15.30 times higher than that of nirK gene, respectively, in different irrigation treatments. However, the Alpha diversity indices of the nirK-denitrifying bacterial community were higher than those of the nirS- and nosZ-denitrifying bacterial communities. Proteobacteria was the predominant phylum for all the denitrifying bacterial communities, and significant differences were observed in relative abundance of Alphaproteobacteria and Betaproteobacteria in predominant class between different irrigation treatments for the nirS- and nosZ-denitrifying bacterial communities, respectively. Irrigation significantly affected the abundance, Shannon and Invsimpson indices, and structure of the nirS- and nosZ-denitrifying bacterial communities, whereas it only minor influenced the structure of the nirK-denitrifying bacterial community. Furthermore, the shifts in abundance, diversity, and structure of the nirS- and nosZ-denitrifying bacterial communities correlated significantly with the soil property variations; however, no soil property was significantly correlated with the abundance and Alpha diversity index of the nirK-denitrifying bacterial community. Our results demonstrate that different long-term irrigation regimes greatly altered the abundance, diversity, and structure of the nirS- and nosZ- rather than the nirK-denitrifying bacterial communities.

Bioaugmented compost was created by inoculating petroleum-degrading bacteria into mature compost. The petroleum hydrocarbon degradation efficiencies were investigated by applying this enhanced compost to petroleum-contaminated soil under low temperatures. The results showed that the degrading bacteria can be enriched in the mature compost. After 30 d of remediation, the removal efficiency of TPH, alkanes, and PAHs in the soil was 27.0%, 19.6%, and 10.0%, compared to natural attenuation (CK), which was 4.5%, 9.5%, and 2.3%, respectively. In response to remediation, the relative abundance of Proteobacteria and Actinobacteria phyla decreased from 53.4% and 25.9% to 48.9% and 14.1%, respectively, and Bacteroidetes phylum increased from 5.0% to 24.5%. At the genus level, the relative abundance of Acinetobacter and Pseudomonas increased from 0.02% and 3.4% to 15.2% and 4.6%, respectively. The results indicated that the bioaugmented compost may efficiently facilitate and speed up the bioremediation of petroleum-contaminated soil under low-temperature conditions. Soil microbial diversity and structure of microbial communities are sensitive to the remediation.

Soil microcosm incubation, molecular ecology techniques including denaturing gradient gel electrophoresis and Illumina MiSeq high-throughput sequencing, and bioinformatics analysis were carried out to investigate the effect of long-term fertilization with chemical fertilizers (NPK) and organic manure (OM) on soil nitrification activity and the autotrophic nitrifying communities in acidic upland soils. No fertilization soil (CK) was the control. Relationships between soil nitrification activities, autotrophic nitrifying communities, and soil characteristics were further evaluated. Long-term fertilization significantly increased the soil organic carbon and inorganic nitrogen contents. Fertilization with organic manure significantly increased soil pH and total nitrogen contents, but decreased soil C/N. Autotrophic nitrification dominated soil nitrification, and accounted for 73.60%-85.32% of total nitrification. Fertilization significantly increased soil autotrophic nitrification activity and the highest value was observed in the OM soil. During the microcosm incubation, the absolute abundances of amoA genes and the relative abundances of 16S rRNA genes of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the OM soil significantly increased. The relative abundances of 16S rRNA genes of the AOA greatly increased in both CK and NPK soils. These results suggested the remarkable activity of AOA in the three soils (the predominant population was Nitrososphaera ,>99.30%) and implied that AOB was active in the OM soil (the predominant population was Nitrosospira ,>99.99%). We also found the activity of nitrite-oxidizing bacteria (NOB) in the OM soil, and the predominant population was Nitrospira (>96.69%). Stepwise regression analysis demonstrated that soil autotrophic nitrification activity was significantly affected by soil total nitrogen content, whereas the abundances of archaeal and bacterial amoA genes were significantly affected by soil organic carbon content and soil pH, respectively. We also found significant positive correlation between the relative abundance of Nitrososphaera and soil nitrate content and a negative correlation between the relative abundance of Nitrosospira and Nitrospira with soil C/N. Overall, our results showed that long-term fertilization greatly increased soil nitrification activity and altered the autotrophic nitrifying communities in acidic upland soils. Soil autotrophic nitrification activity was significantly stimulated by soil total nitrogen content. The Nitrososphaera group played a critical role in nitrification of acidic upland soils. The increased soil pH and decreased soil C/N stimulated the growth of Nitrosospira .

