Seasonal variations in abundance and activity of nitrifiers in four arable cropping systems

Ammonium and nitrite oxidizers were counted with the most probable number (MPN) method and potential ammonium- and nitrite-oxidation rates were determined with a chlorate inhibition technique in an arable soil over a 3-year period. Samples were taken from the topsoil once a month for 2 years and a few times during a third year in four cropping systems: unfertilized lucerne ley and barley, and nitrate fertilized grass ley and barley. The distribution of nitrifiers was determined and their activities measured at various soil depths and between and within plant rows of fertilized barley.The numbers and activities of ammonium oxidizers were highest in the spring and autumn samples. Numbers of ammonium oxidizers ranged from 0.2 to 19×10⁴ and nitrite oxidizers from 3 to 870×10⁴ cells g^–1 dry soil. Potential ammonium-oxidizer activities ranged from 120 to 1,060 and nitrite-oxidizer activities ranged from 280 to 680 ng N g^–1 dry soil hour^–1. Lucerne and grass leys generally showed the highest, whereas unfertilized barley had the lowest, abundances and activities.Abundance estimates and activities were 10–20 times higher in the plow layer than in underlying sand and clay layers. A strong correlation was found between organic matter content vs numbers and activities of both ammonium and nitrite oxidizers. Only nitrite oxidizer counts were significantly higher within plant rows compared to between plant rows.     

Soil microbial populations after wildfire

Abstract Population fluctuations were increased by burning, which also modified the incubation patterns and the densities of several microbial groups, although without changing the order of their population sizes. In the short term, fire produced a sharp increase in microbes but affected the groups studied differently. Aerobic heterotrophic bacteria, including the acidophilic and sporulating ones, were stimulated by fire while cyanobacteria, algae and fungi (propagules as well as hyphae length) were clearly depressed. In the long term, the positive effect of fire on bacteria was nullified except on the sporulating ones; fungal propagules, but not mycelium, reached the unburned soil values, cyanobacteria and algae also increased. Soil incubation both improved the beneficial and diminished the negative fire effect on the microbiota.     

杭州西湖水域微生物的生态调查

对杭州西湖水域微生物生态调查结果表明:(1)有机营养型细菌在富营养化程度较重的岳湖分布较多,而无机营养型细菌在水质较好的小南湖丰度较大;(2)许多微生物类群在温度较高的季节数量反而较少;(3)西湖经综合治理后,异养型细菌和大肠菌群数量有显着减少,但近年又有增加的趋势;(4)西湖水体中的微生物以假单胞菌属的细菌较多,而底泥中芽孢杆菌属的细菌占优势。       

Variations of soil structure and microbial population in a compost amended soil

Changes in soil structure and in microbial population were recorded in a long term field experiment over the growing season of maize (June–November). Determinations were made on samples from plots which had received, for two years, the following treatments: mineral fertilizers, farmyard manure and three rates of compost. Seasonal variations were observed for the stability of soil aggregates, total porosity, pore size distribution, mycorrhizal infection and aerobic cellulolytic microorganisms. The stability of the soil aggregates changed in a similar way to that found for both mycorrhizal infection and the number of aerobic cellulolytic microorganisms. Physical characteristics were not affected in any instance by the organic dressings and microbiological populations were generally influenced only by the higher doses of compost.     

The occurrence of chemolitho-autotrophic nitrifiers in water-saturated grassland soils

Relatively high most probable number (MPN) counts of chemolithotrophic nitrite oxidizers were present in water-saturated soils compared with MPNs and activity of ammonia oxidizers. These high numbers of nitrite oxidizers were confirmed by fluorescent antibody counts and potential activity measurements. Application of different nitrite concentrations in the MPN procedure discriminated within the community of nitrite oxidizers and revealed a large number of nitrite-sensitive nitrite oxidizers and a subcommunity of nitrite-insensitive nitrite oxidizers. The size of this subcommunity was small but corresponded with the low numbers of ammonium oxidizers. Numbers of nitrite-sensitive nitrite oxidizers outnumbered the ammonia oxidizing bacteria by 2–4 orders of magnitude in these soils. The possibility is discussed that the fraction of the nitrite-insensitive cells was active as aerobic nitrite oxidizers, whereas the nitrite-sensitive cells represented an inactive group of nitrite oxidizers growing as heterotrophs or as anaerobes reducing nitrite. In this situation, both MPN enumerations at a low nitrite concentration and activity measurements could give false information about the size of the in situ nitrite-oxidizing community.     

