Response of ammonia oxidizing archaea and bacteria to changing water filled pore space

This study examined the effect of water filled pore space (WFPS) on gross N fluxes and community structure and abundance of ammonia oxidizing archaea and bacteria in a semi-arid soil. Different WFPS altered the community structure of both AOA and AOB. Ammonia oxidizer communities (for both archaea and bacteria) from ‘wet’ soils (95, 85 and 75% WFPS) and ‘dry’ soils (25, 45 and 55% WFPS) were distinctly different from one another. Additionally there was a significant relationship between community structure and gross rates of nitrification. There was also a significant relationship between WFPS and bacterial amoA abundance but not archaeal amoA abundance suggesting that bacterial ammonia oxidizers are more responsive to changes in soil water availability. These results are in agreement with other studies suggesting that both groups of ammonia oxidizers have distinct physiological characteristics and ecological niches with consequences for nitrification in response to WFPS. Overall findings from this study indicate that nitrification, both in terms of process rates and populations responsible for nitrification activity, is highly responsive to soil water availability.     

A positive relationship between the abundance of ammonia oxidizing archaea and natural abundance δ15N of ecosystems

We present a significant relationship between the natural abundance isotopic composition of ecosystem pools and the abundance of a microbial gene. Natural abundance ¹⁵N of soils and soil DNA were analysed and compared with archaeal ammonia oxidizer abundance along an elevation gradient in northern Arizona and along a substrate age gradient in Hawai'i. There was a significant positive correlation between the abundance of archaeal amoA genes and natural abundance δ¹⁵N of total soil or DNA suggesting that ammonia oxidizing archaea play an important role in ecosystem N release.     

Effects of inorganic fertilizer and manure on soil archaeal abundance at two experimental farms during three consecutive rotation-cropping seasons

Soil archaeal population dynamics at two experimental sites of the same clay-loam type in Ottawa and Woodslee, Ontario, were investigated to determine fertilizer and manure effects following their different long-term crop rotation and fertilization schemes. Phylogenetic analysis of cloned soil archaeal 16S rRNA gene libraries of both sites identified them with group 1.1b of Thaumarchaeota. The gene population dynamics subtly varied in the order of 10⁷ copies g⁻¹ soil when monitored by quantitative real-time PCR during three growing seasons (2007–2009). In Ottawa, where plots were amended with dairy-farm manure, soil thaumarchaeal gene abundance was double of the unamended plots. At the Woodslee N-P-K-fertilized plots, it remained at least 30% fewer than that of the unfertilized ones. These cultivated plots showed soil carbon limitation while the fertilized ones were low in soil pH (ca. 5.5). Surface soils from an unfertilized sod plot and an adjacent deciduous forest had higher total carbon content (C:N ratio of 9 and 11, respectively). Their thaumarchaeal gene abundance varied up to 4.8 × 10⁷ and 7.0 × 10⁷ copies g⁻¹ soil, respectively. The former value was also attained at the manure-amended plots in Ottawa, where the C:N ratio was just below 10. Where soil pH was above 6.0, there was a weak and positive correlation between soil total C and the estimated gene abundance. Such gene population dynamics consistently demonstrated the stimulating and suppressive effects of dairy-farm manure (Ottawa site) and inorganic fertilizers (Woodslee site), respectively, on soil thaumarchaea. At both sites archaeal amoA and 16S rRNA gene abundance were similarly affected. Archaeal amoA gene abundance also outnumbered bacterial amoA abundance, suggesting that ammonia-oxidizing archaea might be dominant in these soils. Only minor crop effects on gene population dynamics were detected.     

Fluctuations in the abundance of ammonia oxidizers and the contents of inorganic nitrogen in solarized soil

