Reclamation of lignite mine areas with Triticum aestivum: The dynamics of soil functions and microbial communities

In this paper is studied the dynamics of the soil microbial structure and function, and enzymatic activities during a chronosequence (0, 5, 10, 15 and 20 years) after reclamation of coal mine areas with wheat (Triticum aestivum). Due to the homogeneity induced by monoculture all over the sites, similarity in the dynamics of structural and functional soil attributes was expected. Moreover, the idea of Whisenant (2002) claiming non monotonic succession unfolding during the reclamation process was checked. Soil samples were collected from the upper 12 cm of cultivated fields differing in their post-reclamation age, and they were analyzed for physicochemical variables, microbial community structure (PLFAs), catabolic profiles (Biolog Ecoplates) and enzymatic activities (β-glucosidase, urease and alkaline phosphatase). Fields outside the mine area, cultivated with the same species were used as controls. Exhibiting rapid growth from 0 to 4–5 years after reclamation, slow decline from 5 to 10 years and stabilization after 10 years, the abundances of the microbial groups (Gram⁺, Gram⁻, fungi, protozoa) showed similar dynamics. Similar dynamics displayed also the activity of alkaline phosphatase and β-glucosidase, which increased gradually from 0 to 10 years and stabilized afterwards. By contrast, the activity of urease showed an inverse temporal pattern. After 15 years, the microbial abundances, the functional diversity (Shannon index), and the soil enzymatic activities of the reclaimed soils converged to values recorded in the controls fields. Significant shifts in the microbial community structure were not detected, probably because of the type of reclamation (agricultural use). However, when the overall PLFA and carbon utilization data sets were analyzed, it was revealed that the microbial community structure changed non monotonically in the transition between 0 and 5 years after reclamation, while the carbon utilization profiles exhibited more complex successional patterns. Above findings support the idea of non monotonic successional processes in soil microbial communities.     

Impact of cattle grazing and inorganic fertiliser additions to managed grasslands on the microbial community composition of soils

A study was undertaken to determine if cattle grazing on managed grasslands had an impact on the microbial community composition of soils. Microbial community molecular profiles of bacteria, actinomycetes, pseudomonads and fungi were generated by polymerase chain reaction (PCR) amplification of rDNA sequences from community DNA isolated from soils. PCR products were profiled using denaturing gradient gel electrophoresis (DGGE) and analysed by principal co-ordinate analysis. PCR–DGGE profiles indicated that cattle grazing had an impact on the pseudomonad community structure only, and that the addition of inorganic nitrogen (N) fertiliser impacted on bacterial, actinomycete and pseudomonad community structure. There was no difference in the community profiles of fungi from grazed and N fertilised grassland plots. Analysis of phospholipid fatty acid (PLFA) profiles revealed that both cattle grazing and N fertiliser impacted on microbial community structure. The abundance of individual PLFAs differed between treatments, with bacterial (15:0), actinomycete (10Me18:0) and fungal (18:2ω6) PLFAs not affected directly by grazing cattle and N fertiliser, however, there were significant grazing–fertiliser interactions. Bacterial plate counts were highest in the N fertilised plots and fungal plate counts were highest in the cattle grazed plots. Analysis of molecular microbial community profiles with PLFA and background soil data revealed several significant correlations. Notably, soil pH was positively correlated with PCO1 of the pseudomonad community profiles and negatively correlated with the fungal PLFA 18:2ω6. Fungal DGGE profiles were negatively correlated with the fungal PLFA 18:2ω6, and bacterial and fungal plate counts positively correlated with each other. Correlation analysis using PC1 from PLFA profile data showed no significant relationship with soil organic matter, pH, total C and total N. The results indicate that cattle grazing and N fertiliser addition to grasslands impact on the community composition of specific groups of micro-organisms. The consequences of such changes in population structure may have implications regarding the dynamics of nutrient turnover in soils.     