Grasslands in semi-arid Northern China are widely desertified, thus inducing the formation of a large area of moving sand lands. Revegetation of the sandy land is commonly adopted to restore degraded grasslands. The structure of the soil microbial community might dramatically change during degradation and recovery because microorganisms are one of the major drivers of ecological process through their interactions with plants and soil. Assuming that soil properties are the key determinants of the structure of soil bacterial community within the same soil type, whether the vegetation type causes the significant difference in the structure of soil bacterial community during revegetation and restoration of the degraded grasslands remains poorly understood. Our study aimed to (1) investigate the response of soil bacterial communities to the changes during vegetation degradation and recovery and (2) evaluate whether the soil bacterial communities under plantations return to their native state. We detected the shifts in diversities and compositions of the soil bacterial communities and the relative abundance of dominant bacterial taxa by using the high-throughput Illumina MiSeq sequencing technique in an area covered by 32-year-old Caragana microphylla, Artemisia halodendron, Hedysarum fruticosum, Pinus sylvestris var. mongolica, Populus simonii, and Salix gordejevii sand-fixing plantations and in the native community (NC) dominated by elm, and moving sandy dune (MS). We found that the obtained operational taxonomic units by 16S rRNA gene sequencing and diversity index in MS were all significantly lower than those in NC, and the number and composition of dominant genera were significantly different between NC and MS. Interestingly, the compositions of bacterial communities and the dominant genera in different sand-fixation plantations (C. microphylla, A. halodendron, H. fruticosum, P. sylvestris var. mongolica, P. simonii, and S. gordejevii) were all similar to those of the native soil of NC, suggesting that the plantation type and soil properties exhibit a minimal effect on the compositions of soil microbial communities within a continuous landscape. These results revealed that the structure of the soil bacterial community of degraded sandy grassland (even degenerated into a mobile sand dunes) in semi-arid region can be reversibly restored by planting indigenous shrub or semi-shrub plantation on human time scales.

Roxarsone is a feed additive widely used in the broiler and swine industries that has the potential to contaminate the environment, mainly via the use of poultry manure as fertilizer, which results in release of inorganic arsenic to the soil and water. This study was conducted to investigate roxarsone degradation and the response of the microbial community under different culture conditions using high-throughput sequencing technology. Poultry litter was incubated for 288 h in the presence of roxarsone under light aerobic, dark aerobic, or dark anaerobic conditions. The results showed that roxarsone was completely degraded after 48 h of dark anaerobic incubation, while 79.9% and 94.5% of roxarsone was degraded after 288 h of dark aerobic and light aerobic incubation, respectively. Under dark aerobic conditions with microbial inhibitor sodium azide, roxarsone was rarely degraded during the 288 h of incubation, illustrating that microorganisms play an important role in roxarsone degradation. Microbial community structure was significantly different among various culture conditions. Olivibacter, Sphingobacterium, and Proteiniphilum were the top 3 genera in the control samples. Sphingobacterium and Alishewanella dominated the light aerobic samples, while the dominant microflora of the dark aerobic samples were Acinetobacter spp. Pseudomonas and Advenella were the predominant genera of dark anaerobic samples. This study emphasizes the potential importance of microbes in roxarsone degradation and expands our current understanding of microbial ecology during roxarsone degradation under different environmental conditions.

The biological oxidation capacity and change of microbial community structure of typical landfill cover soil cultured in situ by methane and trichloroethylene (TCE) were studied. The rates of CH 4 oxidation and TCE degradation were 0.20-0.87 Μmol·g -1 soil·h -1 and 0.009-0.013 mg·L -1 ·h -1 among these landfill cover soils, respectively. The activity of CH 4 oxidation in Shandong landfill cover soil was higher than that in landfill cover soils sampled from Guangdong, Shanghai and Chongqing. The α-diversity and microbial community structure before and after co-metabolism degradation were then investigated in all landfill cover soils by Illumina MiSeq sequencing. The results indicated that bacterial Operational Taxonomic Units (OTUs) were assigned to 39 phyla, 85 classes and 562 genera in all the commented OTUs clustering. The dominant bacterial populations were Proteobacteria, Bacteroidetes, Chloroflexi and Acidobacteria and the sum of the proportion was over 77.4% in all landfill cover soils. In addition, total percent of γ-Protebacteria, β--Protebacteria, α-Proteobacteria, Actinobacteria and Acidobacteria was over 26.5%. Specifically, the relative abundances of Methylophilaceae_uncultured, Anaerolineaceae_uncultured, Arthrobacter and Pseudomonas increased obviously after acclimated by TCE. These results suggested that there were co-metabolism degradation with non-methane compounds and aerobic assimilation of TCE besides the widely-agreed co-metabolism degradation by methanotrophs.