Solarization makes a great impact on the abundance of ammonia oxidizers and nitrifying activity in soil. To elucidate fluctuations in the abundance of ammonia oxidizers and nitrification in solarized soil, copy numbers of amoA gene of ammonia-oxidizing bacteria (AOB) and archaea (AOA), viable number of ammonia oxidizers and inorganic nitrogen contents were investigated in greenhouse experiments. The copy number of amoA gene and the viable number of ammonia oxidizers were determined by the quantitative polymerase chain reaction and most probable number methods, respectively. Abundance of AOB based on the estimation of amoA gene copy numbers and viable counts of ammonia oxidizers was decreased by the solarization treatment and increased during the tomato (Solanum lycopersicum L.) cultivation period following the solarization. Effect of solarization on the copy number of amoA gene of AOA was less evident than that on AOB. The proportion of nitrate in inorganic nitrogen contents was declined by the solarization and increased during the tomato cultivation period following the solarization. Positive correlations were found between the proportion of nitrate in inorganic nitrogen content and the copy number of bacterial or archaeal amoA gene or the viable number of ammonia oxidizers; the copy number of bacterial amoA gene showed a strong correlation with the viable number of ammonia oxidizers. The present study revealed influences of solarization on the fluctuation in the abundance of ammonia oxidizers and dynamics of inorganic nitrogen contents in soil and the results indicate that the determination of amoA gene of AOB is possibly a quick and useful diagnostic technique for evaluating suppression and restoration of nitrification following solarization.     

Response of microbial characteristics to heavy metal pollution of mining soils in central Tibet,China

Soil microbial activity plays a crucial role in soil microbiological processes, which can be used as a useful indicator to determine the ecological effects of heavy metal pollution on soils. The objective was to determine the effects of heavy metal pollution on mining soils at the Lawu mine of central Tibet, China on soil enzyme activities (sucrase, urease and acid phosphatase), microbial biomass C, N and P (MBC, MBN, and MBP), basal respiration, metabolic quotients, and N mineralization. Sixteen soil samples around the mine were sampled, and one soil sample, 2 km from the mine center, was taken as the control. Compared to the control, mining soils were polluted by heavy metals, Cu, Zn, Pb and Cd, resulting in decreases of sucrase activities, urease activities, acid phosphatase activities, MBC, MBN, MBP, and N mineralization, and increases of basal respiration and qCO₂. Multivariate analysis (cluster analysis [CA], principle component analysis [PCA] and canonical correlation analysis [CCA]) indicated nine microbial variables were only reduced to one principal component explaining 72% of the original variances, and MBC (R² = 0.93) had the highest positive loadings on the principal component. Mining soils polluted by heavy metals were perfectly clustered into four groups, which were highly distinguished by MBC. There were significant canonical correlations between soil heavy metals and microbial indexes on two canonical variates (R1 = 0.99, p < 0.001; R2 = 0.97, p < 0.01), which further demonstrated significant correlations between soil heavy metal contents and microbial characteristics. Hence, our results suggested that MBC may be used a sensitive indicator for assessing changes in soil environmental quality in metal mine of central Tibet.     

Linking plant identity and interspecific competition to soil nitrogen cycling through ammonia oxidizer communities

Both plants and microbes influence soil nutrient cycling. However, the links between plants, microbes and nutrient cycling are poorly understood. In this study, we investigated how plant identity and interspecific competition influence soil nitrogen cycling and attempted to link plant identity and interspecific competition to community structures of bacterial and archaeal ammonia oxidizers based on terminal restriction fragment length polymorphism analysis (T-RFLP) of bacterial and archaeal ammonia monooxygenase (amoA) genes. Faba bean and maize monocultures and a faba bean/maize mixture were planted with two nitrogen levels (0 and 100 mg N kg⁻¹ soil as urea). Soil mineral nitrogen, ammonia oxidizer function (potential nitrification activity, PNA) and community structures were measured 28 and 54 days after plant emergence. Faba bean and maize substantially differed in their influences on mineral nitrogen concentrations and PNA in rhizosphere soils. Soil mineral nitrogen and PNA in the rhizosphere soils of the faba bean/maize mixture were closer to those of the maize monoculture than to those of the faba bean monoculture. T-RFLP with restriction enzymes BsaJI and Hpy8I distinguished variations in bacterial and archaeal ammonia oxidizers community structure, respectively, and detected both between-cluster and within-cluster variations in bacterial ammonia oxidizers. T-RFLP data showed that nitrogen addition favored part of a Nitrosospira cluster 3b sequence type and suppressed part of a cluster Nitrosospira 3a sequence type of bacterial ammonia oxidizers, while it had no influence on the archaeal ammonia oxidizer community structure. Although multivariate analysis showed that the function and community structure of bacterial ammonia oxidizers were significantly correlated, plant species and interspecific competition did not significantly change the community structure of bacterial and archaeal ammonia oxidizers. These results indicate that plant species and interspecific competition regulate soil nitrogen cycling via a mechanism of other than alteration in the community structure of ammonia oxidizers as investigated by DNA based methods.     

