The relative contribution of nitrifiers to autotrophic nitrification across a pH-gradient in a vegetable cropped soil

Purpose

Microbial nitrification plays an important role in nitrogen cycling in ecosystems. Nitrification is performed by ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB) including complete ammonia oxidizers. However, the relative importance of nitrifiers in autotrophic nitrification in relation to soil pH is still unclear.

Materials and methods

Combining DNA-based stable isotope probing (SIP) and molecular biological techniques, we investigated the abundance, structure, and activity of AOA, AOB, and NOB along a pH-gradient (3.97–7.04) in a vegetable cropped soil.

Results and discussion

We found that AOA abundance outnumbered AOB abundance and had a significantly negative relationship with soil pH. The abundances of NOB Nitrospira 16S rRNA, nxrB gene, and Nitrobacter nxrA gene were affected by soil pH. Incubation of soil with ¹³CO₂ and DNA-SIP analysis demonstrated that significant ¹³CO₂ assimilation by AOA rather than by AOB occurred in the acidic soils, whereas the labeled ¹³C level of AOA was much less in the neutral soil than in the acidic soils. There was no evidence of ¹³CO₂ assimilation by NOB except for Nitrobacter with NxrB gene at pH 3.97. Phylogenetic analysis of AOA amoA gene in the ¹³C- and ¹²C-labeled treatments showed that the active AOA mainly belonged to Nitrososphaera in the acidic soils.

Conclusions

These results suggested that the main performer of nitrification was AOA in the acidic soils, but both AOA and AOB participated in nitrification in the neutral soil with low nitrification activity. NOB Nitrospira and Nitrobacter did not grow in the soils with pH 4.82–7.04 and other populations of NOB were probably involved in nitrite oxidation in the vegetable cropped soil.

     

铅胁迫对黄褐土微生物区系和功能多样性的影响

为了筛选出黄褐土中对铅污染敏感的指示微生物,本研究采用室内培养试验研究不同铅浓度对土壤微生物区系和功能多样性的影响。结果表明,向土壤中添加硝酸铅显著降低了可培养细菌、放线菌和真菌微生物的种群数量,这种抑制作用随着铅浓度的升高而增强,随着培养时间的延长而减弱。铅浓度、细菌、真菌和放线菌数量两两间呈极显著负相关关系。低浓度铅处理（100 mg kg?1）在培养初期（1 d）显著减少了可培养细菌和放线菌的数量,降低率分别为27.43%和30.89%;高浓度铅处理（2500 mg kg?1）在整个培养期内均对真菌数量产生显著抑制作用,且抑制率维持在90%左右。从培养初期到中期（1 ~ 14 d）,随着铅浓度升高土壤微生物群落活性和功能多样性指数显著下降（中浓度铅处理除外）,培养后期（28 d）各个浓度铅处理的土壤微生物的丰富度和优势度均显著增加。与对照、低浓度铅和高浓度铅处理相比,中浓度铅处理（500 mg kg?1）更有利于保持黄褐土较高的微生物的群落代谢活性和功能多样性。本研究中3 种可培养微生物功能群对黄褐土添加硝酸铅的敏感度依次是放线菌,细菌和真菌。研究表明,在黄褐土地区真菌可以用来指示较为严重的土壤铅污染状况,放线菌和细菌可以用来指示铅污染程度较轻的土壤环境状况。     

Influence of PAH contamination on soil ecological status

Purpose

The purpose of this paper is to study the responses of soil biological parameters as indicator of ecological status on PAH-contaminated soil.

Materials and methods

Studies are conducted on the soils and natural grassy vegetation of monitoring plots subjected to Novocherkassk power station (NPS) emissions. Monitoring plots were established at different distances from the NPS (1.0–20.0 km).

