水稻土好氧甲烷氧化菌对大气CO2浓度升高的适应规律

CH4是仅次于CO2的第二大温室气体,而稻田是CH4的主要排放源,但未来大气CO2浓度升高情景下（elevated CO2, eCO2）,水稻土好氧甲烷氧化过程及其功能微生物群落适应规律尚不清楚。本研究依托中国FACE（Free Air CO2 Enrichment）水稻田试验平台,通过13C-CH4示踪的室内微宇宙培养实验,采用稳定性同位素核酸探针（DNA-SIP）和高通量测序技术,研究了未来大气CO2浓度升高对水稻土甲烷氧化活性及其功能微生物的影响规律。研究结果表明：与常规大气CO2浓度（ambient CO2, aCO2）相比,eCO2条件下的甲烷氧化活性显著增加,从243 nmol g-1 d.w.s h-1增加至302 mol g-1 d.w.s h-1,增幅高达24.3%,甲烷氧化菌数量则增加了1.1~1.2倍。通过超高速离心获得活性甲烷氧化菌同化13CH4后合成的13C-DNA,高通量测序发现,未来大气CO2升高情景下水稻土活性好氧甲烷氧化微生物群落极可能发生明显演替,与对照相比,类型I甲烷氧化菌甲基杆菌属Methylobacter的相对丰度增加16.2%~17.0%,而甲基八叠球菌属Methylosarcina的相对丰度下降4.7%-11.1%;同时刺激了食酸菌属Acidovorax和假单胞菌属Pseudomonas等非甲烷氧化菌的活性。这些研究结果表明：未来大气CO2升高情景下,水稻土好氧甲烷氧化微生物群落结构发生分异,促进了甲烷氧化通量,而甲烷氧化的代谢产物可能引发土壤中微生物食物网的级联反应,是土壤碳储存和周转的重要功能微生物群。     

Rapid changes in the rhizosphere bacterial community structure during re-colonization of sterilized soil

Diversity has been shown to be pivotal in ecosystem stability and resilience. It is therefore important to increase our knowledge about the development of diversity. The aim of this study was to investigate the temporal dynamics of the bacterial community structure in the rhizosphere of wheat plants growing in a soil in which the initial conditions for bacterial re-colonization were modified by mixing different amounts of sterilized with native soil at ratios of 19:1, 9:1, 4:1 and 1:1. Additional treatments comprised sterilized soil or native soil. Plant dry weight at day 20 decreased with increasing percentage of native soil in the mix. The bacterial community structure in the rhizosphere was assessed by polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) at days 3, 14 and 20 after planting. The bacterial community in the sterilized soil had a lower diversity and evenness than the native soil. Both diversity and evenness increased with time in the sterilized soil. Community structure in the different mixes changed over time and the changes were mix-specific. Principal component analyses of the DGGE banding patterns showed clear differences between the treatments particularly at day 3 and day 14 and revealed changes in community structure within a few days in a given treatment. The results of the present study show that bacterial communities rapidly re-colonize sterilized soil. During re-colonization, the community structure changes rapidly with a general trend towards higher diversity and evenness. The changes in community structure over time are also affected by the amount of sterile substrate to be re-colonized.     

Elevated CO<Subscript>2</Subscript> alters the abundance but not the structure of diazotrophic community in the rhizosphere of soybean grown in a Mollisol

The effect of elevated CO₂ (eCO₂) on rhizospheric diazotrophic community in cropland has little been studied, although eCO₂ facilitates nodulation and N₂ fixation in legumes. In this study, four soybean cultivars (Xiaohuangjin, Suinong 8, Suinong 14, and Heinong 45) were grown in Mollisols for 65 days under ambient CO₂ (aCO₂) (390 ppm) or eCO₂ (550 ppm). Quantitative PCR and Illumina MiSeq sequencing targeting the nifH gene that reflects the composition of diazotrophic community were determined. Elevated CO₂ significantly increased the abundance of nifH gene copies in the rhizospheres of the Suinong 8 and Heinong 45 cultivars, but not in the Suinong 14 and Xiaohuangjin cultivars. The nifH abundance correlated negatively with nodule density (p?≤?0.01) but positively with nodule size (p?≤?0.01). Elevated CO₂ did not significantly alter the composition of diazotrophic community, nor shift dominant bacterial operational taxonomic units (OTUs). These results indicated that eCO₂ stimulated the growth but did not alter the community composition of diazotrophs in the rhizosphere of soybean, which depended on cultivar and might contribute to nodulation responses to eCO₂.     