Structural diversity and enzyme activity of volcanic soils at different stages of development and response to experimental disturbance

We investigated the phospholipid fatty acid (PLFA) diversity and enzyme activities in soils from the volcano, Mt. Etna (Sicily). The soils were at sites which have been developing for different periods of time and have formed in volcanic lava of differing ages that have been supplemented with volcanic ejecta from subsequent eruptions. However, the plant communities indicated a marked successional difference between the sites and we have used this as a proxy for developmental stage. We have compared the structural and functional properties of the microbial communities in soils from the two sites and tested experimentally the hypothesis that the more diverse community was more resistant and resilient to disturbance. The experimental disturbance imposed was heating (60 °C for 48 h) and the recovery of enzyme activities (β-glucosidase, acid phosphatase and arylsulfatase) and structural properties (PLFA profiles) were then followed over six months. The microbial community in the soil from the older site was more structurally diverse and had a larger total PLFA concentration before disturbance than that of the soil from the younger site. The older soil community was not more resistant and resilient following an environmental disturbance as the younger soil community was equally or more resistant and resilient for all parameters. Changes in enzyme activities following disturbance were almost entirely attributable to changes in biomass (total PLFA).     

施肥对中国农田土壤微生物群落结构与酶活性影响的整合分析

【目的】 施肥能直接或间接改变农田生态系统的养分平衡,从而影响土壤的物理、化学和生物学特性。本研究探讨不同种植制度和土壤条件下施肥对农田土壤生物学特性的影响程度,为合理施肥和土壤肥力提升提供科学依据。 【方法】 通过收集近10年 (2008—2018年) 来发表的文献,建立了包含185组微生物量及群落结构等相关内容的数据库。采用整合分析方法(Meta-analysis),定量分析了施肥对土壤微生物量、群落结构以及酶活性的影响。 【结果】 与不施肥相比,施肥显著提高了土壤微生物磷脂脂肪酸 (PLFA) 和微生物量碳、氮含量,提高幅度分别为28.5%、30.9%和41.6%。施用 (单施或配施) 有机物料对土壤微生物总PLFA含量及微生物量碳、氮含量的提高幅度分别为47.3%、50.4%和58.7%,相当于施用化肥的2.8、2.4和3.9倍。与不施肥相比,施肥均能增加各类微生物菌群PLFA含量,对细菌、真菌及放线菌的提高幅度为23.8%～30.4%,对革兰氏阴性菌(G–)和革兰氏阳性菌 (G+) 的提高幅度为37.8%～43.2%,且施用有机物料处理对各类微生物菌群PLFA含量的提高幅度显著高于施化肥处理。施用化肥对土壤微生物总PLFA含量的提高幅度在一年两熟制区为17.9%,在水田和水旱轮作条件下为18.3%～27.6%,而在一年一熟制区及旱地条件下对土壤微生物总PLFA含量无显著影响。在不同pH的土壤中,施用有机物料对微生物总PLFA的提高幅度均显著高于施化肥处理。在pH < 6与pH > 8的土壤上施用化肥对微生物总PLFA含量无明显影响。施肥显著提高了与土壤有机质分解相关的β-葡萄糖苷酶(42.4%)和乙酰氨基葡萄糖苷酶(174.5%)的活性,对与氮循环相关的亮氨酸氨基肽酶活性无显著影响。统计分析还表明,施肥并未改变土壤微生物的真菌细菌比(F∶B)和革兰氏阳性菌革兰氏阴性菌比(G +∶G–)。 【结论】 在不同种植制度、土地利用类型和土壤pH下,施肥显著改变了土壤微生物量和与有机质分解相关的酶活性,但未改变土壤微生物的真菌细菌比(F∶B)和革兰氏阳性菌革兰氏阴性菌比(G+∶G–)。单施或配施有机物料均有利于提高农田土壤微生物总量及各类菌群的生物量,效果显著好于单施化肥。      

Short-term effect of tillage and crop rotation on microbial community structure and enzyme activities of a clay loam soil