Results and discussion

The level of polycyclic aromatic hydrocarbons (PAHs) around NPS is the highest at the monitoring plot located at distance 1.6 km to the northwest through the prevailing wind direction. Gradually, decrease of PAHs was observed while increasing the distance from the NPS through the prevailing wind direction. Calculation of correlations between PAH level and biological activity parameters of soils showed lack of dependence with total and every PAH content in all 12 studied monitoring plots. The most significant correlations were found between PAH content and enzyme activity in the monitoring plots situated through the prevailing wind direction from NPS.

Conclusions

The main pollution source in the studied area is NPS. It was found that contamination of soil by PAHs has a direct dependence on the activity of all biological communities in chernozems, as well as the activities of dehydrogenase and the phytotoxicity of soils. Inverse correlations have been revealed between the PAH contamination and abundance of soil bacteria.

     

High contribution of ammonia-oxidizing archaea (AOA) to ammonia oxidation related to a potential active AOA species in various arable land soils

Purpose

Ammonia oxidation is the limiting step in soil nitrification and critical in the global nitrogen cycle. The discovery of ammonia-oxidizing archaea (AOA) has improved our knowledge of microbial mechanisms for ammonia oxidation in complex soil environments. However, the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to ammonia oxidation remain unclear.

Materials and methods

In this study, through large geographical scale sampling in China, totally nine samples representing various types of arable land soils were selected for analyzing the ammonia oxidation activity. The AOA and AOB activities were separately determined by using the dicyandiamide and 1-octyne inhibition method. High-throughput pyrosequencing and DNA stable-isotope probing (DNA-SIP) analysis were applied to investigate the distribution and activity of Candidatus Nitrosocosmicus franklandus in the arable land soils.

Results and discussion

In this study, AOA abundance (3.2?×?10⁷–3.4?×?10⁹ copies g^?1) and activity (0.01–1.33 mg N kg^?1 dry soil day^?1) were evaluated for nine selected arable land soils and accounted for 4–100% of ammonia oxidation. By separately determining AOA and AOB rates, we observed that archaeal ammonia oxidation dominated the ammonia oxidation process in six soils, revealing a considerable contribution of AOA in ammonia oxidation in arable land soils. Based on high-throughput pyrosequencing analysis, the AOA species Ca. N. franklandus with relatively low abundance (0.6–13.5% in AOA) was ubiquitously distributed in all the tested samples. Moreover, according to the DNA-SIP analysis for Urumqi sample, the high activity and efficiency of Ca. N. franklandus in using CO₂ suggests that this species plays an important role in archaeal ammonia oxidation in arable land soils.

Conclusions

Through determining the AOA activity and analyzing the potential predominant functional AOA species, this study greatly improves our understanding of ammonia oxidation in arable land soils.

     

Effects of 3,4-dimethylpyrazole phosphate (DMPP) on the abundance of ammonia oxidizers and denitrifiers in two different intensive vegetable cultivation soils

Purpose

Nitrification and denitrification in the N cycle are affected by various ammonia oxidizers and denitrifying microbes in intensive vegetable cultivation soils, but our current understanding of the effect these microbes have on N₂O emissions is limited. The nitrification inhibitor, 3,4-dimethylpyrazole phosphate (DMPP), acts by slowing nitrification and is used to improve fertilizer use efficiency and reduce N losses from agricultural systems; however, its effects on nitrifier and denitrifier activities in intensive vegetable cultivation soils are unknown.

Materials and methods

In this study, we measured the impacts of DMPP on N₂O emissions, ammonia oxidizers, and denitrifying microbes in two intensive vegetable cultivation soils: one that had been cultivated for a short term (1 year) and one that had been cultivated over a longer term (29 years). The quantitative PCR technique was used in this study. Three treatments, including control (no fertilizer), urea alone, and urea with DMPP, were included for each soil. The application rates of urea and DMPP were 1800 kg ha^?1 and 0.5% of the urea-N application rate.