种植年限对蔬菜日光温室土壤微生物区系和酶活性的影响

以种植2、4、6、11、13、16、19年的蔬菜日光温室土壤为研究对象,并以露地菜田为对照,测定了土壤微生物区系及酶活性的变化.结果表明: 随着种植年限的增加,土壤中细菌、放线菌和微生物总数均呈现先增加后减少的趋势,在种植11年时达到最大值,分别比对照增加了54.8%、63.7%和55.4%,差异达显著水平;而真菌数量持续上升,种植19年约为对照的2.2倍.微生物生理类群中,纤维素分解菌、自生固氮菌、亚硝酸细菌、反硝化细菌和硫化细菌数量的变化趋势与细菌相似, 种植11年分别为对照的1.5、1.6、1.9、1.4和1.1倍;而氨化细菌数量则呈现先减少后增加的趋势,在种植13年时达到最小值,为对照的56.0%.土壤中脲酶、多酚氧化酶、蔗糖酶、蛋白酶、纤维素酶和碱性磷酸酶活性随种植年限的增加呈现先增强后减弱的趋势,而过氧化氢酶活性较稳定.相关分析表明,细菌、放线菌和微生物总数与各土壤酶均呈显著正相关;而真菌数量与脲酶、蔗糖酶、过氧化氢酶和碱性磷酸酶均呈负相关,其中与过氧化氢酶的相关性达到显著水平.     

Does fire severity influence shrub resprouting after spring prescribed burning?

Prescribed burning is commonly used to reduce the risk of severe wildfire. However, further information about the associated environmental effects is required to help forest managers select the most appropriate treatment. To address this question, we evaluated if fire severity during spring prescribed burning significantly affects the resprouting ability of two common shrub species in shrubland under a Mediterranean climate in NW Spain. Fire behaviour and temperatures were recorded in tagged individuals of Erica australis and Pterospartum tridentatum during prescribed burning. The number and length of resprouted shoots were measured three times (6, 12 and 18 months) after the prescribed burning. The influence of a series of fire severity indicators on some plant resprouting vigour parameters was tested by canonical correlation analysis. Six months and one year after prescribed burning, soil burn severity (measured by the absolute reduction in depth of the organic soil layer, maximum temperatures in the organic soil layer and the mineral soil surface during burning and the post-fire depth of the organic soil layer) reduced the resprouting vigour of E. australis and P. tridentatum. In contrast, direct measurements of fire effects on plants (minimum branch diameter, duration of temperatures above 300 °C in the shrub crown and fireline intensity) did not affect the post-fire plant vigour.Soil burn severity during spring prescribed burning significantly affected the short-term resprouting vigour in a mixed heathland in Galicia. The lack of effects eighteen months after prescribed burning indicates the high resilience of these species and illustrates the need to conciliate fire prevention and conservation goals.     

Microflora of dissimilative nitrate reduction in a denitrifying reactor

The predominant denitrifiers and ammonifiers from methanogenic, aerobic and denitrifying reactor sludge were isolated and characterised. The population of ammonifiers increased by three orders of magnitude during the operation of the denitrifying reactor treating landfill leachate. The predominant ammonifiers were enterobacteria, and the predominant denitrifiers belonged to the genera Alcaligenes and Pseudomonas. Studies in pure culture showed that ammonia production by ammonifiers was favoured by fermentable substrates and by high C/N ratios. For acetate, only nitrite was obtained as the reduction product of nitrate, even at high C/N ratios. Furthermore, for glucose, nitrite addition caused a shift in fermentation products, with an increase in the acetate/ethanol ratio, with no significant differences in growth rates. Received: 14 January 1998 / Received revision: 11 May 1998 / Accepted: 21 May 1998     

Changes in Diversity and Functional Gene Abundances of Microbial Communities Involved in Nitrogen Fixation, Nitrification, and Denitrification in a Tidal Wetland versus Paddy Soils Cultivated for Different Time Periods