Impact of artificial root exudates on the bacterial community structure in bulk soil and maize rhizosphere

Bacterial densities, metabolic signatures and genetic structures were evaluated to measure the impact of soil enrichment of soluble organic carbon on the bacterial community structures. The exudates chosen were detected in natural maize exudates (glucose, fructose, saccharose, citric acid, lactic acid, succinic acid, alanine, serine and glutamic acid) and were used at a rate of 100 μg C g⁻¹ day⁻¹ for 14 days. Moreover two synthetic solutions with distinct carbon/nitrogen ratios (20.5 and 40.1), obtained by varying carboxylic and amino acids concentrations, were compared in order to evaluate the potential role of organic N availability. The in vitro experiment consisted of applying exudate solutions to bulk soil. In the case of the control, only distilled water was added. Both solutions significantly increased bacterial densities and modified the oxidation pattern of Biolog® GN2 plates with no effect of the C/N ratio on these two parameters. Genetic structure, measured by means of ribosomal intergenic spacer analysis (RISA), was also consistently modified by the organic amendments. N availability levels led to distinct genetic structures. In a second experiment, one of the previous exudate solutions (C/N 20.5) was applied to 15-day-old maize plants to determine the structural influence of exudates on the rhizosphere microbial community (in situ experiment). Bacterial densities were significantly increased, but to a lesser extent than had been found in the in vitro experiment. Metabolic potentials and RISA profiles were also significantly modified by the organic enrichment.     

Influence of introduced potential biocontrol agents on maize seedling growth and bacterial community structure in the rhizosphere

Two species of Pseudomonas chromosomally tagged with gfp, which had shown antagonistic activity against the tomato pathogen Ralstonia solanacearum in a previous study, were assessed for their impact in the rhizosphere of maize. Plant growth characteristics, numbers of indigenous heterotrophic bacteria, changes in the bacterial community structure according to the r/K strategy concept, and shifts in MIDI-FAME profiles of culturable bacterial fractions as well as total rhizosphere microbial communities were determined in relation to seed and soil treatment with the exogenous pseudomonads. The maize rhizosphere proved to be a suitable habitat for the introduced P. chlororaphis IDV1 and P. putida RA2, which showed good survival after introduction. However, both inoculants showed a small growth-reducing effect towards maize, which might have been caused by the high densities of inoculants used (i.e. competition for nutrients and action of metabolites produced) and/or changes in microbial community structure (both culturable bacterial fraction and the total microflora). Probably, an altered balance among the indigenous maize rhizosphere populations occurred. Thus, the culturable bacteria, as well as the total microflora in the rhizosphere, changed in response to the introduced pseudomonads, and their development was dependent on the growth stage of the plant. The FAME analyses showed that these microbial communities comprised different populations, and were separated according to, first, the method used (direct versus cultivation-based), second, sampling time, and, finally, inoculation level.     

Growth,phosphorus uptake,and rhizosphere microbial‐community composition of a phosphorus‐efficient wheat cultivar in soils differing in pH

In a pot experiment, the P‐efficient wheat (Triticum aestivum L.) cultivar Goldmark was grown in ten soils from South Australia covering a wide range of pH (four acidic, two neutral, and four alkaline soils) with low to moderate P availability. Phosphorus (100 mg P kg^–1) was supplied as FePO₄ to acidic soils, CaHPO₄ to alkaline, and 1:1 mixture of FePO₄ and CaHPO₄ to neutral soils. Phosphorus uptake was correlated with P availability measured by anion‐exchange resin and microbial biomass P in the rhizosphere. Growth and P uptake were best in the neutral soils, lower in the acidic, and poorest in the alkaline soils. The good growth in the neutral soils could be explained by a combination of extensive soil exploitation by the roots and high phosphatase activity in the rhizosphere, indicating microbial facilitation of organic‐P mineralization. The plant effect (soil exploitation by roots) appeared to dominate in the acidic soils. Alkaline phosphatase and diesterase activities in acidic soils were lower than in neutral soils, but strongly increased in the rhizosphere compared with the bulk soil, suggesting that microorganisms contribute to P uptake in these acidic soils. Shoot and root growth and P uptake per unit root length were lowest in the alkaline soils. Despite high alkaline phosphatase and diesterase activities in the alkaline soils, microbial biomass P was low, suggesting that the enzymes could not mineralize sufficient organic P to meet the demands of plants and microorganisms. Microbial‐community composition, assessed by fatty acid methylester (FAME) analysis, was strongly dependent on soil pH, whereas other soil properties (organic‐C or CaCO₃ content) were less important or not important at all (soil texture).     