A field study was carried out to analyze the short-term (2 years) effect of tillage and crop rotation on microbial community structure and enzyme activities of a clay loam soil. The experimental design was a split-plot arrangement of treatments, consisting of two tillage treatments—ridge tillage (RT) and no-tillage (NT)—in combination with two crop rotation treatments—corn (Zea mays L.) monoculture and a 2-year corn-soybean (Glycine max L.) rotation. Phospholipid fatty acid (PLFA) profiles were used to assess soil microbial community structure. No-tillage resulted in significantly higher total PLFAs compared to the RT treatment, which was accompanied by higher activities of protease, β-glucosaminidase, and β-glucosidase. This suggests a close link between soil microbial communities and enzyme activities in response to tillage. The increase of total microbial lipid biomass in the NT soils was due to the increase in both fungal and bacterial PLFAs. Crop rotation had little effect on soil bacterial communities and enzyme activities, but it significantly influenced soil fungal communities, particularly arbuscular mycorrhizal fungi. Soils under monoculture corn had higher fungal biomass than soils under corn-soybean rotation regardless of tillage treatment.     

Shifts in rhizosphere microbial communities and enzyme activity of Poa alpina across an alpine chronosequence

This study quantifies the influence of Poa alpina on the soil microbial community in primary succession of alpine ecosystems, and whether these effects are controlled by the successional stage. Four successional sites representative of four stages of grassland development (initial, 4 years (non-vegetated); pioneer, 20 years; transition, 75 years; mature, 9500 years old) on the Rotmoos glacier foreland, Austria, were sampled. The size, composition and activity of the microbial community in the rhizosphere and bulk soil were characterized using the chloroform-fumigation extraction procedure, phospholipid fatty acid (PLFA) analysis and measurements of the enzymes β-glucosidase, β-xylosidase, N-acetyl-β-glucosaminidase, leucine aminopeptidase, acid phosphatase and sulfatase. The interplay between the host plant and the successional stage was quantified using principal component (PCA) and multidimensional scaling analyses. Correlation analyses were applied to evaluate the relationship between soil factors (C_org, N_t, C/N ratio, pH, ammonium, phosphorus, potassium) and microbial properties in the bulk soil. In the pioneer stage microbial colonization of the rhizosphere of P. alpina was dependent on the reservoir of microbial species in the bulk soil. As a consequence, the rhizosphere and bulk soil were similar in microbial biomass (ninhydrin-reactive nitrogen (NHR-N)), community composition (PLFA), and enzyme activity. In the transition and mature grassland stage, more benign soil conditions stimulated microbial growth (NHR-N, total amount of PLFA, bacterial PLFA, Gram-positive bacteria, Gram-negative bacteria), and microbial diversity (Shannon index H) in the rhizosphere either directly or indirectly through enhanced carbon allocation. In the same period, the rhizosphere microflora shifted from a G⁻ to a more G⁺, and from a fungal to a more bacteria-dominated community. Rhizosphere β-xylosidase, N-acetyl-β-glucosaminidase, and sulfatase activity peaked in the mature grassland soil, whereas rhizosphere leucine aminopeptidase, β-glucosidase, and phosphatase activity were highest in the transition stage, probably because of enhanced carbon and nutrient allocation into the rhizosphere due to better growth conditions. Soil organic matter appeared to be the most important driver of microbial colonization in the bulk soil. The decrease in soil pH and soil C/N ratio mediated the shifts in the soil microbial community composition (bacPLFA, bacPLFA/fungPLFA, G⁻, G⁺/G⁻). The activities of β-glucosidase, β-xylosidase and phosphatase were related to soil ammonium and phosphorus, indicating that higher decomposition rates enhanced the nutrient availability in the bulk soil. We conclude that the major determinants of the microflora vary along the successional gradient: in the pioneer stage the rhizosphere microflora was primarily determined by the harsh soil environment; under more favourable environmental conditions, however, the host plant selected for a specific microbial community that was related to the dynamic interplay between soil properties and carbon supply.     