In many areas of China, tidal wetlands have been converted into agricultural land for rice cultivation. However, the consequences of land use changes for soil microbial communities are poorly understood. Therefore, we investigated bacterial and archaeal communities involved in inorganic nitrogen turnover (nitrogen fixation, nitrification, and denitrification) based on abundances and relative species richness of the corresponding functional genes along a soil chronosequence ranging between 50 and 2,000 years of paddy soil management compared to findings for a tidal wetland. Changes in abundance and diversity of the functional groups could be observed, reflecting the different chemical and physical properties of the soils, which changed in terms of soil development. The tidal wetland was characterized by a low microbial biomass and relatively high abundances of ammonia-oxidizing microbes. Conversion of the tidal wetlands into paddy soils was followed by a significant increase in microbial biomass. Fifty years of paddy management resulted in a higher abundance of nitrogen-fixing microbes than was found in the tidal wetland, whereas dominant genes of nitrification and denitrification in the paddy soils showed no differences. With ongoing rice cultivation, copy numbers of archaeal ammonia oxidizers did not change, while that of their bacterial counterparts declined. The nirK gene, coding for nitrite reductase, increased with rice cultivation time and dominated its functionally redundant counterpart, nirS, at all sites under investigation. Relative species richness showed significant differences between all soils with the exception of the archaeal ammonia oxidizers in the paddy soils cultivated for 100 and 300 years. In general, changes in diversity patterns were more pronounced than those in functional gene abundances.     

Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment

The oxidation of ammonia plays a significant role in the transformation of fixed nitrogen in the global nitrogen cycle. Autotrophic ammonia oxidation is known in three groups of microorganisms. Aerobic ammonia-oxidizing bacteria and archaea convert ammonia into nitrite during nitrification. Anaerobic ammonia-oxidizing bacteria (anammox) oxidize ammonia using nitrite as electron acceptor and producing atmospheric dinitrogen. The isolation and cultivation of all three groups in the laboratory are quite problematic due to their slow growth rates, poor growth yields, unpredictable lag phases, and sensitivity to certain organic compounds. Culture-independent approaches have contributed importantly to our understanding of the diversity and distribution of these microorganisms in the environment. In this review, we present an overview of approaches that have been used for the molecular study of ammonia oxidizers and discuss their application in different environments.     

The effect of long‐term repeated burning and fire exclusion on above‐ and below‐ground Blackbutt (Eucalyptus pilularis) forest vegetation assemblages

We used a long‐term fire experiment in south‐east Queensland, Australia, to determine the effects of frequent prescribed burning and fire exclusion on understorey vegetation (<7.5 m) richness and density in Eucalyptus pilularis forest. Our study provided a point in time assessment of the standing vegetation and soil‐stored vegetation at two experimental sites with treatments of biennial burning, quadrennial burning since 1971–1972 and no burning since 1969. Vegetation composition, density and richness of certain plant groups in the standing and soil‐stored vegetation were influenced by fire treatments. The density of resprouting plants <3 m in height was higher in the biennially burnt treatment than in the unburnt treatment, but resprouters 3–7.5 m in height were absent from the biennial burning treatment. Obligate seeder richness and density in the standing vegetation was not significantly influenced by the fire treatments, but richness of this plant group in the seed bank was higher in the quadrennial treatment at one site and in the long unburnt treatment at the other site. Long unburnt treatments had an understorey of rainforest species, while biennial burning at one site and quadrennial burning at the other site were associated with greater standing grass density relative to the unburnt treatment. This difference in vegetation composition due to fire regime potentially influences the flammability of the standing understorey vegetation. Significant interactions between fire regime and site, apparent in the standing and soil‐stored vegetation, demonstrate the high degree of natural variability in vegetation community responses to fire regimes.     