Population size of indigenous Rhizobium leguminosarum biovar trifolii in long-term field experiments with sewage sludge cake,metal-amended liquid sludge or metal salts: Effects of zinc,copper and cadmium

There is conflicting evidence, and therefore continuing concern, as to whether metals in sewage sludge are deleterious to soil microbial processes and long-term agricultural productivity. Nine field experiments with sewage sludge cakes, three with metal-amended liquid sludges and three with inorganic metal salts were set up across Britain in 1994 to give individual metal dose–response treatments to try to answer this question. This study reports on the effects of Zn, Cu and Cd on the population size of Rhizobium leguminosarum biovar trifolii, a nitrogen fixing symbiont of white clover (Trifolium repens), in soils from these experiments over 11 years. Significant (P < 0.05) reductions in indigenous rhizobial numbers occurred on the Zn metal dose–response treatments at eight of the sludge cake sites in 2005, but few consistent effects were evident on the Cu or Cd metal dose–response treatments during the 11-year monitoring period. The soil total Zn concentrations where effects occurred were near to the UK statutory limit of 300 mg kg^?1 for soils receiving sewage sludge. No significant reductions occurred in any treatments on the metal-amended liquid sludge or inorganic metal salt experiments in which the metals would be expected to be in a more bioavailable form, even after 11 years. The effects in the sludge cake experiments were related consistently with soil total Zn, with no recovery to date. The reductions in clover rhizobial numbers in the sludge cake experiments were due to Zn effects on free-living rhizobia in the soil, with gradual die-off over a long time with increasing soil total Zn concentrations. Currently, no consistent adverse effects on rhizobia have been seen at the UK limits for Cu and Cd of 135 and 3 mg kg^?1, respectively.     

Soil properties and metal accumulation by earthworms in the Siena urban area (Italy)

This paper reports the results of a study focused on the metal (Cd, Co, Cr, Cu, Ni, Pb, Sb, U and Zn) distribution in soils and uptake and accumulation by earthworms Nicodrilus caliginosus (Savigny) from urban, peri-urban, green-urban and non-urban zones of Siena municipality (central Italy). The main goal was to define the influence of soil properties and metal soil contents on the uptake of these contaminants by earthworms. Data indicated that Cd, Cu, Pb, Sb and Zn soil contents increased in the following order: non-urban < green-urban < peri-urban < urban soils, suggesting that vehicular traffic affects the distribution of these metals. Pb and Sb were the main soil contaminants and their highest enrichments were found in urban sites where stop-and-go traffic occurs. Concentrations of these traffic-related metals in earthworms showed a distribution pattern similar to that in soil, suggesting that soil contamination influenced the uptake of Cd, Cu, Pb, Sb and Zn by N. caliginosus. There were significant positive correlations between Cd, Pb and Sb earthworm concentrations and their soil contents. The lack of correlation for Cu and Zn could be due to the physiological regulation of these elements by earthworms. Statistical analysis pointed out that the uptake and accumulation of Cd, Cu, Pb, Sb and Zn by earthworms were affected by some soil physicochemical properties such as the organic carbon and carbonate contents that are able to rule the bioavailability of metals in soils.     

Comparative diversity and abundance of ammonia monooxygenase genes in mulched and vegetated soils

Soil microbial habitats are altered by mulching, a common practice in urban areas during which vegetation is removed and soils covered to suppress weeds and retain moisture. Soil microorganisms drive nitrogen-cycling processes in mulched soils, because living plants no longer take up ammonium-N released during decomposition of residual organic matter. Because ammonia oxidizers carry out the first, rate-limiting step of nitrification, we compared ammonia oxidizers in experimental, unfertilized plots of mulched and vegetated soils. We hypothesized that mulched and vegetated soils would support contrasting communities of bacterial and archaeal ammonia oxidizers, as determined by quantitative PCR and primers specific for genes encoding ammonia monooxygenase subunit A (amoA). Clone libraries of archaeal amoA also were constructed to compare diversity in soil cores, duplicate blocked plots, and treatments (bark-mulched, gravel-mulched, and unmanaged old field vegetation). Gene copies from ammonia-oxidizing bacteria (AOB) ranged from 2.2 × 10⁶ to 2.7 × 10⁷ gene copies per gram dry soil and did not differ across treatments. In contrast, gene copies from ammonia-oxidizing archaea (AOA) ranged from 9.1 × 10⁵ to 1.0 × 10⁸ copies per gram dry soil, with bark-mulched soils having significantly lower abundance. Community structure of AOA in gravel-mulched soils was distinct from the other two treatments. At 97% amino acid similarity, 22 operational taxonomic units, or OTUs, were identified, with only one OTU found in all 18 clone libraries. This ubiquitous OTU-1, which was highly similar to published amoA sequences recovered from soils, comprised 55% of all 482 translated sequences. Greater variability in OTU richness was observed among cores from mulched soils than from vegetated soils. Our observations supported our hypothesis that AOA communities differ in mulched and vegetated soils, with mulched soils providing altered and variable microniches for these N cycling microorganisms.     