Excessive application of chlorimuron-ethyl has led to soil contamination and limited crop rotation; therefore, tactics to decrease and eliminate residual chlorimuron-ethyl in the environment have attracted increasing attention. In this study, two chlorimuron-ethyl-degrading bacterial strains (Rhodococcus sp. D310-1; Enterobacter sp. D310-5) were used to ferment and prepare a chlorimuron-ethyl-degrading bacterial consortium. To improve the degradation efficiency of the bacterial consortium, the cultivation conditions were optimized using response surface methodology (RSM). The maximum biodegradation rate (87.42%) was obtained under optimal conditions (carbon concentration, 9.21gL -1 ; temperature, 26.15°C; pH, 6.95). The rate of chlorimuron-ethyl degradation by the bacterial consortium in the chlorimuron-ethyl-contaminated soil was monitored and reached 80.02% at the end of a 60-d incubation period. Illumina MiSeq sequencing results showed that microbial diversity was high, and 33 phyla were identified in the analyzed samples. Proteobacteria, Acidobacteria, Acidobacteria, Firmicutes and Bacteroidetes were present in relatively high abundances in the samples. The bacterial consortium made a positive impact on the remediation of chlorimuron-ethyl-contaminated soil and somewhat altered the composition of the bacterial community in the chlorimuron-ethyl-contaminated soil. These findings provide highly valuable information on the production of bacterial consortium for the remediation of chlorimuron-ethyl and other sulfonylurea-herbicide-contaminated soil., (Copyright © 2017 Elsevier Inc. All rights reserved.)

While numerous studies both in laboratory and field have showed short term impacts of biochar on soil microbial community, there have been comparatively few reports addressing its long term impacts particular in field condition. This study investigated the changes of microbial community activity and composition in a rice paddy four years after a single incorporation of biochar at 20 and 40t/ha. The results indicated that biochar amendment after four years increased soil pH, soil organic C (SOC), total N and C/N ratio and decreased bulk density, particularly for the 40t/ha treatment compared to the control (0t/ha). Though no significant difference was observed in soil basal respiration, biochar amendment increased soil microbial biomass C and resulted in a significantly lower metabolic quotient. Besides, dehydrogenase and β-glucosidase activities were significantly decreased under biochar amendment relative to the control. The results of Illumina Miseq sequencing showed that biochar increased α-diversity of bacteria but decreased that of fungi and changed both bacterial and fungal community structures significantly. Biochar did not change the relative abundances of majority of bacteria at phylum level with the exception of a significant reduction of Actinobacteria, but significantly changed most of bacterial groups at genus level, particularly at 40t/ha. In contrast, biochar significantly decreased the relative abundances of Ascomycota and Basidiomycota by 11% and 66% and increased the relative abundances of Zygomycota by 147% at 40t/ha compared to the non-amended soil. Redundancy analysis (RDA) indicated that biochar induced changes in soil chemical properties, such as pH, SOC and C/N, were important factors driving community composition shifts. This study suggested that biochar amendment may increase microbial C use efficiency and reduce some microorganisms that are capable of decomposing more recalcitrant soil C, which may help stabilization of soil organic matter in paddy soil in long term., (Copyright © 2016 Elsevier B.V. All rights reserved.)