Results and discussion

The application of N significantly increased N₂O emissions in both soils. The abundance of ammonia-oxidizing bacteria (AOB) increased significantly with high rate of N fertilizer application in both soils. Conversely, there was no change in the growth rate of ammonia-oxidizing archaea (AOA) in response to the applied urea despite the presence of larger numbers of AOA in these soils. This suggests AOB may play a greater role than AOA in the nitrification process, and N₂O emission in intensive vegetable cultivation soils. The application of DMPP significantly reduced soil NO₃^?-N content and N₂O emission, and delayed ammonia oxidation. It greatly reduced AOB abundance, but not AOA abundance. Moreover, the presence of DMPP was correlated with a significant decrease in the abundance of nitrite reductase (nirS and nirK) genes.

Conclusions

Long-term intensive vegetable cultivation with heavy N fertilization altered AOB and nirS abundance. In vegetable cultivation soils with high N levels, DMPP can be effective in mitigating N₂O emissions by directly inhibiting both ammonia oxidizing and denitrifying microbes.

     

Nitrapyrin affects the abundance of ammonia oxidizers rather than community structure in a yellow clay paddy soil

Purpose

Yellow clay paddy soil (Oxisols) is a low-yield soil with low nitrogen use efficiency (NUE) in southern China. The nitrification inhibitor nitrapyrin (2-chloro-6- (tricholoromethyl)-pyridine, CP) has been applied to improve NUE and reduce environmental pollution in paddy soil. However, the effects of nitrapyrin combined with nitrogen fertilizers on ammonia oxidizers in yellow clay paddy soil have not been examined.

Materials and methods

A randomized complete block design was set with three treatments: (1) without nitrogen fertilizer (CK), (2) common prilled urea (PU), and (3) prilled urea with nitrapyrin (NPU). Soil samples were collected from three treatments where CK, PU, and NPU had been repeatedly applied over 5 years. Soil samples were analyzed by quantitative PCR and 454 high-throughput pyrosequencing of the amoA gene to investigate the influence of nitrapyrin combined with nitrogen on the abundance and community structure of ammonia oxidizers in yellow clay paddy soil.

Results and discussion

The potential nitrification rate (PNR) of the soil was significantly correlated with the abundances of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Application of urea significantly stimulated AOA and AOB growth, whereas nitrapyrin exhibited inhibitory effects on AOA. Phylogenetic analysis showed that the most dominant operational taxonomic units (OTUs) of AOA and AOB were affiliated with the Nitrosotalea cluster and Nitrosospira cluster 12, respectively. AOA and AOB community structures were not altered by urea and nitrapyrin application.

Conclusions

Nitrogen fertilization stimulated nitrification and increased the population sizes of AOA and AOB. Nitrapyrin affected the abundance, but not community structure of ammonia oxidizers in yellow clay soil. Our results suggested that nitrapyrin improving NUE and inhibiting PNR was attributable to the inhibition of AOA growth.

     

Distributions and environmental drivers of archaea and bacteria in paddy soils

Purpose

The aim of this study is to investigate the abundance, diversity, and distribution of archaea and bacteria as affected by environment parameters in paddy soils, with focus on putative functional microbial groups related to redox processes. Because there is generally a high iron content in the soil, we also want to test a hypothesis that soil iron concentration significantly affects microbial diversity and distribution.

Materials and methods

Quantitative PCR and barcoded pyrosequencing of 16S ribosomal RNA genes were employed to investigate the abundance and community composition of archaeal and bacterial communities in 27 surface paddy soil samples. Pearson’s correlation, analysis of variance, partial least squares regression, principal coordinates analysis, and structural equation models were performed for the analyses of gene copy numbers, α-diversity, β-diversity, and relative abundances of archaea and bacteria and their relationships with environmental factors.