Evaluation of Bacillus thuringiensis bioinsecticidal protein effects on soil microorganisms

The effect of B. thuringiensis and its crystal protein on plant growth and on functional groups of microorganisms is not well understood. Soybean (Glycine max) var. Br 322 was grown in non-sterile soil infested with three B. thuringiensis (Bt) inocula: insecticidal crystal protein producer (Cry+), a mutant non-producer (Cry–), or insecticidal crystal protein (ICP), at a rate of 10⁷ cells g^–1 dry soil or 1.25 mg of protein g^–1 dry soil. Non-inoculated plants were maintained as control. Measurements were carried out on soil samples before sowing (time zero) and after sowing and inoculation (5, 15, 25, 35 and 45 d) on samples of rhizosphere soil. The effect of spore and crystal protein produced by B. thuringiensis on the populations of functional groups of microorganisms (bacteria including actinomycetes and fungi) involved in the biogeochemical cycling of carbon (cellulolytic, amylolytic and proteolytic), phosphorus (arbuscular mycorrhizal fungi), and nitrogen (number of nodules and proteolytic) were evaluated. Population sizes of culturable heterotrophic bacteria and saprophytic fungi were also evaluated. No difference was found in heterotrophic bacterial populations inoculated with B. thuringiensis. Difference was observed in functional groups of C-cycling microorganisms. Nodule formation and plant growth were increased by Cry+ strain and ICP when compared with uninoculated plants. Crystal protein did not show any effect on arbuscular mycorrhiza (AM) colonization. However, a deleterious effect was observed with Cry+ and Cry– strains that inhibited colonization of AM fungi when compared with uninoculated plants.     

Soil phosphorus and microbial response to a long-term wildfire chronosequence in northern Sweden

In the prolonged absence of major disturbances, ecosystems may enter a stage of retrogression, which is characterized by decreased ecosystem process rates both above and belowground, and often reduced availability of phosphorus (P). Disturbance through wildfire can increase soil P losses through leaching or erosion, but in the long-term absence of fire, soil P could potentially become increasingly bound in more stable forms that are less available to microbes. We studied forms of P and microbial respiration kinetics in the humus layer of a group of islands that vary considerably in wildfire frequency (40–5,300 years since last fire), and which are known to enter retrogression in the prolonged absence of fire. We found a decrease in labile P with decreasing fire frequency but no change in total P. Soil microorganisms responded more strongly to N than to P addition, and microbial biomass N:P ratios remained unchanged across the gradient. However, the concentration of labile P was the best predictor of microbial respiration responses across the islands, and this provides some evidence that declining access to P could contribute to the decline in soil microbial activity during retrogression. Our results show that even though N is arguably the main limiting nutrient during retrogression in this chronosequence, long term absence of fire also causes a decline in P availability which negatively affects microbial activity. This in turn could potentially impair microbially driven processes such as decomposition and mineralization and further contribute to the reduced availability of soil nutrients during retrogression.     

蚯蚓对秸秆还田土壤细菌生理菌群数量和酶活性的影响

在连续7a稻麦轮作系统中,通过测定作物收获后表层土壤(0-20cm)中4种细菌生理菌群数量和4种酶活性的变化,研究接种蚯蚓(Metaphire guillelmi)对秸秆(表施或混施)还田土壤的细菌生理菌群数量和酶活性的影响。试验设5个处理:对照、秸秆表施、秸秆混施、秸秆表施且接种蚯蚓、秸秆混施且接种蚯蚓。结果表明,单独秸秆还田促进了土壤氨化细菌、固氮菌、纤维素分解菌和无机磷分解菌数量增加,且土壤酶活性显著地增强;在秸秆表施方式下,接种蚯蚓使得上述4种细菌生理菌群微生物的数量增加;秸秆混施方式下,接种蚯蚓增加氨化细菌和无机磷分解菌数量,且土壤蛋白酶和蔗糖酶活性显著地增强(P0.05)。另外,蚓粪中4种细菌生理菌群微生物数量和水解酶活性都远远高于其周围土壤。在秸秆还田的作物轮作系统中,蚯蚓活动进一步增加土壤微生物数量和酶活性,对改善农田土壤肥力有着重要意义。     

Influence of Aboveground Biomass Removal on Nitrogen Mineralization in a Restored Tallgrass Prairie