The aim of the present study is to deepen the current understanding of the microbial communities at two poplar phytomanagement sites to reveal the environmental factors that drive the abundance, diversity and composition of microbial communities. A soil analysis revealed that the two soils displayed contrasting physico-chemical characteristics, with significant lower pH and higher Cd, Zn and Mn CaCl2-extractable fractions at Leforest site, compared with Pierrelaye site. The fungal and bacterial community profiles in the poplar roots and soils were assessed through Illumina MiSeq sequencing. Diversity indices and β-diversity measures illustrated that the root microbial communities were well separated from the soil microbial communities at both sites. A detailed study of the fungal composition showed that Ascomycota dominated the overall fungal communities on poplar soil, the root samples at Pierrelaye, and the unplanted soil at the experimental sites. Conversely, Basidiomycota accounted for a much higher percentage of the fungal community in poplar root samples from the Leforest site. The root bacterial communities were dominated by Alphaproteobacteria and Actinobacteria, and the soil samples were dominated by Alphaproteobacteria and Acidobacteria. The occurrence and dominance of the ectomycorrhizal community at Leforest but not at Pierrelaye is the major feature of our data set. Overall, ectomycorrhizal root symbionts appeared to be highly constrained by soil characteristics at the phytomanagement sites. Our data support the view that mycorrhizal inoculation is needed in highly stressed and nutrient-poor environments., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Understanding the response of permafrost microbial communities to climate warming is crucial for evaluating ecosystem feedbacks to global change. This study investigated soil bacterial and archaeal communities by Illumina MiSeq sequencing of 16S rRNA gene amplicons across a permafrost thaw gradient at different depths in Alaska with thaw progression for over three decades. Over 4.6 million passing 16S rRNA gene sequences were obtained from a total of 97 samples, corresponding to 61 known classes and 470 genera. Soil depth and the associated soil physical-chemical properties had predominant impacts on the diversity and composition of the microbial communities. Both richness and evenness of the microbial communities decreased with soil depth. Acidobacteria, Verrucomicrobia, Alpha- and Gamma-Proteobacteria dominated the microbial communities in the upper horizon, whereas abundances of Bacteroidetes, Delta-Proteobacteria and Firmicutes increased towards deeper soils. Effects of thaw progression were absent in microbial communities in the near-surface organic soil, probably due to greater temperature variation. Thaw progression decreased the abundances of the majority of the associated taxa in the lower organic soil, but increased the abundances of those in the mineral soil, including groups potentially involved in recalcitrant C degradation (Actinomycetales, Chitinophaga, etc.). The changes in microbial communities may be related to altered soil C sources by thaw progression. Collectively, this study revealed different impacts of thaw in the organic and mineral horizons and suggests the importance of studying both the upper and deeper soils while evaluating microbial responses to permafrost thaw., (© 2014 John Wiley & Sons Ltd.)

In order to study the effects of adding different types of rice straw on soil bacterial communities under continuous cropping of flue-cured tobacco, fresh rice straw (FS) and rotted rice straw (RS) were added in soil, with no straw as control (CK). The community composition and diversity of soil bacteria and fungi at different times (0, 7, 30, 60 and 90 d) under 3 treatments were studied by high-throughput sequencing. The results showed that fresh rice straw and rotted rice straw could significantly improve the diversity and richness of soil microbial community. After 90 d in FS and RS treatments, the Chao 1 index, Shannon index and Simpson index of bacteria and the Chao 1 index of fungi were significantly improved. The analysis of community structure composition showed that FS and RS treatments increased the relative abundances of Proteobacteria, Spirochaetes and Verrucomicrobia. FS treatment increased the relative abundance of Basidiomycota, and decreased the relative abundances of Chytridiomycota and Rozellomycota. RS treatment increased the relative abundances of Ascomycota and Basidiomycota, and decreased the relative abundances of Zygomycota and Chytridiomycota. In summary, the addition of fresh rice straw and rotted rice straw could change the community composition of soil bacteria and fungi, improve the health status of soil with continuous cropping of flue-cured tobacco. Compared with rotted rice straw treatment, fresh rice straw treatment increased the abundance of pathogenic fungi. [ABSTRACT FROM AUTHOR]