Soil microbial diversity of four German long-term field experiments

Abstract

The understanding of agro-ecosystems is the key to estimating the influence of long-term agricultural production methods on the environment. The present study aimed to improve the knowledge of functional and structural soil microbial diversity influenced by differentiated fertilization at four German long-term field experiments. Soil microbial biomass, β-glucosidase, protease, alkaline phosphatase, DMSO-reduction and TTC-dehydrogenase were evaluated in soils from three different fertilizer treatments (control, farmyard manure, mineral fertilizer) at four sites (Lauterbach, Bad Lauchstädt, Halle, Thyrow). Profiles of 29 identified phospholipid fatty acids were used for the evaluation of structural diversity. The results obtained showed that fertilization applied over several decades or even more than a century has led to distinct alterations of the soil ecosystem. There was a clear separation of the sites by microbial biomass and metabolic activities into dependence of soil properties and fertilization treatments. In contrast to the control, microbial biomass and enzyme activities of the FYM soils increased more strongly than in the NPK plots. The results of PLFA analyses indicate that the community of the autochthonous microflora has differently changed among sites and fertilizer application. Principle component analyses revealed that bacteria especially Gram-positive bacteria and eukaryotes were responsible for these differences.     

不同土地利用方式下围垦海涂微生物群落和土壤酶特征

利用DGGE技术,从微生物多样性的角度,结合土壤酶活性研究不同农林利用方式对围垦海涂养分特征的影响。结果表明:未利用海涂盐分含量最高,而有机质和碱解氮含量最低;相比于蔬菜地和林地,棉花地和水稻田的有机质、碱解氮、过氧化氢酶和蛋白酶活性更高。四种利用方式土壤的脲酶和磷酸酶活性差异不显著。细菌是土壤中的主要种群,其数量与土壤有机质、碱解氮等养分特征呈显著正相关,表现为水稻田、棉花地>蔬菜地、林地>未利用。DGGE图谱分析结果显示未利用土壤shannon多样性指数最高为2.81,与水稻田、棉花地较为接近,其次为蔬菜地和林地,分别为2.52和2.38。围垦利用引起土壤中的Gaetbulibacter marinus与Gillisia mitskevichiae种属变化。围垦利用后土壤质量优于未利用海涂。相比而言,种植水稻对提高土壤肥力水平,维持土壤质量较为有利。     

Soil moisture and plant residue addition interact in their effect on extracellular enzyme activity

Water availability strongly affects soil microbial activity and community composition. In a laboratory incubation we investigated the combined effect of soil moisture potential (−10 kPa, −135 kPa, and <−1500 kPa) and plant residue addition on soil enzyme activities (protease, β-glucosidase, β-glucosaminidase and exocellulase) and phospholipid fatty acid (PLFA) profiles. Soil respiration was positively correlated with soil moisture potential and significantly increased with the addition of residue. In the unamended soil, enzyme activities were little affected by soil moisture potential, nor did they change much over time. The addition of residue, however, significantly increased enzyme activity at each moisture level. Furthermore, all four enzyme activities were considerably higher in the amended dry soil than in amended samples with a higher moisture potential. In contrast, in the amended dry soil, respiration and microbial biomass were reduced compared to the amended samples with a higher moisture potential. The low microbial biomass in the amended dry soil was mainly due to a decrease in Gram-negative bacteria, while the fungal biomass reached similar levels at all water potentials. Therefore, shifts in microbial community composition alone cannot explain the increased enzyme activities in the dry soil. Other factors, such as increased fungal activity, stronger interactions between enzymes and soil particles due to thinner water films, may have contributed to the observed effects. Our results suggest that under dry conditions, potential enzyme activities may be decoupled from microbial biomass and respiration in the presence of substrates.     