Density, structure, and diversity of the cultivable arylsulfatase-producing bacterial community in the rhizosphere of field-grown rape and barley

In this study we investigated the arylsulfatase-producing bacterial community (ARS-BC) in the rhizosphere soils of field-grown rape in comparison with that of barley. For this, the rhizosphere soils from both plant species were sampled four times during plant growth. Soil arylsulfatase (ARS) activity and the density and the structure of the cultivable ARS-BC on M9-Xsulf medium were then determined. ARS activity in rape rhizosphere was greater than in barley rhizosphere and evolved along the phenology in the two rhizosphere soils. In parallel, the average density of ARS-BC in the rape rhizosphere was higher than that in the barley rhizosphere. Moreover, ARS activity is correlated with ARS-BC density both in rape and barley rhizosphere soils. The structure of the ARS-BC in the rape rhizosphere was different from that in the barley rhizosphere. In the rape rhizosphere, the ARS-BC was substantially more structured than in the barley rhizosphere. Among the ARS-BC, Actinobacteria and Pseudomonads were significantly present in the both rhizosphere soils. Actinobacteria predominated in the barley rhizosphere while Pseudomonads were mostly represented under rape. It is possible that the differences in ARS activity observed between rape and barley can be attributed to a different ARS-BC size and/or a different ARS-BC structure under these two plant covers. This impact of rape may be connected to a selective effect of rhizodeposits released by rape roots to the functional bacterial community. Our findings suggest that plant species, via their rhizodeposits, may affect the functional bacterial community and thus influence the dynamic of S in soil.     

Responses of nematode‐community structure in turfgrass soil to microbial filtrates from municipal–solid waste compost

Actinomycetes, Bacillus subtilis, and Bacillus thuringiensis were isolated from municipal–solid waste (MSW) compost, and different microbial liquid filtrates (MLF) were prepared. Sterile culture media with no microbes were used as their controls. The effects of MLF on soil nematode communities were examined in pot‐grown Festuca arundinacea Schreb. Fifteen genera of nematodes in background soil were identified, of which Helicotylenchus and Rotylenchus were dominant. The inoculation of MLF strongly affected the abundance and community structure of soil nematodes. Compared with their controls, lower total nematode numbers following MLF incorporation were found. Actinomycetes inoculation changed community structure of soil nematodes, transforming the dominant genera from Helicotylenchus and Rotylenchus into Cephalobus, Chiloplacus, and Aphelenchus. Actinomycetes incorporation resulted in a significant decrease of plant‐parasitic nematodes relative to control pots. Only plant‐parasitic and omnivorous‐predatory nematodes were found in treatments following B. subtilis inoculation, and Helicotylenchus, Rotylenchus were dominant genera with relative abundance of 76.2% and 14.3%, respectively. Although the dominant genera were still Helicotylenchus and Rotylenchus, B. thuringiensis inoculation led to a marked decrease in populations of plant‐parasitic nematodes and an increase in populations of fungivorous and bacterivorous nematodes relative to control. Shannon's diversity index (H′), evenness index (J′), richness index (SR), and Wasilewska index (WI) in pots treated with actinomycetes and B. thuringiensis filtrates were significantly higher than those of their controls, whereas significant lower dominance index (λ) in actinomycetes and B. thuringiensis treatments was observed than their controls. Plant growth was improved in the treatments inoculated with three microbes. The findings highlight that actinomycetes can most effectively suppress plant‐parasitic nematodes, increase community diversity, evenness, and richness, thus improving soil environment for turf growth.     

