Structure and diversity of nirK-type denitrifying microbial community in marsh soils at different invasion stages of Spartina alterniflora in the Minjiang River estuary, China.

No studies have examined the effect of experimental warming on the microbial biomass and community composition of soil in agricultural ecosystem on the Qinghai-Tibet Plateau. Thus it is unclear whether the influences of experimental warming on microbial communities in soil are related to warming magnitude in croplands on this Plateau. This study performed warming experiment (control, low- and high-level) in a highland barley system of the Lhasa River in May 2014 to examine the correlation between the response of microbial communities in soil to warming and warming magnitude. Topsoil samples (0–10 and 10–20 cm) were collected on September 14, 2014. Experimental warming at both low and high levels significantly increased soil temperature by 1.02 °C and 1.59 °C, respectively at the depth of 15 cm. Phospho lipid fatty acid (PLFA) method was used to determine the microbial community in soil. The low-level experimental warming did not significantly affect the soil's total PLFA, fungi, bacteria, arbuscular mycorrhizal fungi (AMF), actinomycetes, gram-positive bacteria (G+), gram-negative bacteria (G–), protozoa, the ratio of fungi to bacteria (F/B ratio), and ratio of G+ to G– (G+/G– ratio) at the 0–10 and 10–20 cm depth. The low-level experimental warming also did not significantly alter the composition of microbial community in soil at the 0–10 and 10–20 cm depth. The high-level experimental warming significantly increased total PLFA by 74.4%, fungi by 78.0%, bacteria by 74.0%, AMF by 66.9%, actinomycetes by 81.4%, G+ by 67.0% and G– by 74.4% at the 0–10 cm depth rather than at 10–20 cm depth. The high-level experimental warming significantly altered microbial community composition in soil at the 0–10 cm depth rather than at 10-20 cm depth. Our findings suggest that the response of microbial communities in soil to warming varied with warming magnitudes in the highland barley system of the Lhasa River.

Transition of populations from rural to urban living causes landscape changes and alters the functionality of soil ecosystems. It is unclear how this urbanization disturbs the microbial ecology of soils and how the disruption influences nitrogen cycling. In this study, microbial communities in turfgrass-grown soils from urban and suburban areas around Xiamen City were compared to microbial communities in the soils from rural farmlands. The potential N2O emissions, potential denitrification activity, and abundances of denitrifiers were higher in the rural farmland soils compared with the turfgrass soils. Ammonia oxidizing archaea (AOA) were more abundant than ammonia oxidizing bacteria (AOB) in turfgrass soils. Within turfgrass soils, the potential nitrification activities and AOA abundances were higher in the urban than in the suburban soils. These results indicate a more pivotal role of AOA in nitrification, especially in urban soils. Microbial community composition was distinctly grouped along urbanization categories (urban, suburban, and rural) classified according to the population density, which can in part be attributed to the differences in soil properties. These observed changes could potentially have a broader impact on soil nutrient availability and greenhouse gas emissions.

A transgenic Bt cotton (Sukang-103) and its non-Bt cotton counterpart (Sumian-12) were investigated to evaluate the potential risk of transgenes on the soil ecosystem. The activities of urease, phosphatase, dehydrogenase, phenol oxidase, and protease in cotton rhizosphere were assayed during the vegetative, reproductive, and senescing stages of cotton growth and after harvest. A Biolog system was used to evaluate the functional diversity of microbial communities in soils after a complete cotton growth cycle. Enzymatic activities in soils amended with cotton biomass were also assayed. Results showed that there were few significant differences in enzyme activities between Bt and non-Bt cottons at any of the growth stages and after harvest; amendment with cotton biomass to soil enhanced soil enzyme activities, but there were no significant difference between Bt and non-Bt cotton; the richness of the microbial communities in rhizosphere soil did not differ between Bt and the non-Bt cotton, and close to that of control soil; the functional diversity of microbial communities were not different in rhizosphere soils between Bt and non-Bt cotton. All results suggested that there was no evidence to indicate any adverse effects of Bt cotton on the soil ecosystem in this study.