Forest floor microbial communities in relation to stand composition and timber harvesting in northern Alberta

With the growing interest in silvicultural techniques that more closely emulate natural disturbance regimes, there is a need to better understand how partial harvesting affects the soil microbial community in stands with varying ecological characteristics, e.g., tree species composition. Four and a half and 5.5 years post-harvest, we used phospholipid fatty acid (PLFA) and substrate-induced respiration (SIR) analyses to compare the microbial biomass and microbial community structure of forest floors from stands dominated by white spruce (Picea glauca; SPRUCE) or by trembling aspen (Populus tremuloides; ASPEN) and from mixed-species (MIXED) stands in northern Alberta, Canada, that had been clearcut, partial-cut with 20% retention, partial-cut with 50% retention or left uncut (controls). PLFA and SIR analyses revealed that ASPEN forest floors supported a larger microbial biomass with a very different community structure than MIXED or SPRUCE forest floors. The microbial community structure of these soils appeared to be strongly affected by the presence of white spruce and the composition of the understory vegetation. There were no effects of timber harvesting detected within or across stand types on any of the variables measured, with the exception of the PLFA 16:1ω5, which was relatively more abundant in the clearcuts and 50% retention treatments than in the uncut controls, perhaps in response to an increased forest floor pH and grass cover in the disturbed areas. The resilience to timber harvesting of the forest floors from these stands may be the result of efforts to minimize soil disturbance during harvesting and to allow vegetation to regenerate naturally. From the perspective of the forest floor microbial community, partial harvesting does not appear to have any benefit over clearcut harvesting at these boreal forest sites.     

Short-term effects of organic and inorganic fertilizers on soil microbial community structure and function

A field study was carried out to analyze the short-term impacts of replacing mineral by organic fertilizers on the microbial and biochemical parameters relevant for soil fertility and crop yield. Three types of fertilization regimes were compared: (1) conventional fertilizer regime with inorganic fertilizer, and combined integrated fertilizer regimes in which 25 % of the nutrients were supplied by either (2) rabbit manure or (3) vermicompost. The effects on microbial community structure and function (phospholipid fatty acid [PLFA] profiles, bacterial growth, fungal growth, basal respiration, β-glucosidase, protease and phosphomonoesterase activities), soil biochemical properties (total C, dissolved organic carbon [DOC], N-NH₄ ⁺, N-NO₃ ^?, PO₄, total K) and crop yield were investigated in the samples collected from the experimental soil at harvest, 3 months after addition of fertilizer. The integrated fertilizer regimes stimulated microbial growth, altered the structure of soil microbial community and increased enzyme activity relative to inorganic fertilization. Bacterial growth was particularly influenced by the type of fertilizer regime supplied, while fungal growth only responded to the amount of fertilizer provided. The use of manure produced a fast increase in the abundance of PLFA biomarkers for Gram-negative bacteria as compared to inorganic fertilizer. Nutrient supply and crop yield with organic fertilizers were maintained at similar levels to those obtained with inorganic fertilizer. The effects of the organic amendments were observed even when they involved a small portion of the total amount of nutrients supplied; thereby confirming that some of the beneficial effects of integrated fertilizer strategies may occur in the short term.     

Soil microbial community composition and land use history in cultivated and grassland ecosystems of coastal California

Phospholipid ester-linked fatty acid (PLFA) profiles were used to evaluate soil microbial community composition for 9 land use types in two coastal valleys in California. These included irrigated and non-irrigated agricultural sites, non-native annual grasslands and relict, never-tilled or old field perennial grasslands. All 42 sites were on loams or sandy loams of similar soil taxa derived from granitic and alluvial material. We hypothesized that land use history and its associated management inputs and practices may produce a unique soil environment, for which microbes with specific environmental requirements may be selected and supported. We investigated the relationship between soil physical and chemical characteristics, management factors, and vegetation type with microbial community composition. Higher values of total soil C, N, and microbial biomass (total PLFA) and lower values of soil pH occurred in the grassland than cultivated soils. The correspondence analysis (CA) of the PLFA profiles and the canonical correspondence analysis (CCA) of PLFA profiles, soil characteristics, and site and management factors showed distinct groupings for land use types. A given land use type could thus be identified by soil microbial community composition as well as similar soil characteristics and management factors. Differences in soil microbial community composition were highly associated with total PLFA, a measure of soil microbial biomass, suggesting that labile soil organic matter affects microbial composition. Management inputs, such as fertilizer, herbicide, and irrigation, also were associated with the distinctive microbial community composition of the different cultivated land use types.     