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Background and aims: Root-rot disease, a catastrophic disease of Panax quinquefolium L. causes yield reduction and serious economic losses. However, knowledge of the relationship between rhizosphere microbial community and root-rot disease is limited. This study is aim to test whether the bacteria and fungi community differed between the soil attached to healthy and rotten roots of American ginseng. Moreover, the effects of American ginseng cultivation for 4 years on changes of soil physiochemical properties and microbial community were also investigated. Methods: High-throughput sequencing (Illumina MiSeq) was used to investigate the difference of microbial communities in the soils of new farmland (C) and the rhizosphere soils around healthy (H) and root rot diseased ginseng (R). Results: Cultivation of American ginseng for 4 years not only changed the soil physicochemical properties, but also significantly increased the richness of the soil bacteria and decreased the fungal richness and diversity. Compared with other genera, the bacterial genera Nitrospira and the fungal genera Gibberella and Podospora were strongly enriched in the soil of new farmland. However, the relative abundance of Janthinobacterium, Nitrospira and Pedomicrobium in bacterial community, and Mrakia, Paradendryphiella, Sporopachydermia, Myrothecium and Racocetra in fungal community were significantly decreased after culture of American ginseng. The results also showed that the bacteria and fungi community differs between the soil attached to healthy and rotten roots of American ginseng. The richness indices of fungal community showed a significant decrease in rhizosphere soils of R comparing with H. The bacteria Rhodoplanes and Kaistobacter were the dominant genera in the H sample, whereas Sphingobium was dominant in the R sample. Notably, Monographella was significantly higher in the R sample (23.13%) than that of H sample (2.90%). In addition, the fungi Melanophyllum and Staphylotrichum were the most differently abundant in the H sample, whereas Mortierella and Cistella were the differently abundant genera in the R sample. Conclusions: Our results indicate that cultivation of American ginseng changed the edaphic factors and the soil microbial community, and there are significant differences in the microbial community between the soil attached to healthy and rotten roots of American ginseng. [ABSTRACT FROM AUTHOR]

Soil salinity, poor soil structure and macronutrient deficiencies are three important limitations responsible for poor crop yields in coastal saline soils. Here we used humic fertilizer and vermicompost to ameliorate salt-induced stress by regulating the soil bacterial community and aggregates in different growth stages of winter wheat. Soil salinity, aggregates, nutrient availability, the soil bacterial community from next-generation high-throughput sequencing, and wheat yield were determined in this study. The results indicated that humic fertilizer and vermicompost could efficiently alleviate salt accumulation (by 16.8-41.1 and 13.3-42.7%, respectively) in topsoil by inhibiting resalinization and increase the proportion of soil macroaggregates (by 26.7-85.9 and 31.6-105.5%, respectively) in the wheat growth stages. Skermanella, Arthrobacter and Sphingomonas were the dominant genera in the study soil. Humic fertilizer and vermicompost could improve soil total N (by 4.7-15.6 and 2.4-25.2%, respectively), available P (by 15.9 and 7.3-64.4%, respectively), and exchangeable K (by 3.9-18.4 and 0.7-12.1%, respectively) by increasing the abundance of Arthrobacter and Pedobacter, consequently improving shoot biomass (by 41.1 and 52.8%, respectively) and grain yield (by 45.1 and 60.2%, respectively) of wheat. Therefore, vermicompost and humic fertilizer ameliorate salt-induced stress in coastal saline soil through the integrated improvement of soil physical, chemical and biological properties. [ABSTRACT FROM AUTHOR]

Nutrient inputs to forest ecosystems significantly influence aboveground plant community structure and ecosystem functioning. However, our knowledge of the influence of nitrogen (N) and/or phosphorus (P) inputs on belowground microbial communities in subtropical forests is still unclear. In this study, we used quantitative polymerase chain reaction and Illumina Miseq sequencing of the bacterial 16S rRNA gene to investigate bacterial abundance, diversity, and community composition in a Chinese fir plantation. The fertilization regimes were as follows: untreated control (CK), P amendment (P), N amendment (N), and N with P amendment (NP). Additions of N decreased soil pH and bacterial 16S rRNA gene abundance by 3.95 (from 4.69 to 3.95) and 3.95 × 109 copies g-1 dry soil (from 9.27 × 109 to 3.95 × 109 g-1 dry soil), respectively. Bacterial richness and diversity decreased with N addition (N and NP) rather than only P input. Proteobacteria, Acidobacteria, and Actinobacteria were the major phylum across all treatments. Nitrogen addition increased the relative abundance of Proteobacteria and Actinobacteria by 42.0 and 10.5%, respectively, while it reduced that of Acidobacteria by 26.5%. Bacterial community structure in the CK and P treatments was different from that in the N and NP treatments upon principle coordinates analysis. Phosphorus addition did not significantly affect soil bacterial communities, and no interactions between N and P inputs on microbial traits were observed. Soil pH and mineral N availability appeared to have a cooperative effect on bacterial abundance and community structure, with soil pH being the key influencing factor by canonical correspondence analysis. These results indicate that inorganic N rather than P fertilization affected both bacterial abundance and community composition in subtropical forests. [ABSTRACT FROM AUTHOR]