连作对再植枸杞根际细菌群落多样性和群落结构的影响研究

受枸杞道地产区土地资源等因素限制,连作障碍已成为影响枸杞产业发展的重要原因之一,导致严重的经济损失.研究连作条件下枸杞农田土壤生态系统微生物群落的演替规律对枸杞产业的可持续发展具有重要的理论意义.以宁夏银川市南梁农场连作多年的枸杞地为研究对象,利用Illumina MiSeq测序技术分析了连作对再植枸杞根际/非根际细菌群落的影响.结果表明,连作地显著抑制再植枸杞苗地径的增加,且其土壤pH较对照样地显著降低(p<0.05).测序结果证实,与对照样地相比,连作地再植枸杞根际土壤细菌物种数显著降低(p<0.05),细菌群落α多样性下降(p>0.05).主坐标分析表明,连作和对照样地间枸杞非根际细菌群落结构无明显差异,但连作显著改变再植枸杞根际细菌的群落结构.对细菌群落丰度的统计分析发现,连作地枸杞根际浮霉菌门、非根际假单胞菌门的相对丰度较对照样地显著降低(p<0.05).此外,冗余分析结果表明:枸杞园土壤pH和有效磷含量是影响枸杞非根际土壤细菌群落结构变化的主要因素,分别解释了41.8%和35.4%的群落结构变化(p<0.05),其他土壤因子无统计学意义,但土壤理化因子对再植枸杞根际细菌群落结构变化的影响均未达显著水平.这些结果证实连作能够显著抑制再植枸杞生长、影响再植枸杞根际细菌群落结构和多样性,干扰枸杞与土壤细菌群落间的互作关系.这些研究结果将为解析枸杞连作障碍机制提供理论基础.     

Climate change goes underground: effects of elevated atmospheric CO<Subscript>2</Subscript> on microbial community structure and activities in the rhizosphere

General concern about climate change has led to growing interest in the responses of terrestrial ecosystems to elevated concentrations of CO₂ in the atmosphere. Experimentation during the last two to three decades using a large variety of approaches has provided sufficient information to conclude that enrichment of atmospheric CO₂ may have severe impact on terrestrial ecosystems. This impact is mainly due to the changes in the organic C dynamics as a result of the effects of elevated CO₂ on the primary source of organic C in soil, i.e., plant photosynthesis. As the majority of life in soil is heterotrophic and dependent on the input of plant-derived organic C, the activity and functioning of soil organisms will greatly be influenced by changes in the atmospheric CO₂ concentration. In this review, we examine the current state of the art with respect to effects of elevated atmospheric CO₂ on soil microbial communities, with a focus on microbial community structure. On the basis of the existing information, we conclude that the main effects of elevated atmospheric CO₂ on soil microbiota occur via plant metabolism and root secretion, especially in C3 plants, thereby directly affecting the mycorrhizal, bacterial, and fungal communities in the close vicinity of the root. There is little or no direct effect on the microbial community of the bulk soil. In particular, we have explored the impact of these changes on rhizosphere interactions and ecosystem processes, including food web interactions.     

Short‐term sequestration of slurry‐derived carbon and nitrogen in temperate grassland soil as assessed by 13C and 15N natural abundance measurements