Results and discussion

Archaeal abundance was correlated greatest with temperature, but bacterial abundance was affected mainly by soil organic matter and total nitrogen content. Soil pH and concentrations of different ions were associated with archaeal and bacterial β-diversity. The relative abundances of Euryarchaeota and Thaumarchaeota were 61.3 and 13.1% of archaea and correlated with soil pH, which may affect the availability of substrates to methanogens and ammonia oxidizers. Dominant bacterial phyla were Proteobacteria (32.4%), Acidobacteria (17.8%), Bacteroidetes (9.3%), and Verrucomicrobia (6.0%). The relative abundances of putative bacterial reducers of nitrate, Fe(III), sulfate, and sulfur, and oxidizers of ammonia, nitrite, reduced sulfur, and C1 compounds had positive, negative, or non-significant correlations with the concentrations of their substrates. Soil iron concentration was correlated only with the distributions of some putative iron-reducing bacteria.

Conclusions

In paddy soils characterized by dynamic redox processes, archaea and bacteria differ in relationships of abundance, diversity, and distribution with environmental factors. Especially, the concentrations of electron donors or acceptors can explain the distributions of some but not all the putative functional microbial groups related to redox processes. Depending on pH range, soil pH has a strong impact on microbial ecology in paddy soils.

     

Growth of comammox Nitrospira is inhibited by nitrification inhibitors in agricultural soils

Purpose

The discovery of comammox Nitrospira being capable of complete oxidising ammonia to nitrate radically challenged the conventional concept of two-step nitrification. However, the response of comammox Nitrospira to nitrification inhibitors (NIs) and their role in soil nitrification remain largely unknown, which has hindered our ability to predict the efficiency of NIs in agroecosystems.

Materials and methods

We evaluated the effect of four NIs, 2-chloro-6-(trichloromethyl) pyridine (nitrapyrin), 3,4-dimethylpyrazole phosphate (DMPP), allylthiourea (ATU) and dicyandiamide (DCD) on the growth of comammox Nitrospira, ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) in two pasture and arable soils.

Results and discussion

The amendment of nitrogen fertiliser significantly increased soil nitrate concentrations over time, indicating a sustaining nitrification activity in both soils. The addition of all the four NIs effectively reduced the production of nitrate in both soils, but to varying degrees during incubation. The abundances of comammox Nitrospira clade A were significantly increased by addition of nitrogen fertilisers and significantly impeded by the four NIs in the pasture soil, but their abundances were only remarkably hindered by nitrapyrin in the arable soil. All the four NIs obviously inhibited the AOB abundances in both soils. Except for DMPP, the other three NIs effectively suppressed the AOA abundances in both soils.

Conclusions

We provided new evidence that growth of comammox Nitrospira clade A can be stimulated by nitrogen fertilisers and inhibited by various nitrification inhibitors, suggesting their potential role in nitrification of agricultural soils.

     

The short-term effects of nitrification inhibitors on the abundance and expression of ammonia and nitrite oxidizers in a long-term field experiment comparing land management

Microcosms were set up to evaluate the effect of nitrification inhibitors (DCD, c-PTiO, and NaClO₃) on the abundance and expression of ammonia-oxidizing bacteria (AOB) and archaea (AOA), as well as the nitrite-oxidizing bacteria (NOB) Nitrospira and Nitrobacter. Both DCD and NaClO₃ inhibited the net nitrification rate, while c-PTiO had no significant effects, and NaClO₃ had a much greater inhibitory effect (> 60%) in all soils than DCD. No significant changes in total microbial abundance were observed with DCD and NaClO₃. DCD limited only the growth of AOB; however, NaClO₃ inhibited growth of both AOA and Nitrospira-NOB with no significant effects on AOB and Nitrobacter-NOB. Probably NaClO₃ inhibited both ammonia oxidation and nitrite oxidation. This is the first report to reveal the inhibitory effects of NaClO₃ on a specific nitrification process, helping to clarify the ecological niche of nitrifiers and the potential of nitrification inhibitors applied to soil.     