Effect of soil aggregate size and dicyandiamide on N2O emissions and ammonia oxidizer abundance in a grazed pasture soil

Nitrous oxide (N₂O) is a potent greenhouse gas, which is mainly produced from agricultural soils. Ammonia oxidation is the rate‐determining step in N₂O production, and the process is carried out by ammonia oxidizers, bacteria and archaea. Soil aggregate size has been shown to alter soil properties, which affect N₂O emissions and bacterial communities. However, the effect of aggregate size on temporal and total N₂O emissions and ammonia‐oxidizing bacteria (AOB) and archaea (AOA) is not fully understood. This incubation study investigated the effect of three different soil aggregate sizes on N₂O emissions and ammonia oxidizer abundance under high urine‐N concentrations and the effectiveness of a nitrification inhibitor, dicyandiamide (DCD), at reducing N₂O emissions in different aggregate soils. It was found that temporal patterns of N₂O emissions were affected by aggregate size with higher peak emissions in the large and medium aggregates. However, the total emissions were the same due to a ‘switch’ in emissions at day 66, after which smaller aggregates produced higher N₂O emissions. It is suggested that the switch was caused by an increase in aggregate disruption in the small aggregates, following the urine application, due to their higher surface area to volume ratio. AOB and AOA abundances were not significantly affected by aggregate size. DCD was effective in reducing N₂O emissions in all aggregate sizes by an average of 79%. These results suggest that similar ammonia oxidizer abundance is found in soils of different aggregate sizes, and the efficacy of DCD in reducing N₂O emissions was not affected by aggregate size of the soil.     

pH-dependent distribution of soil ammonia oxidizers across a large geographical scale as revealed by high-throughput pyrosequencing

Purpose

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are ubiquitous and important for nitrogen transformations in terrestrial ecosystems. However, the distribution patterns of these microorganisms as affected by the terrestrial environments across a large geographical scale are not well understood. This study was designed to gain insights into the ecological characteristics of AOA and AOB in 65 soils, collected from a wide range of soil and ecosystem types.

Materials and methods

Barcoded pyrosequencing in combination with quantitative PCR was employed to characterize the relative abundance, diversity, and community composition of archaeal 16S rRNA gene, and AOA and AOB amoA genes in 65 soil samples.

Results and discussion

The operational taxonomic unit richness and Shannon diversity of Thaumarchaeota, AOA, and AOB were highly variable among different soils, but their variations were best explained by soil pH. Soil pH was strongly correlated with the overall community composition of ammonia oxidizers, as measured by the pairwise Bray–Curtis dissimilarity across all sites. These findings were further corroborated by the evident pH-dependent distribution patterns of four thaumarchaeal groups (I.1a-associated, I.1b, I.1c, and I.1c-associated) and four AOB clusters (2, 3a.1, 10, and 12). The ratios of AOA to AOB amoA gene copy numbers significantly decreased with increasing pH, suggesting a competitive advantage of AOA over AOB in acidic soils.

Conclusions

These results suggest that the distribution of ammonia oxidizers across large-scale biogeographical settings can be largely predicted along the soil pH gradient, thus providing important indications for the ecological characteristics of AOA and AOB in different soils.     