Wildland fire is increasingly recognized as a driver of bioaerosol emissions, but the effects that smoke-emitted microbes have on the diversity and community assembly patterns of the habitats where they are deposited remain unknown. In this study, we examined whether microbes aerosolized by biomass burning smoke detectably impact the composition and function of soil sinks using lab-based mesocosm experiments. Soils either containing the native microbial community or presterilized by γ-irradiation were inundated with various doses of smoke from native tallgrass prairie grasses. Smoke-inundated, γ-irradiated soils exhibited significantly higher respiration rates than both smoke-inundated, native soils and γ-irradiated soils exposed to ambient air only. Microbial communities in γ-irradiated soils were significantly different between smoke-treated and control soils, which supports the hypothesis that wildland fire smoke can act as a dispersal agent. Community compositions differed based on smoke dose, incubation time, and soil type. Concentrations of phosphate and microbial biomass carbon and nitrogen together with pH were significant predictors of community composition. Source tracking analysis attributed smoke as contributing nearly 30% of the taxa found in smoke-inundated, γ-irradiated soils, suggesting smoke may play a role in the recovery of microbial communities in similar damaged soils. Our findings demonstrate that short-distance microbial dispersal by biomass burning smoke can influence the assembly processes of microbial communities in soils and has implications for a broad range of subjects including agriculture, restoration, plant disease, and biodiversity.

Effects of cultivation of OsrHSA transgenic rice on functional diversity of microbial communities in the soil rhizosphere

Phosphorus (P)-modified biochar demonstrates dual capabilities for heavy metal immobilization and soil quality enhancement. However, the underlying mechanism of microbial response to changes in soil properties is still unclear. In this study, P-modified biochar, prepared by co-pyrolysis of apple tree branches with K3PO4, was used for removal of heavy metals from the soils near a mining area. Effects of P-modified biochar on the microbial communities in soil were investigated and the key driving factors were identified. Adding P-modified biochar reduced the bioavailable cadmium and lead contents of the soil by 28.21% and 28.64%, respectively, mainly through improved co-precipitation and cation exchange. In turn, the cadmium and lead concentrations in maize grains were reduced by 36.52% and 61.82% respectively. Meanwhile, the richness and diversity of soil bacteria significantly decreased with the addition of P-modified biochar (P < 0.05). Microbial multi-trophic ecological network module analysis and partial least squares pathway modeling indicated that biochar changed the capacity of the soil to provide microorganisms with nitrogen and P, requiring the key microbial taxa (modules 1 and 3) to adjust. Modules 1 and 3 played important but opposite functions in the nitrogen and P cycle of the soil. This further led to variations in the composition and structure of microbial communities in soil. Particularly, changes in the bioavailability of heavy metals showed a negligible effect on soil microbial communities. This study emphasizes that P-modified biochar can efficiently reduce soil heavy metal bioavailability and alter the microbial community by regulating nutrient supply balance. Graphical Abstract

Pollution due to heavy metals is a serious global environmental problem, particularly in China. It is thus important to study the effects of heavy metal pollution, especially in mining areas. Cadmium(Cd) and lead(Pb) severely damage the microbial life in soil. The concentration of heavy metals and their toxic effects on microbes and enzymes in soil were examined in this study using contaminated soil samples. The Biolog method was used to analyze the characteristics of the microbial community. The results showed that the addition of Cd2+ and Pb2+ in different concentrations has a significant impact on microbial and enzyme activity in soil. With an increase in their concentrations, activities of the microbial community and enzymes decreased gradually. Each index related to the structure of the microbial community in soil decreased, indicating that pollution due to Cd and Pb reduced its size and functional activity. This study provides a reference for future research on the functional diversity of the microbial community in soil and plays its role in their environmental management.