Response of microbial communities to different doses of chromate in soil microcosms

The toxic effect of chromate on soil microbial communities is not well documented, although microorganisms control biogeochemical cycling, contribute to formation of soil structure, regulate the fate of organic matter applied to soil. In this study the effects of short- and middle-term chromate on the soil microbial community were investigated. The shifts in the size and in the diversity of culturable heterotrophic bacterial community, the resistance to Cr(VI) of heterotrophic bacteria, the presence of cyanobacteria, the activity of 19 enzymes, and the ATP content were monitored over time (120 days) in soil microcosms artificially contaminated with three concentrations of chromate (50, 250 and 1000 mg kg⁻¹ soil). The chromate contamination affected the structure and the diversity of the soil bacterial community. Bacterial strains isolated from the microcosm contaminated with the highest concentration of chromate were identified by 16S rDNA gene sequencing. All isolates belonged to the genus Pseudomonas, were able to reduce Cr(VI), and showed a high resistance to chromate. To our knowledge, this is the first report that shows Pseudomonas strains having the capability to resist up to 40 mM of Cr(VI) on minimal medium. The cyanobacterial group was more sensitive to chromate contamination than culturable heterotrophic bacteria. No cyanobacterial growth was detected in enrichment cultures from the soil polluted with the highest chromate concentration. Some enzymes were inhibited by high concentrations of chromate, whereas others were stimulated. The ATP content in microcosms was strongly affected by chromate. We conclude that the soil microbial community responds to chromate pollution through changes in community structure, in metabolic activity, and in selection for Cr(VI)-resistance.     

Factors Affecting Nitrification in Soils

Abstract

Nitrification in soil converts relatively immobile ammonium‐nitrogen (N) to highly mobile nitrate‐N (via nitrite), and this has implications for N‐use efficiency by agricultural systems as well as for environmental quality, especially in situations where the potential for loss of soil or added N is high following nitrate formation. The literature on various physical, environmental, and chemical factors and their interactions on nitrification in soil is reviewed and discussed with examples from natural and agro‐ecosystems. Among the various factors, soil matrix, water status, aeration, temperature, and pH have strong influence on nitrification. The information on factors that influence nitrification is useful when developing strategies for regulating nitrification in soils by employing chemical or biological nitrification inhibitors.     

Effect of humic preparation on winter wheat productivity and rhizosphere microbial community under herbicide-induced stress

Purpose

The aim of the present work was to study the effect of humic preparation on the yielding capacity of winter wheat, the dynamics of mineral nutrients in the rhizosphere, and the activity of rhizosphere microbial community, as well as the protective properties of humate treatment under the stress caused by the application of a sulfonylurea herbicide.

Materials and methods

The humic preparation BIO-Don is prepared from vermicompost by alkaline extraction. The effect of humic preparation was estimated in a field experiment. The contents of the mobile ammonium and nitrate, exchangeable potassium, phosphorus, and humus were determined. Sampling and nutrient determination were performed in the tillering, booting, and grain maturing stages. Production experiments on the study of the combined effect of the humic preparation and the sunfonylurea pesticide Granstar Pro were performed in 2015 and 2017. The dynamics of mobile phosphorus in soil was studied. The abundance of culturable bacteria in the rhizosphere and bacterial species with different ecological strategies was determined. The dominant bacterial species were identified by MALDI-TOF mass spectrometry.

Results and discussion

The results of a small-plot experiment showed that at the tillering stage, the use of humic preparation has led to significantly higher supply of soil with mobile phosphorus. The winter wheat yield was 32.0 dt/ha in the control and 39.2 dt/ha with humic preparation or 22.5% gain in yield. The results of production experiment show that the application of sulfonylurea herbicide induced a chemical stress on winter wheat plants, but the use of humic preparation reduced this effect and increased the availability of phosphorus compounds. The treatment of plants with pesticides caused the general decrease in abundance of bacteria in the rhizosphere. The effect on quickly growing bacteria is more pronounced, while slowly growing bacteria and fungi are more resistant to this impact.

Conclusions

The application of humic preparation to winter wheat plantations allows to decrease the toxic effect of sulfonylurea herbicide, improve the supply of soil with mineral nutrients, and increase the crop yield. The favorable effects of humic preparation can be related to the active regulation of phosphorus mobilization by plants through the mechanism of root exudates due to the activation of root microbiota.