Land application of animal wastes from intensive grassland farming has caused growing environmental problems during the last decade. This study aimed to elucidate the short‐term sequestration of slurry‐derived C and N in a temperate grassland soil (Southwest England) using natural abundance ¹³C and ¹⁵N stable isotope techniques. Slurry was collected from cows fed either on perennial ryegrass (C3) or maize (C4) silages. 50 m³ ha^—1 of each of the obtained C3 or C4 slurries (δ¹³C = —30.7 and —21.3‰, δ¹⁵N = +12.2 and + 13.8 ‰, respectively) were applied to a C₃ soil with δ¹³C and δ¹⁵N values of —30.0 ± 0.2‰ and + 4.9 ± 0.3‰, respectively. Triplicate soil samples were taken from 0—2, 2—7.5, and 7.5—15 cm soil depth 90 and 10 days before, at 2 and 12 h, as well as at 1, 2, 4, 7, and 14 days after slurry application and analyzed for total C, N, δ¹³C, and δ¹⁵N. No significant differences in soil C and N content were observed following slurry application using conventional C and N analysis techniques. However, natural abundance ¹³C and ¹⁵N isotope analysis allowed for a sensitive temporal quantification of the slurry‐derived C and N sequestration in the grassland soil. Our results showed that within 12 hours more than one‐third of the applied slurry C was found in the uppermost soil layer (0—2 cm), decreasing to 18% after 2 days, but subsequently increasing to 36% after 2 weeks. The tentative estimate of slurry‐derived N in the soil suggested a decrease from 50% 2 hours after slurry application to only 26% after 2 weeks, assuming that the increase in δ¹⁵N of the slurry plots compared to the control is proportional to the amount of slurry‐incorporated N. We conclude that the natural abundance tracer technique can provide a rapid new clue to the fate of slurry in agricultural C and N budgets, which is important for environmental impacts, farm waste management, and climate change studies.     

Soil organic carbon temperature sensitivity of different soil types and land use systems in the Brazilian semi‐arid region

Quantifying the sensitivity of soil organic matter decomposition (SOM) to global warming is critical for predict future impacts of climate change on soil organic carbon stocks (SOC) and soil respiration, especially in semi‐arid regions such as north‐eastern Brazil, where SOC stocks are naturally small. In this study, the responses of the labile and recalcitrant carbon components and soil respiration dynamics were evaluated in three different soil types and land use systems (native vegetation, cropland and pasture) of the Brazilian semi‐arid region, when submitted to temperature increase. After 169 days of incubation, the results showed that an increase of 5°C generated an average increase in CO₂ emission of 12.0%, but which could reach 28.1%. Overall, the labile carbon (LC) in areas of native vegetation showed greater sensitivity to temperature than in cropland areas. It was also observed that recalcitrant carbon (RC) was more sensitive to warming than LC. Our results indicate that Brazil's semi‐arid region presents a substantial vulnerability to global warming, and that the sensitivity of RC and of LC in areas of native vegetation to warming can enhance SOC losses, contributing to positive feedback on climate change, and compromising the productive systems of the region. However, further studies evaluating other types of soil and texture and management systems should be carried out to consolidate the results obtained and to improve the understanding about SOM decomposition in the Brazilian semi‐arid region.     

Microbial community abundance and structure are determinants of soil organic matter mineralisation in the presence of labile carbon

Altered rates of native soil organic matter (SOM) mineralisation in the presence of labile C substrate (‘priming’), is increasingly recognised as central to the coupling of plant and soil-biological productivity and potentially as a key process mediating the C-balance of soils. However, the mechanisms and controls of SOM-priming are not well understood. In this study we manipulated microbial biomass size and composition (chloroform fumigation) and mineral nutrient availability to investigate controls of SOM-priming. Effects of applied substrate (¹³C-glucose) on mineralisation of native SOM were quantified by isotopic partitioning of soil respiration. In addition, the respective contributions of SOM-C and substrate-derived C to microbial biomass carbon (MBC) were quantified to account for pool-substitution effects (‘apparent priming’). Phospholipid fatty acid (PLFA) profiles of the soils were determined to establish treatment effects on microbial community structure, while the ¹³C-enrichment of PLFA biomarkers was used to establish pathways of substrate-derived C-flux through the microbial communities. The results indicated that glucose additions increased SOM-mineralisation in all treatments (positive priming). The magnitude of priming was reduced in fumigated soils, concurrent with reduced substrate-derived C-flux through putative SOM-mineralising organisms (fungi and actinomycetes). Nutrient additions reduced the magnitude of positive priming in non-fumigated soils, but did not affect the distribution of substrate-derived C in microbial communities. The results support the view that microbial community composition is a determinant of SOM-mineralisation, with evidence that utilisation of labile substrate by fungal and actinomycete (but not Gram-negative) populations promotes positive SOM-priming.     