PLFA法和DGGE法分析堆肥细菌群落变化

同时采用PLFA（Phospholipid fatty acid）谱图分析法和DGGE（Denaturing gradient gel electrophoresis）法分析农业废物堆肥化过程中细菌群落的变化。结果表明：（1）单体PLFA数据显示样品之间的群落结构有明显差异,随着堆肥进程的进行,群落在不断演替,PLFA数据可以较为明确地表征微生物生物量的变化,但不能给出具体的物种变化信息;（2）DGGE分析显示堆肥过程中的样点和DGGE条带数据都存在3大主要类别,堆肥过程中细菌群落结构至少经历了3个阶段的演替,即嗜温细菌群落、高温细菌群落和腐熟期细菌群落。堆肥过程是微生物群落结构与堆肥温度相互制约的过程;（3）虽然两类方法显示的信息并不完全一致,但也因此说明了不同方法显示的信息并不是绝对的,采用各类方法组合研究堆肥微生物的信息变化是很有必要的。     

Changes in soil microbial community composition in response to fertilization of paddy soils in subtropical China

Repeated fertilizer applications to cultivated soils may alter the composition and activities of microbial communities in terrestrial agro-ecosystems. In this study, we investigated the effects of different long term fertilization practices (control (CK), three levels of mineral fertilizer (N₁P₁K₁, N₂P₂K₂, and N₃P₃K₃), and organic manure (OM)) on soil environmental variables and microbial communities by using phospholipid fatty acid (PLFA) biomarkers analysis in subtropical China. Study showed that OM treatment led to increases in soil organic carbon (SOC), total nitrogen (TN) and total phosphorus (TP) contents, while the mineral fertilizer treatment led to increases in dissolved organic carbon (DOC) content. Changes in soil microbial communities (eg. bacteria, actinomycetes) were more noticeable in soils subjected to organic manure applications than in the control soils or those treated with mineral fertilizer applications. Fungal PLFA biomarkers responded differently from the other PLFA groups, the numerical values of fungal PLFA biomarkers were similar for all the OM and mineral fertilizer treatments. PCA analysis showed that the relative abundance of most PLFA biomarkers increased in response to OM treatment, and that increased application rates of the mineral fertilizer changed the composition of one small fungal PLFA biomarker group (namely 18:3ω6c and 16:1ω5c). Further, from the range of soil environmental factors that we examined, SOC, TN and TP were the key determinants affecting soil microbial community. Our results suggest that organic manure should be recommended to improve soil microbial activity in subtropical agricultural ecosystems, while increasing mineral fertilizer applications alone will not increase microbial growth in paddy soils.     

Phyllostachys edulis (moso bamboo) rhizosphere increasing soil microbial activity rather than biomass

Purpose

Rhizosphere and fertilization might affect soil microbial activities, biomass, and community. This study aimed to evaluate the impacts of Phyllostachys edulis (moso bamboo) rhizospheres on soil nutrient contents and microbial properties in a moso bamboo forest with different fertilizer applications and to link soil microbial activities with abiotic and biotic factors.

Materials and methods

The experiment included three treatments: (1) application of 45% slag fertilizer (45%-SF); (2) application of special compound fertilizer for bamboos (SCF); and (3) the control without any fertilizer application (CK). Simultaneously, bulk soils and 0.5, 2.5, 4.5, and 6.5-year-old (y) bamboo rhizosphere soils were selected. Soil nutrient contents were analyzed. Microbial activities were evaluated based on the activities of soil enzymes including β-glucosidase, urease, protease, phosphatase, and catalase. The total microbial biomass and community were assessed with the phospholipid fatty acids (PLFAs) method.

Results and discussion

In the CK and SCF treatments, organic matter contents of rhizosphere soils were significantly higher than those of bulk soils. Soil β-glucosidase, urease, protease, phosphatase, and catalase activities in rhizosphere soils were higher than those of bulk soils, with the sole exception of β-glucosidase of 0.5 y rhizosphere soil in the 45%-SF treatment. Compared with the CK treatment, fertilizer applications tended to increase soil total PLFAs contents and changed soil microbial community. Moso bamboo rhizospheres did not significantly increase the total microbial biomass. In the SCF treatment, the Shannon index of bulk soil was significantly lower than those of rhizosphere soils.