     

Source identification and assessment of heavy metal contamination in urban soils based on cluster analysis and multiple pollution indices

Purpose

To identify the sources and levels of contamination with anthropogenically derived heavy metals (HMs) for appropriate pollution control. We quantified anthropogenic influences with respect to HM pollution in soil, based on multiple pollution indices and cluster analysis derived from the results of an annual nationwide survey conducted in Korea.

Methods

Contamination levels of HMs in soils were quantitatively evaluated using multiple pollution indices: contamination factor (CF), geo-accumulation index (I_geo), Nemerow’s integrated pollution index (NIPI), and pollution load index (PLI). Hierarchical cluster analysis was conducted to elucidate the correlations between HMs and contamination sources. A total of 2214 HM concentration data including six contamination sources were used to evaluate the pollution state of anthropogenic effects of HMs.

Results

The CFs for Zn and Cu revealed a broad enrichment of these HMs in all pollution sources. Scrap recycling sites (SRS) had the highest likelihood of pollutant distribution in soil surfaces. NIPI and PLI varied with the extent of anthropogenic activities or land use, especially in SRS, waste disposal sites (WDS), transport maintenance sites (TMS), and industrial sites (INS), and anthropogenic sources were divided into three discrete clusters: INS-TMS-LDS (land development sites), SRS-WDS, and vicinities of industrial sites (VIS).

Conclusion

Our results confirmed that soil pollution indices combined with cluster analysis were useful to identify sources of anthropogenic HMs in urban soil, as well as to assess the levels of HM contamination.

     

Vermicompost improves microbial functions of soil with continuous tomato cropping in a greenhouse

Purpose

At present, the improvement of soil microbial function by the application of vermicompost in long-term monoculture system is rarely reported. We took advantage of a greenhouse pot experiment that examined the effects of vermicompost on soil microbial properties, enzyme activities, and tomato yield.

Materials and methods

Three soils subjected to 0, 5, and 20 years of continuous tomato cropping in a greenhouse were collected for a pot experiment. Treatments include chemical fertilizer (CF), vermicompost (VM), and poultry manure compost (PM). No fertilization was established as a control (CK). Biolog Eco microplates were used to measure soil microbial function.

Results and discussion

The results showed that compared to the CF and PM treatments, the VM treatment increased the abundances of bacteria (Bac, average 41% and 103%, respectively) and actinomycetes (Act, average 8.59% and 16.36%, respectively), while decreased the abundance of fungi (Fun, average 39% and 29%, respectively), and had the highest ratio of bacteria to fungi. Soil microbial activity, which was represented as the average well color development (AWCD), and microbial functional diversity were higher in the VM treatment than in the CF and PM treatments. The VM treatment led to greater improvement in soil health than the PM treatment, which expressed as the higher utilization of carboxylic acids and phenolic compounds in each type of soil. Catalase (Cat) and polyphenoloxidase (Ppo) activities in the VM treatment were significantly higher than those in the CF and PM treatments. We also found that the soil Cat activity, pH, available P, acid phosphatase (Pac) activity, and Ppo activity were important contributors to variation in the microbial population. Moreover, compared to CK, fruit yield in the VM treatment increased by 74%, 43%, and 28% in soils subjected to 0, 5, and 20 years of planting, respectively.

Conclusions

Our findings indicated that vermicompost can replace poultry manure compost to improve soil quality in greenhouse due to the ability of vermicompost to improve soil microbial functions.