C and N mineralization and microbial biomass in heavy-metal contaminated soil

Heavy metals such as arsenic (As), lead (Pb), copper (Cu) and zinc (Zn) can be found in large concentrations in mine spills in Mexico. Interest in contamination by these heavy metals has increased recently as they can change the functioning of soil ecosystems qualitatively and quantitatively. They disturb the activities of soil fauna and contaminate drinking water in large parts of the world, which severely affects human health. Little, however, is known how heavy metals might affect the biological functioning of a soil. Soil was sampled from eight locations along a gradient of heavy-metal contamination with distance from a mine in San Luis Potosí (Mexico) active since about 1800 AD. Microbial biomass was determined with the original chloroform fumigation incubation (CFI) as well as extraction (CFE) techniques and the substrate induced respiration (SIR) technique while C and N mineralization were measured. Total concentrations of As in the top 0–10 cm soil layer ranged from 8 to 22992 mg kg^–1, from 31 to 1845 mg kg^–1 for Pb, from 27 to 1620 mg kg^–1 for Cu and from 81 to 4218 mg kg^–1 for Zn. There was a significant negative correlation (P < 0.0001) between microbial biomass, soil organic carbon, total N and C mineralization and the heavy metal content of the soil. The microbial biomass C to organic C ratio, which varied from 0.4 to 1.9%, specific respiratory activity (qCO₂), and oxidation of NO₂^– were not affected by heavy metals. It was found that long-term contamination of soil with heavy metals had an adverse effect on the amount of soil microorganisms as evidenced by a marked decrease in microbial biomass C, but not some of their characteristics. According to principal components analysis (PCA), the correlation matrix showed three distinct factors explaining 71% of the variance. A first factor including heavy metals (As, Pb, Cu and Zn) with a negative loading and total N, organic C, soil microbial biomass with a positive loading characterized the soil organic matter and contamination status. Loam and sand combined for the second factor characterizing the textural classification while the third factor was loaded by CEC and clay content.     

Uptake and bioaccumulation of heavy elements by two earthworm species from a smelter contaminated area in northern Kosovo

As, Cd, Cu, Pb, Sb and Zn concentrations were determined in two earthworm species (Allolobophora rosea and Nicodrilus caliginosus) from a mining and industrial area in northern Kosovo and compared with their contents in the bulk soil and the main soil fractions. Earthworm specimens were collected at fifteen sites located at different distances from a Pb–Zn smelter along a gradient of decreasing contamination. Individuals of A. rosea and N. caliginosus showed similar tissue levels of As, Cd, Cu, Pb, Sb and Zn, suggesting that earthworm species belonging to the same eco-physiological group have a similar propensity to uptake and bioaccumulate heavy elements. Cd, Pb, Sb and Zn concentrations in both earthworm species were positively correlated with the respective total soil contents and generally decreased with distance from the smelter. The bioaccumulation factor (BAF) revealed that Cd and Zn were the only elements bioaccumulated by earthworms. The rank order of BAF values for both species was as follows: Cd > > Zn > > Cu > As = Pb = Sb. The absorption of Cd, Pb, Sb and Zn by earthworms mostly depended on the extractable, reducible and oxidable soil fractions, suggesting that the intestine is likely the most important uptake route. The extractable soil fraction constantly influenced the uptake of these heavy elements, whereas the reducible fraction was important mainly for Pb and Zn. The water soluble fraction had an important role especially for the most mobile heavy elements such as Cd and Zn, suggesting that dermal uptake is not negligible. As a whole, the analytical data indicate that soil fractionation patterns influence the uptake of heavy elements by earthworms, and the extractable fraction is a good predictor of heavy element bioavailability to these invertebrates in soil.     

Direct and indirect influence of arbuscular mycorrhizal fungi on abundance and community structure of ammonia oxidizing bacteria and archaea in soil microcosms

Both arbuscular mycorrhizal (AM) fungi and ammonia oxidizers are important soil microbial groups in regulating soil N cycling. However, knowledge of their interactions, especially the direct influences of AM fungi on ammonia oxidizers is very limited to date. In the present study, a controlled microcosm experiment was established to examine the effects of AM fungi and N supply level on the abundance and community structure of ammonia oxidizing bacteria (AOB) and archaea (AOA) in the rhizosphere of alfalfa plants (Medicago sativa L.) inoculated with AM fungus Glomus intraradices. Effects were studied using combined approaches of quantitative polymerase chain reaction (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP). The results showed that inoculation with AM fungi significantly increased the plant dry weights, total N and P uptake. Concomitantly, AM fungi significantly decreased the amoA gene copy numbers of AOA and AOB in the root compartment (RC) but not in the hyphal compartment (HC). Moreover, AM fungi induced some changes in AOA community structure in HC and RC, while only marginal variations in AOA composition were observed to respond to N supply level in HC. Neither RC nor HC showed significant differences in AOB composition irrespective of experimental treatments. The experimental results suggested that AM fungi could directly shape AOA composition, but more likely exerted indirect influences on AOA and AOB abundance via the plant pathway. In general, AM fungi may play an important role in mediating ammonia oxidizers, but the AOA community appeared to be more sensitive than the AOB community to AM fungi.     