Effects of solarization on microbial communities in soil were investigated with an incubation experiment and in a greenhouse experiment with isolated bed culture of tomato (Solanum lycopersicum L.) by molecular techniques. Microbial biomass carbon in soil was decreased by about half in the incubation experiment treated with 45°C for 14 days and the greenhouse experiment with solarization for 45 days. Bacterial and fungal communities in soil were affected by the heat and solarization treatments in both the experiments and greatly different from the communities in the unheated soil or the soil before solarization. Copy number of amoA gene of ammonia-oxidizing bacteria in soil was decreased to one-tenth or less by the treatments in both the experiments. This study revealed that the solarization made a great impact on the abundance and composition of microbial communities in soil.

Characterization of redox-related soil microbial communities along a river floodplain continuum by fatty acid methyl ester (FAME) and 16S rRNA genes

Heavy metals can severely influence the mineralisation of organic pollutants in a compound-polluted environment. However, to date, no study has focused on the effects of heavy metals on the active organic pollutant-degrading microbial communities to understand the bioremediation mechanism. In this study, toluene was used as the model organic pollutant to explore the effects of soils with different levels of heavy metal pollution on organic contaminant degradation in the same area via stable isotope probing (SIP) and 16S rRNA high-throughput sequencing. Heavy metals can seriously affect toluene biodegradation and regulate the abundance and diversity of microbial communities. SIP revealed a drastic difference in the community structure of active toluene degraders between the unpolluted and heavy metal-polluted soils. All SIP-identified degraders were assigned to nine bacterial classes, among which Alphaproteobacteria, Gammaproteobacteria, and Bacilli were shared by both treatments. Among all active degraders, Nitrospira, Nocardioides, Conexibacteraceae, and Singulisphaera were linked to toluene biodegradation for the first time. Notably, the type of active degrader and microbial diversity were strongly related to biodegradation efficiency, indicating their key role in toluene biodegradation. Overall, heavy metals can affect the microbial diversity and alter the functional microbial communities in soil, thereby influencing the removal efficiency of organic contaminants. Our findings provide novel insights into the biodegradation mechanism of organic pollutants in heavy metal-polluted soils and highlight the biodiversity of microbes involved in toluene biodegradation in compound-polluted environments.

IntroductionPine wilt disease (PWD) is recognized as a destructive forest disease worldwide, leading to massive mortality of many Pinus spp., including the Korean white pine Pinus koraiensis. Current work has focused on underlying development of this disease occurring aboveground, but few studies have assessed soil consequences from the destruction in pine forest by PWD.MethodsIn this study, we collected soil samples from one stand of PWD-resistant species Larix olgensis, and from four stands of PWD-susceptible P. koraiensis (n = 8) following a natural chronosequence of PWD development (healthy, diseased, killed, and clear-cut P. koraiensis). We aimed to investigate the shifts in soil microbial and nematode communities under the canopy of P. koraiensis over the PWD progression.ResultsThe α-diversity e.g., species richness of bacterial community in soil of healthy P. koraiensis was ca. 17% lower than in soil of diseased pines. The species richness of fungal community in the soil of healthy P. koraiensis was also 24.5% lower than in soil of killed pines. The diseased and killed pines also exhibited different compositions in soil microbial community from the healthy pines, although these damaged trees did not differ themselves in the composition. In particular, the relative abundance of the methane-cycling Methylomirabilota became higher in bacterial community and the ectomycorrhizal Agaricomycetes was lower in fungal community in soil of the diseased or killed pines than healthy ones, suggesting an overall decrease in soil health caused by PWD. Although the α-diversity of soil nematode community did not vary over the development of PWD, its composition was significantly altered by the disease. Consequently, we observed a lower inter-kingdom network complexity in the soil community of the pines following the PWD, in which the bacterial networks decreased but fungal networks increased in complexity. The nematode community also showed a lower network complexity in soil of PWD-destructed pines, albeit that this only occurred when the pines were diseased rather than killed.DiscussionBy recording the structure dynamics of soil microbial and nematode communities in pines following the progression of PWD, this study helps to understand the impacts of PWD on soil biotic processes, thus providing an important reference for better assessing the ecological consequences of this devastating disease.