     

Inhibition of nitrification by potassium ethyl xanthate in soil and in liquid culture

Inhibition of nitrification by potassium ethyl xanthate has been investigated in liquid batch culture and in soil, using axenic cultures of Nitrosomonas and Nitrobacter. In all cases the major effect was induction of a prolonged lag rather than a reduction in specific oxidation rates, although this was also found for Nitrosomonas at high xanthate concentrations. Inhibition of both ammonium and nitrite oxidation was reduced in soil, because of immobilization of xanthate or its breakdown products at the soil surface. However, in liquid culture nitrite oxidation was more sensitive while ammonium oxidation was more sensitive in soil. It is proposed that this also results from accumulation of xanthate, or its breakdown products at the soil surface. Xanthate was shown to have a bacteriostatic, rather than bactericidal effect, but xanthate-treated cells exhibited a significantly longer lag when transferred to xanthate-free medium, emphasizing the need for caution when using the most probable number method in such studies.     

Effect of fulvic and humic acids on nitrificationPart 1: In vitro production of nitrite and nitrate

Abstract

Mixed opinions exist on the effect of organic matter on nitrification in soils as well as the lack of data on the effect of fulvic (FA) and humic (HA) acids on this biochemical process. This in vitro investigation was conducted to study the effect of FA and HA on oxidation of NH⁺ ₄ and NO^‐ ₂ by soil nitrifiers and on the delay period (t') and maximum nitrification rate (K_max). Soil extracts containing an ammonium‐oxidizer population were incubated in vitro for 3 weeks at 25C in the presence of (NH₄)₂SO₄and 0 to 320 mg FA or HA/L at pH 7.0 or 8.0. A similar experiment was conducted with soil extracts containing a nitrite‐oxidizer population, but with KNO₂ as the N source. An additional experiment was conducted with the nitrite‐oxidizer extracts for the determination of t’ and K_max values. Nitrite production tended to increase linearly as a result of FA and HA treatments from 0 to 320 mg/L at pH 7.0 or 8.0. Fulvic acid appeared to be more effective than HA in increasing the oxidation process. Differences in pH had only a slight effect. On the other hand, nitrate production was decreased linearly by FA or HA treatments from 0 to 320 mg/L which provided some justification for reports of lower nitrate, but higher nitrite concentrations in soils high in organic matter content. Humic acid treatments increased the delay period (t¹), and at the same time decreased the maximum nitrification rate (K_max). The latter suggests that in the presence of HA more time is required to reach a maximum nitrification rate.     

Soil enzyme activities and abundance of microbial functional genes involved in nitrogen transformations in an organic farming system

Organic farming systems receive organic amendments to maintain soil fertility and supply nutrients for plant growth. This study investigated the effect of organic fertilizers (no amendment as control, compost, and manure), and their interaction with cover crops (millet, buckwheat, and black turtle bean) on soil enzyme activities, N transformation rates, and functional gene abundances under an organic production system. Organic N fertilizers had a stronger effect than cover crop type on soil function and functional gene abundances. Soil enzyme activities were increased by both compost and manure, but there were few differences between these treatments. Nitrification potential, nitrite oxidation potential, and denitrification potential were significantly higher in manure-treated than in control and compost-treated soils, indicating application of manure had a higher N loss potential than compost application in this organic farming system. Organic N fertilizers significantly increased the abundance of some genes involved in N mineralization, ammonification, and nitrification (sub, ureC, bacterial amoA and nxrB). The activity of ammonia-oxidizing bacteria and archaea were both increased by organic N fertilizers, and their activities were higher in manure-treated than in compost-treated soils. Overall, the abundance of functional genes was significantly correlated with their corresponding enzyme activity. However, functional gene abundance was less important than soil chemical and microbiological properties in explaining the variation in the corresponding enzyme activity.     

Nitrogen mineralization and nitrifier activity in limed and urea‐treated soils

Abstract

The effect of liming on mineralization and soil nitrifier activity (NA) was investigated with Brookston clay (pH 5.7) and Haldimand clay (pH 4.7). Liming increased the rate of mineralization in both soils but at a rate about 4‐times greater in Haldimand clay than Brookston clay. A significant increase in N mineralization due to liming occurred in both soils only when pH was raised above 6.0. The rate of mineralization was greater than nitrification in the Haldimand soil resulting in NH₄ ⁺ accumulation. Nitrifier activity increased with liming of Brookston clay, but decreased in Haldimand clay after 15 days of incubation. There was a significant increase in nitrifier activity due to liming from 15 to 60 days in Haldimand clay. After 60 days nitrifier activity in limed treatments increased by five times over the unlimed control.