Prescribed burning in prairies influences soil nitrogen (N), which is the primary nutrient that limits plant growth and is an important factor in plant competition and diversity. The primary objective of the experiment described here was to better understand the changes in net N mineralization that occur after a fire. We compared soil properties after a fire with those following vegetation removal by mowing and raking in a restored prairie in southeastern Minnesota. The treatments occurred in the spring of two consecutive years. Calcium oxide, burnt lime, was added to some of the raked plots in the first year to mimic the deposition of basic cations during a fire, which cause an increase in soil pH. Aboveground biomass removal by raking or by burning had similar effects on soil moisture, temperature, and inorganic N. The removal treatments caused warmer and drier soil than in the untreated plots. The change in net N mineralization after raking was unaffected by the addition of lime. In the first year, with low rainfall, removal caused net N mineralization rates similar to those in the untreated controls, but during the second year, with heavy rainfall, net N mineralization rates were significantly higher after removal. We predict that if water is sufficient, increased soil temperature after biomass removal will increase soil microbial activity and net N mineralization, but during drought, water will limit microbial activity. Furthermore, depending on soil N concentrations, which are very high at this study site, altered soil microbial activity will have variable effects on net N mineralization.     

Influence of antibiotics (benzylpenicillin,pharmazin, and nystatin) on the number of microorganisms in ordinary chernozem

In model experiments, the influence of pharmaceutical antibiotics (benzylpenicillin, pharmazin, and nystatin) in different doses (100, 300, 450, and 600 mg/kg) on a number of microorganisms of the chernozem region has been studied. All the studied doses of antibiotics had reliable and overwhelming impacts on the amount of soil microorganisms. The time between a dose of antibiotics and a change in the number of microorganisms in the soil is shown to have a linear dependence. The studied groups of soil microorganisms in relation to pharmaceutical antibiotics showed a hierarchy of resistance (high concentration): Azotobacter > amylolytic bacteria > ammonifying bacteria > micromycetes.     

Establishment of microscale vegetation pattern in maritime chaparral after fire

We quantified microscale pattern in vegetation and seed assemblages along a 24 m transect before and for two years following a controlled burn in chamise (Adenostoma fasciculatum) chaparral in central coastal California. Our objective was to document scale-dependent correlation between pre-burn seed assemblages, pre-burn canopy cover, microtopography, soil temperatures during burning, post-burn seed assemblages and post-burn vegetation. Scale-dependent correlations among pre- and post-burn seed densities, maximum soil temperatures during burning, microtopography and post-burn vegetation were measured based on two-term local covariance analysis.Seed distribution varied among species prior to fire, with seeds of some annual species concentrated in gap areas. Maximum soil temperatures during burning ranged from less than 50 °C to 225 °C, and were generally lowest in gaps in the pre-burn canopy. These gaps were associated with local topographic depressions. After burning, readily germinable seeds were concentrated in or near gaps in the pre-burn canopy. Germination of different species was variously enhanced, diminished or unchanged by the passage of fire. Post-burn vegetation was very patchy, with some areas nearly devoid of seedlings and other areas, especially pre-burn canopy gaps, supporting numerous seedlings. Seedling recruitment patterns in the second year were generally highly correlated with patterns in pre-burn seed banks and first year vegetation. Although many species exhibited similar recruitment patterns, several different mechanisms may have been responsible for the origin of those patterns.     

Moderately thermophilic nitrifying bacteria from a hot spring of the Baikal rift zone

Samples from three hot springs (Alla, Seya and Garga) located in the northeastern part of Baikal rift zone (Buryat Republic, Russia) were screened for the presence of thermophilic nitrifying bacteria. Enrichment cultures were obtained solely from the Garga spring characterized by slightly alkaline water (pH 7.9) and an outlet temperature of 75 degrees C. The enrichment cultures of the ammonia- and nitrite oxidizers grew at temperature ranges of 27-55 and 40-60 degrees C, respectively. The temperature optimum was approximately 50 degrees C for both groups and thus they can be designated as moderate thermophiles. Ammonia oxidizers were identified with classical and immunological techniques. Representatives of the genus Nitrosomonas and Nitrosospira-like bacteria with characteristic vibroid morphology were detected. The latter were characterized by an enlarged periplasmic space, which has not been previously observed in ammonia oxidizers. Electron microscopy, denaturing gradient gel electrophoresis analyses and partial 16S rRNA gene sequencing provided evidence that the nitrite oxidizers were members of the genus Nitrospira.