Differences in the activity and bacterial community structure of drained grassland and forest peat soils

The microbial activity and bacterial community structure were investigated in two types of peat soil in a temperate marsh. The first, a drained grassland fen soil, has a neutral pH with partially degraded peat in the upper oxic soil horizons (16% soil organic carbon). The second, a bog soil, was sampled in a swampy forest and has a very high soil organic carbon content (45%), a low pH (4.5), and has occasional anoxic conditions in the upper soil horizons due to the high water table level. The microbial activity in the two soils was measured as the basal and substrate-induced respiration (SIR). Unexpectedly, the SIR (μl CO₂ g⁻¹ dry soil) was higher in the bog than in the fen soil, but lower when CO₂ production was expressed per volume of soil. This may be explained by the notable difference in the bulk densities of the two soils. The bacterial communities were assessed by terminal restriction fragment length polymorphism (T-RFLP) profiling of 16S rRNA genes and indicated differences between the two soils. The differences were determined by the soil characteristics rather than the season in which the soil was sampled. The 16S rRNA gene libraries, constructed from the two soils, revealed high proportions of sequences assigned to the Acidobacteria phylum. Each library contained a distinct set of phylogenetic subgroups of this important group of bacteria.     

Economic and Soil Environmental Benefits of Using Controlled‐Release Bulk Blending Urea in the North China Plain

Crop production must be increased in order to ensure a sustainable food supply for the growing world population. Controlled‐release urea (CRU) improves nutrient use efficiency and saves labor, but its use in crop production is limited due to its high cost. Bulk blending urea (BBU) consists of both CRU and conventional urea and could be an excellent substitute or replacement for CRU. Nevertheless, its economic benefits and soil environment impact are unknown. A 3‐year field experiment was conducted to investigate the effects of two different nitrogen management practices in terms of economic benefits, soil mineral nitrogen availability, aggregate stability, and soil microbial communities. Split applications of conventional urea (UREA) and a single application of BBU were tested on winter wheat (Triticum aestivum L.) and summer maize (Zea mays L.) in the North China Plain between 2010 and 2013. Crop yields were measured after each harvest, and soil environmental parameters were determined after the 3‐year crop sequence. Relative to UREA, BBU significantly increased net revenue, soil inorganic nitrogen concentration, and the functional diversity of the soil microbial community without adverse effects on the soil bacterial community composition. On the other hand, BBU reduced the amount of soil macro‐aggregates and the mean weight diameter value of soil water‐stable aggregates. Although BBU showed great potential for improving wheat–maize cropping systems in the North China Plain, future studies should focus on optimizing the nitrogen dosage and the CRU ratio in BBU to decrease nitrogen leaching, avoid soil aggregate deterioration, and maintain crop yield. Copyright © 2017 John Wiley & Sons, Ltd.     

Changes in microbial‐community structure with depth and time in a chronosequence of restored grassland soils on the Loess Plateau in northwest China

Microbial‐community structure is closely associated with plant‐community composition. The objective of this study was to evaluate the effects of depth and revegetation time on the microbial‐community structure of restored grassland soils of the Loess Plateau of China. Microbial‐community structure at 0–10 cm (depth 1) and 10–20 cm (depth 2) of eight sites of a grassland chronosequence with revegetation time ranging from 1 to 78 y was determined using phospholipid fatty acid (PLFA) analysis. Except for the youngest site microbial‐community structure at the two depths varied distinctly with actinomycetes and vesicular arbuscular mycorrhiza as the most important discriminators. Total PLFA content decreased with depth and increased with revegetation time. Protozoa were the only functional group whose proportion did not change with depth. Their relative abundance tended to decrease with increasing revegetation time. The microbial community at all sites was bacteria‐dominated with Gram‐negative bacteria representing the largest proportion. Principal‐component and cluster analysis revealed that microbial‐community structure in the surface soil (depth 1) of the older sites (23–78 y of revegetation) was rather similar which may be due to only small effects of the plant species present on the soil environment. Differences in microbial‐community composition at 0–20 cm depth of the eight sites were partly related to variations in the physico‐chemical characteristics. Relations to organic C, alkali‐extractable N, pH, and available P were found. Revegetation of former agricultural sites on the Loess Plateau improves the soil status and leads to shifts in microbial‐community structure more pronounced with depth than time.