The nitrification of urea powder (1000 mg N.kg^‐1) mixed into the soil was also studied in several soils incubated at 15°C for 28 days. There was evidence up to 14 days that nitrification of urea was correlated with initial nitrifier activity. Between 14 and 28 days, other factors such as soil pH and possible ammonia toxicity in coarser textured soils as well as nitrifier activity were important. Accumulation of nitrite occurred mainly in soils with a pH above 7.0 up to 28 days especially where nitrifier population enrichment was not done.     

Nematodes as indicators of soil recovery in tailings of a lead/zinc mine

Trophic groups and functional guilds of soil nematodes were measured under four mine tailing subsystems in the Baoshan lead/zinc mine, Hunan Province, southern China to test the indicator value of nematodes for heavy metal pollution. No obvious correlation was found between heavy metal concentration and the total number of nematodes. However, the densities of c–p3, c–p4 and c–p5 nematodes were negatively correlated with Pb and Zn concentrations, suggesting that the abundance of nematode groups of high c–p values is useful indicators of heavy metal contamination. The “weighted faunal analysis” provided a better assessment of soil health condition than Maturity Index (MI) in situations where there were extremely low numbers of soil nematodes. Results showed that the effect of heavy metal contamination on soil nematodes might be strongly influenced by plants. Although the abundance of plant-feeding nematodes did not reflect the heavy metal conditions in the soil, it might be used as an index for assessing the soil remediation potential of pioneering plants. Patrinia villosa seems superior to Viola baoshanensis as a pioneer plant species for soil remediation based on analysis of rhizosphere nematode community.     

Biogeochemical responses of soil ecosystems to raw coal pollution in Xuanhua,China

Purpose

China is the world’s largest coal producer and consumer. Despite extensive studies on coal-burning pollution, the effect of raw coal pollutants caused by transportation and turnover on soil along the road received little attention. The main purpose of the study was to clarify the biogeochemical response of soil ecosystems to raw coal pollution.

Materials and methods

The raw coal and unpolluted soil from the coal distribution area in Xuanhua, China were collected for the incubation experiments. Combined with the determination of soil physicochemical properties, including pH, electric conductivity, soluble ions, dissolved organic carbon, and available heavy metals, the biogeochemical responses of soil to raw coal pollution, such as soil enzyme activities (β-glucosidase, alkaline phosphatase, and Urease), microbial community composition, and soil respiration, were systematically studied. In addition, a q-PCR analysis of the urease was performed to clarify the inhibitory mechanism of urease by coal pollution. Furthermore, a simple field investigation was carried out to confirm the incubation results.

Results and discussion

Raw coal pollution not only changed the soil physicochemical properties but also made the available Zn, Ni, and Co accumulate significantly. A positive priming effect in soil with the low-dose raw coal addition was trigged, but soil respiration rate and soil enzyme activity, such as β-glucosidase and alkaline phosphatase, were inhibited to different degrees with the increased pollution. Urease activity also decreased under the higher coal contamination, which was due to inhibition of ureC gene expression. In addition to the slight soil acidification caused by coal pollution, microbial communities and diversity was also found to be affected. The relative abundances of the microorganisms related to urease, alkaline phosphatase, and β-glucosidase changed accordingly. The incubation results are in good agreement with the field survey results.

Conclusions

Low-dose raw coal pollution can trigger the soil positive priming effect. However, as the coal pollution increased, the β-glucosidase, alkaline phosphatase, and urease in the soil were inhibited to varying degrees. The compounding effects of soil acidification, increased electric conductivity, and the accumulation of available heavy metals such as Zn, Ni, and Co are the key causes for the biogeochemical response of soil to coal pollution.