Effects of municipal solid waste compost,farmyard manure and chemical fertilizers on wheat growth,soil composition and soil bacterial characteristics under Tunisian arid climate

The use of municipal solid waste compost (MSWC) as soil organic amendment is of an economic and environmental interest. However, little is known about the effectiveness of MSWC application on agricultural soil in northern Africa arid climate. We assessed the impact of five years' applications of different organic and mineral fertilizers on wheat grain yields and soil chemical and microbial characteristics. Soils were treated with MSWC at rates of 40 (C1) and 80 (C2) Mg ha^?1, farmyard manure at a rate of 40 Mg ha^?1 (M), chemical fertilizers (Cf) and the combinations (C1Cf, C2Cf, MCf). Wheat grain yield was enhanced with all amendments. Parallel increases of heavy metal levels and faecal coliform were also recorded except for Cf treatments. Based on wheat grain yield, heavy metal and faecal coliform data, we determined the treatment effectiveness index (E_xx), calculated by dividing the pollutant increase ratio by the grain yield increase ratio. The treatment effectiveness index E_C1 indicated lower faecal and heavy metal pollution with positive gains in wheat yields. Despite polluting effects on soil determined by the different treatments, no significant differences between treatments were observed in total bacterial count and soil bacterial community structure, as shown by 16S rRNA gene PCR-denaturing gradient gel electrophoresis banding patterns and 16S rRNA gene Length Heterogeneity-PCR analysis. According to the collected data, the use of MSWC at a rate of 40 Mg ha^?1 might be recommended.     

Short-term changes of metal availability in soil. II: The influence of earthworm activity

This study aimed to evaluate short-term earthworm-induced changes in the availability of metals applied to soil directly (metal-spiked) or via an organic matrix (sludge-amended). A laboratory experiment was performed using destructive sampling of microcosms filled with agricultural soil. A concentration gradient of industrial sludge contaminated predominantly with Cr, Cu, Ni, and Zn, and a soil freshly spiked with the same metal concentrations were applied on top of the soil columns. Individuals of Dendrobaena veneta (mimicking a realistic density of 500 earthworms per m²) were introduced in half of the replicates of each treatment. Total and 0.01 M CaCl₂ extractable metal concentrations were measured in soil after 0, 3, 6 and 12 weeks and metal concentrations in earthworms and percolates were measured after 3, 6, and 12 weeks. Earthworm activity did not affect metal availability of any treatment over time, but Ni and Cu concentrations in D. veneta were higher at the highest treatment levels. Earthworm Zn concentrations were similar in all treatments while Cr concentrations increased with increasing soil total metal content only for sludge treatments. Existing relationships of earthworm metal concentrations with total metal content in soil, taken from the literature, were not able to predict the metal levels measured in D. veneta. Results demonstrated that although over 12 weeks earthworm activity did not affect metal availability in soil, their burrowing activities did influence the metal concentrations of percolates over time.     

Long-term fertilization effects on active ammonia oxidizers in an acidic upland soil in China

The effects of long-term fertilization of acidic soils on ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities and its ecological implications remain poorly understood. We chose an acidic upland soil site under long-term (27-year) fertilization to investigate ammonia oxidizer communities under four different regimes: mineral N fertilizer (N), mineral NPK fertilizer (NPK), organic manure (OM) and an unfertilized control (CK). Soil net nitrification rates were significantly higher in OM soils than in CK, N or NPK soils. Quantitative analysis of the distribution of amoA genes by DNA-based stable isotope probing revealed that AOA dominate in CK, N and NPK soils, while AOB dominate in OM soils. Denaturing gradient gel electrophoresis and clone library analyses of amoA genes revealed that Group 1.1a-associated AOA (also referred to as Nitrosotalea) were the most dominant active AOA population (>92%), while Nitrosospira Cluster 3 and Cluster 9 were predominant among active AOB communities. The functional diversity of active ammonia oxidizers in acidic soils is affected by long-term fertilization practices, and the responses of active ammonia oxidizers to mineral fertilizer and organic manure are clearly different. Our results provide strong evidence that AOA are more highly adapted to growth at low pH and low substrate availability than AOB, and they suggest that the niche differentiation and metabolic diversity of ammonia oxidizers in acidic soils are more complex than previously thought.     