Differences in geological conditions have reshaped the structure and diversity of microbial communities in oily soils

Microplastics and various other contaminants are frequently present in soil. Here we investigated the long-term integrated responses of changes in the microbial community, metabolomics, heavy metal availability, and nutritional properties of the cadmium-cuprum-zinc-contaminated coastal saline soil to the three different microplastics. Various categories of microplastics had notable impacts on the available potassium, organic matter, availability of cadmium and cuprum, as well as the enzymatic activity in soil. Microplastics contamination caused diverse changes in microbial diversity and the composition of bacterial and fungal communities, resulting in the enrichment of Mortierella and a decrease of Bacillus abundance. The metabolites in soil primarily affected by microplastics contamination were the pathways involved organic acids and their derivatives, organoheterocyclic compounds, as well as lipids and lipid-like substances. Therefore, the addition of microplastics to soil may influence soil fertility, metal mobility, and alter the structure and metabolic processes of the microbial community in soil.

Effect of the fungicide tetraconazole on microbial community in silt loam soils from orchard with long history of triazole application and from grassland with no known history of fungicide usage was investigated. Triazole tetraconazole that had never been used on these soils before was applied at the field rate and at tenfold the FR. Response of microbial communities to tetraconazole was investigated during 28-day laboratory experiment by determination of changes in their biomass and structure (phospholipid fatty acids method—PLFA), activity (fluorescein diacetate hydrolysis—FDA) as well as changes in genetic (DGGE) and functional (Biolog) diversity. Obtained results indicated that the response of soil microorganisms to tetraconazole depended on the management of the soils. DGGE patterns revealed that both dosages of fungicide affected the structure of bacterial community and the impact on genetic diversity and richness was more prominent in orchard soil. Values of stress indices—the saturated/monounsaturated PLFAs ratio and the cyclo/monounsaturated precursors ratio, were almost twice as high and the Gram-negative/Gram-positive ratio was significantly lower in the orchard soil compared with the grassland soil. Results of principal component analysis of PLFA and Biolog profiles revealed significant impact of tetraconazole in orchard soil on day 28, whereas changes in these profiles obtained for grassland soil were insignificant or transient. Obtained results indicated that orchards soil seems to be more vulnerable to tetraconazole application compared to grassland soil. History of pesticide application and agricultural management should be taken into account in assessing of environmental impact of studied pesticides.Electronic supplementary materialThe online version of this article (doi:10.1007/s10646-016-1661-7) contains supplementary material, which is available to authorized users.

Understanding the salt tolerance of microbial communities may help to elucidate the effects of salt concentration and other environmental factors on soil biodiversity. Here, high-throughput sequencing of 16S rDNA and ITS was combined to investigate the distribution and salt tolerance of microbial communities in coastal soils and sediments near the Yinggehai saltern field of Hainan Island, China. The microbial communities in the soils and sediments of the land zone (YGHLS), the intertidal zone (YGHIS), and the inshore zone (YGHWS) were compared. PCoA of weighted and unweighted UniFrac distance revealed obvious differences in soil microbial community among different samples. ANOSIM analysis could clearly separate the three samples from each other. Three halotolerant bacteria, including Halomonas, Halobacillus and Wallemia, were found in the samples, which accounted for 0.0335 ± 0.0586%, 0.0241 ± 0.0304%, and 0.0308 ± 0.0445% of the total microbial community, respectively. The relative abundance of Trk system potassium uptake protein, Kdp operon response regulator, and Na+/H+ antiporter in the samples exceeded 0.09%, 0.06%, and 0.02%, respectively, indicating that the Trk system plays a major role in the salt tolerance of halotolerant bacteria in Yinggehai coastal soils and sediments.