Conclusions

Our results suggested that both rhizospheres and fertilizer applications could change the soil microbial community structures and that moso bamboo rhizosphere could increase microbial activity rather than biomass in the forest soils with different fertilizer applications.

     

Impact of the antibiotic sulfadiazine and pig manure on the microbial community structure in agricultural soils

Large amounts of veterinary antibiotics enter soil via manure of treated animals. The effects on soil microbial community structure are not well investigated. In particular, the impact of antibiotics in the presence of manure is poorly understood. In this study, two agricultural soils, a sandy Cambisol (KS) and a loamy Luvisol (ML), were spiked with manure and sulfadiazine (SDZ; 0, 10 and 100 μg g^?1) and incubated for 1, 4, 32 and 61 days. Untreated controls received only water. The microbial community structure was characterised by investigating phospholipid fatty acids (PLFA) and using PCR–denaturing gradient gel electrophoresis (DGGE) of 16S rDNA. The total concentration of PLFA increased with addition of manure and was reduced by both SDZ concentrations at incubation times >4 days. The SDZ addition decreased the bacteria:fungi ratio. The largest stress level, measured as ratio of PLFA (cyc17:0 + cyc19:0)/(16:1ω7c + 18:1ω7c), was found for the controls, followed by the manure treatments and the SDZ treatments. A discriminant analysis of the PLFA clearly separated treatments and incubation times. Both soils differed in total PLFA concentrations and Gram^?:Gram⁺ ratios, but showed similar changes in PLFA pattern upon soil treatment. Effects of manure and SDZ on the bacterial community structure were also revealed by DGGE analysis. Effects on pseudomonads and β-proteobacteria were less pronounced. While community structure remained altered even after two months, the extractable concentrations of SDZ decreased exponentially and the remaining solution concentrations after 32 days were ≤27% of the spiking concentration. Our results demonstrate that a single addition of SDZ has prolonged effects on the microbial community structure in soils.     

Spatial variability of enzyme activities and microbial biomass in the upper layers of Quercus petraea forest soil

Extracellular lignocellulose-degrading enzymes are responsible for the transformation of organic matter in hardwood forest soils. The spatial variability on a 12 × 12 m plot and vertical distribution (0–8 cm) of the ligninolytic enzymes laccase and Mn-peroxidase, the polysaccharide-specific hydrolytic enzymes endoglucanase, endoxylanase, cellobiohydrolase, 1,4-β-glucosidase, 1,4-β-xylosidase and 1,4-β-N-acetylglucosaminidase and the phosphorus-mineralizing acid phosphatase were studied in a Quercus petraea forest soil profile. Activities of all tested enzymes exhibited high spatial variability in the L and H horizons. Acid phosphatase and 1,4-β-N-acetylglucosaminidase exhibited low variability in both horizons, while the variability of Mn-peroxidase activity in the L horizon, and endoxylanase and cellobiohydrolase activities in the H horizon were very high. The L horizon contained 4× more microbial biomass (based on PLFA) and 7× fungal biomass (based on ergosterol content) than the H horizon. The L horizon also contained relatively more fungi-specific and less actinomycete-specific PLFA. There were no significant correlations between enzyme activities and total microbial biomass. In the L horizon cellulose and hemicellulose-degrading enzymes correlated with each other and also with 1,4-β-N-acetylglucosaminidase and acid phosphatase activities. Laccase, Mn-peroxidase and acid phosphatase activities correlated in the H horizon. The soil profile showed a gradient of pH, organic carbon and humic compound content, microbial biomass and enzyme activities, all decreasing with soil depth. Ligninolytic enzymes showed preferential localization in the upper part of the H horizon. Differences in enzyme activities were accompanied by differences in the microbial community composition where the relative amount of fungal biomass decreased and actinomycete biomass increased with soil depth. The results also showed that the vertical gradients occur at a small scale: the upper and lower parts of the H horizon only 1 cm apart were significantly different with respect to seven out of nine activities, microbial biomass content and community composition.     