Characterization of nitrifying bacteria communities of soils from different ecological regions of China by molecular and conventional methods

Soil nitrification rate is very different among soil types, as a result of differences in physical and chemical properties. Little is known about the composition of the nitrifying bacteria community. In this investigation, three soils (fluvo-aquic soil, permeable paddy soil and red earth) from different geo-ecological regions in China were characterized for their nitrification activities and their nitrifying bacteria communities determined either by molecular approaches or by conventional culture methods. A 28-day long-term soil incubation showed that the maximum nitrification potential was found in the fluvo-aquic soil with almost 100% of inorganic N present as NO₃^–-N, while the minimum nitrification potential was in red earth with only a 4.9% conversion rate from ammonium into nitrate. There was no relationship between nitrification potential and numbers of nitrifiers in the soil. The conventional most probable number (MPN) method could enumerate ammonia oxidizers, but failed in enumerating nitrite oxidizers. Therefore, we used an MPN-PCR procedure which gave a convincing nitrite oxidizer count result, instead of MPN-diphylamine. Soils were characterized by denaturing gradient gel electrophoresis (DGGE) of DNA extracted from soils and amplified using a primer specific for the 16S rRNA gene and/or for the amoA gene. The DGGE columns of the three soils differed from each other. There were two similar bands present in DGGE columns of the fluvo-aquic and permeable paddy soils, but no similar band was found in DGGE columns of the red earth. The sequence of amoA indicated that all ammonia oxidizers in these soils were grouped into Nitrosospira clusters 1 and 3, and each soil had a common band similar to the other soils and a special band which differed from the other soils.     

Indication of soil heavy metal pollution with earthworms and soil microbial biomass carbon in the vicinity of an abandoned copper mine in Eastern Nanjing,China

Mining activities can cause severe soil pollution in mining area and its surroundings. Nevertheless, very little is known about the local environmental risk after the mining activities are ended in China. Earthworms and soil microbial biomass carbon (SMBC), which are often used as bioindicators of soil pollution, were studied in order to support chemical analyses in assessing the status of soil heavy metal pollution around an abandoned copper mine in eastern Nanjing, China. Seven earthworm species belonging to three families (Megascolecidae, Moniligastridae, and Lumbricidae) were present. Correlations between earthworm densities or biomass and a range of soil physical and chemical parameters were generally poor; however, several linear regression models based on the soil physicochemical characteristics and metal concentrations in earthworm bodies were established for each metal (Cu, Cd, and Zn) and each earthworm family. Therefore, metal bioaccumulation by soil-dwelling earthworms can be used as an ecological indicator of metal availability for this area. The SMBC, which varied from 83.9 to 499 g kg^?1, did not correlate with the soil heavy metal concentrations, and SMBC is not proposed as a sensitive indicator for evaluating the environmental effects of soil heavy metal pollution in this area.     

Abundance and community structure of ammonia-oxidizing bacteria and archaea in a temperate forest ecosystem under ten-years elevated CO2

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are considered as the key drivers of global nitrogen (N) biogeochemical cycling. Responses of the associated microorganisms to global changes remain unclear. This study was to determine if there was a shift in soil AOB and AOA abundances and community structures under free-air carbon dioxide (CO₂) enrichment (FACE) and N fertilization in Duke Forest of North Carolina, by using DNA-based molecular techniques, i.e., quantitative PCR, restriction fragment length polymorphism (RFLP) and clone library. The N fertilization alone increased the abundance of bacterial amoA gene, but this effect was not observed under elevated CO₂ condition. There was no significant effect of the N fertilization on the thaumarchaeal amoA gene abundance in the ambient CO₂ treatments, while such effect increased significantly under elevated CO₂. A total of 690 positive clones for AOA and 607 for AOB were selected for RFLP analysis. Analysis of molecular variance (AMOVA) indicated that effects of CO₂ enrichment and N fertilization on the community structure of AOA and AOB were not significant. Canonical correspondence analysis also showed that soil pH rather than elevated CO₂ or N fertilization shaped the distribution of AOB and AOA genotypes. A negative linear relationship between the δ¹³C and archaeal amoA gene abundance indicated a positive effect of elevated CO₂ on the growth ammonia oxidizing archaea. On the other hand, the community structures of AOB and AOA are determined by the soil niche properties rather than elevated CO₂ and N fertilization.