The impacts of rice varieties with stacked drought tolerance and insect resistance on soil microbiomes are poorly understood. Hence, the objective of this study was to investigate the effects resulting from the cultivation of the drought-tolerant and insect-resistant rice cultivar, Hanhui3T, on soil physical-chemical properties, and bacterial and fungal community composition. Soil samples of Hanhui3T and conventional rice varieties (Hanhui3 and Zhonghua11) were collected in triplicate at the booting stage, and bacterial and fungal population sizes and community structures were assessed using qPCR and Illumina MiSeq sequencing, respectively. The Bt protein concentration of Hanhui3T was significantly higher than that of Hanhui3 and Zhonghua11, while the pH of Hanhui3T was significantly lower. Bacterial population sizes and community composition were significantly different between Hanhui3T and Hanhui3 (or Zhonghua11), while no similar effects were observed for fungal communities. These differences suggest that the effect of Hanhui3T cultivation on bacterial community composition is stronger than the effect on fungal communities. Moreover, bacterial abundance was positively correlated to soil pH, while bacterial community structure variations were mainly driven by soil pH and Bt protein concentration differences. In conclusion, the abundances and structure of bacterial communities were altered in rhizosphere with Hanhui3T cultivation that changed soil pH and Bt protein concentrations, while fungal communities displayed no such responsiveness. [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]

Purpose: Ammonia oxidation, the first and rate-limiting step of nitrification, can be strongly influenced by agricultural practices, but little is known about the effects of fertilization and irrigation combination on ammonia oxidizers in agricultural soils. This study was designed to reveal how fertilizer type and irrigation frequency affect the ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities in a northern Chinese wheat-maize rotation soil.Materials and methods: Soil samples were collected from a long-term field experiment under different fertilization and irrigation regimes located in Wuqiao Experimental Station of China Agricultural University in June 2016. The abundance, diversity, and composition of AOA and AOB in the soils were investigated by using real-time PCR and Illumina Miseq sequencing approaches.Results and discussion: The abundance of AOA was higher in the irrigated treatments, but lower in the treatments without irrigation, than that of AOB. The AOA abundance was positively correlated with soil moisture, pH, and NO3−-N, while the AOB abundance was positively correlated with TN and NO3−-N. Soil potential nitrification activity (PNA) was significantly positively correlated with the AOB abundance. Both fertilizer type and irrigation frequency significantly affected Shannon, ACE, and Chao1 indices of the AOB community, while only irrigation frequency had a significant impact on Shannon index of the AOA community. PCoA analysis results indicated that irrigation frequency greatly affected the AOA community structure, while fertilizer type played a more important role in affecting the AOB community structure. Mantel test and correlation heatmap analysis results indicated that soil moisture, pH, and NH4+-N were significantly correlated to the AOA community structure, and TN and SOC were significantly correlated to the AOB community structure.Conclusions: This study demonstrated that irrigation frequency greatly influenced the AOA community, while fertilizer type had a stronger effect on the AOB community. It was AOB but not AOA played a more important role in soil nitrification. Moreover, soil moisture, pH, and TN were the main determinants in driving the AOA community and TN and SOC were the main factors in influencing the AOB community. [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]