Investigating microbial community structure in soils by physiological, biochemical and molecular fingerprinting methods

Several biochemical and molecular methods are used to investigate the microbial diversity and changes in microbial community structure in rhizospheres and bulk soils resulting from changes in management. We have compared the effects of plants on the microbial community, using several methods, in three different types of soils. Pots containing soil from three contrasting sites were planted with Lolium perenne (rye grass). Physiological (Biolog), biochemical (PLFA) and molecular (DGGE and TRFLP) fingerprinting methods were employed to study the change in soil microbial communities caused by the growth of rye grass. Different methods of DNA extraction and nested PCR on TRFLP profiles were examined to investigate whether they gave different views of community structure. Molecular methods were used for both fungal and bacterial diversity. Principal component analysis of Biolog data suggested a significant effect of the plants on the microbial community structure. We found significant effects of both soil type and plants on microbial communities in PLFA data. Data from TRFLP of soil bacterial communities showed large effects of soil type and smaller but significant effects of plants. Effects of plant growth on soil fungal communities were measured by TRFLP and DGGE. Multiple Procrustes analysis suggested that both methods gave similar results, with only soil types having a significant effect on fungal communities. However, TRFLP was more discriminatory as it generated more ribotype fragments for each sample than the number of bands detected by DGGE. Neither methods of DNA extraction nor the nested PCR had any effect on the evaluation of soil microbial community structure. In conclusion, the different methods of microbial fingerprinting gave qualitatively similar results when samples were processed consistently and compatible statistical methods used. However, the molecular methods were more discriminatory than the physiological and biochemical approaches. We believe results obtained from this experiment will have a major impact on soil microbial ecology in general and rhizosphere–microbial interaction studies in particular, as we showed that the different fingerprinting methods for microbial communities gave qualitatively similar results.     

Soil moisture pre-treatment effects on enzyme activities as indicators of heavy metal-contaminated and reclaimed soils

Heavy metal contamination can inhibit soil functions but it is often difficult to determine the degree of pollution or when soil reclamation is complete. Enzyme assays offer potential as indicators of biological functioning of soils. However, antecedent water content of soil samples may affect the outcome of biological measurements. In Mediterranean regions, for much of the year ‘field moist’ surface soil can have water content similar to that of air-dry samples. The objectives of this study were to: (1) determine the sensitivity of a range of enzyme assays to detect the degree of pollution from a heavy metal mine spill; (2) evaluate rewetting field-dry soil as a pre-treatment for enzyme assays; and (3) test multivariate analysis for improving discrimination between polluted, reclaimed and non-polluted soils. The Aznalcóllar mining effluent spill provided a unique opportunity to address these objectives. This accident released toxic, heavy metal-contaminated (As, Bi, Cd, Cu, Pb, Tl, Zn…) and acid tailings into the Guadiamar watershed (SW Spain) in 1998, severely affecting the riparian zone along more than 4000 ha. Contaminated soils were collected from the highly polluted upper watershed and less polluted lower watershed along with reclaimed soil at both sites. Enzyme activities (phosphatases, arylsulfatase, β-glucosidase, urease and dehydrogenase) were assessed on both field-moist samples and soils rewetted to 80% of water-holding capacity and then incubated at 21 °C for 7 d prior to the assay. The reclaimed soils had higher activities than polluted soils but, typically, 1.5-3 times lower levels of activity than the non-polluted soil. Regardless of the moisture pre-treatment, all enzymes showed significant effects due to pollution, with urease and β-glucosidase showing the greatest discrimination between degrees of contamination. In general, rewetting field-dried soils increased activities on non-polluted and reclaimed soils which improved discrimination with polluted soils. Another method to increase the potential of soil enzyme activities to detect soil contamination could be to combine them in multivariate analysis, which provides a more holistic representation of the biochemical and microbial functionality of a soil.