Both nitrogen (N) and phosphorus (P) may limit plant production in steppes and affect plant community structure. However, few studies have explored in detail the differences and similarities in the responses of belowground microbial communities to long-term N and P inputs. Using a high-throughput Illumina Miseq sequencing platform, we characterized the bacterial communities in a semi-arid steppe subjected to long-term N or P additions. Our results showed that both the Chao richness and Shannon's diversity were negatively correlated to N input rate, while only Chao richness was significantly and negatively correlated to P input rate. Also, both N and P additions altered the bacterial community structure. The bacterial community between plots of the same N or P input rate was much more dissimilar with the higher input level, indicating more severe niche differentiation in pots with higher N or P input. N Inputs significantly increased the relative abundance of the predicted copiotrophic groups ( Proteobacteria and Firmicutes ) but reduced the predicted oligotrophic groups ( Acidobacteria , Nitrospirae , Chloroflexi ), with the order Rhizobiales being most affected. P additions significantly affected only two phyla (Armatimonadetes and Chlorobi ), which were positively correlated with P source. Results from the structural equation modelling (SEM) showed that N additions affected the bacterial community primarily by changing the pH, while P additions did so mainly by improving P availability. Our results suggest that the below-ground bacterial communities are more sensitive to N inputs, but P inputs can also play an important role in bacterial niche differentiation. These findings improve our understanding of bacterial responses to N and P inputs, and their impacts on bacterial-mediated processes, especially in the context of increasing anthropogenic nutrient inputs. [ABSTRACT FROM AUTHOR]

Characterizing microbial communities associated with disease-suppressive soil is an important first step toward understanding the potential of microbiota to protect crops against plant pathogens. In the present study, we compared microbial communities in suppressive- and conducive-soils associated with Fusarium wilt disease in a vanilla long-term continuous cropping system. Suppressive soil was associated with higher fungal diversity and lower bacterial diversity. The fungal phyla Zygomycota and Basidiomycota , and the bacterial phyla Acidobacteria , Verrucomicrobia , Actinobacteria and Firmicutes were strongly enriched in the suppressive soil. Notably, suppressive soil was dominated by the fungal genus Mortierella , accounting for 37% of the total fungal sequences. The hyper-dominance of Mortierella spp. in suppressive soil suggests that this taxon may serve as an indicator and enhancer of Fusarium wilt disease suppression in vanilla. In addition, Molecular Ecological Network analysis revealed that fungal communities were more connected and showed more co-occurrence relationships in the suppressive versus conducive soils. Our results indicate that fungal communities may be important in the development of soil suppressiveness against vanilla Fusarium wilt disease. [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]

The rhizomicrobiome is composed of microbes that live in association with plant roots. From nutrient cycling to carbon sequestration, soil microorganisms have provided a solid base for natural and agricultural ecosystems to function. The relationship between plant roots and soil microorganisms is especially relevant in food staples such as rice (Oryza sativa L.), as the various properties of these microbes can influence crop yield and plant health, thereby affecting a major portion of the food supply for an ever-growing world population. In this study, we used 16S rRNA gene-based metagenomic analysis to investigate the impact of crop rotation and soil cultivation methods (no-till or tillage) on rhizosphere bacterial diversity and composition in eight crop fields in Arkansas. Illumina MiSeq sequencing revealed 56 Phyla, with four major Phyla: Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes. Soil microbial communities in the samples studied were phylogenetically diverse but with a stable community structure. Crop rotation and tillage did not significantly affect bacterial diversity. [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]

Changes in soil physicochemical properties and bacterial community composition were investigated six years after biochar amendment at 0%, 4%, 8% and 12% (w/w), which were coded as C0, C1, C2 and C3, respectively. Results showed that some soil characteristics were sustainable, as they were still affected by biochar addition after six years. Compared to the control, biochar-treated soils had higher pH, total carbon (TC), C/N, total nitrogen (TN), available phosphorus (AP) and available potassium (AK). Soil pH, C/N and the content of TC, TN and AK all increased along with the increase of biochar dosage. The results of Illumina MiSeq sequencing demonstrated that biochar enhanced soil bacteria diversity and modified the community composition over time. The relative abundance of Nitrospirae and Verrucomicrobia phylum increased but that of Acidobacteria phylum decreased significantly in biochar amended soils. The addition of biochar also enriched some bacterial genera, such as uncultured Nitrosomonadace, uncultured Gemmatimonadac, uncultured Nitrospiraceae and Magnetovibrio. In particular, the relative abundance of uncultured Nitrospiraceae was enhanced by 16.9%, 42.8% and 73.6% in C1, C2 and C3, respectively, compared to C0. Biochar has a potential role in enhancing the abundance of bacteria involved in N cycling. Soil pH, TC, TN, TK and AK, were closely related to alterations in the composition of the soil bacterial community. Meanwhile, these soil properties were significantly influenced by biochar amendment, which indicates that biochar affected the soil microbial community indirectly by altering the soil characteristics in the long term. [ABSTRACT FROM AUTHOR]