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1.

Purpose

Changes of nitrogen (N) cycle caused by N fertilization and precipitation regimes have affected the key ecosystem structure and functions in temperate steppe, which may modify the structure of soil microbial communities involved in N transformation. This paper was designated to examine the response of soil ammonia oxidizers and denitrifiers to the N fertilization and precipitation regimes in a semi-arid steppe where N and water contents are major limiting factors of the grassland productivity.

Materials and methods

This study was based on a long-term N fertilization and precipitation regimes experiment in Inner Mongolia (116° 17′ 20″ E, 42° 2′ 29″ N). The treatments including CK (control), R (reduced precipitation), W (30% increase in precipitation), N (10 g N m?2 y?1), RN (reduced precipitation and 10 g N m?2 y?1), and WN (30% increase in precipitation and 10 g N m?2 y?1). Soil basic chemical properties and microbial activities were analyzed. Molecular methods were applied to determine the abundance, structure and diversity of ammonia oxidizers and denitrifiers. Statistical analysis detected the main and interactive effect of treatments on soil microbial communities and revealed the relationship between soil microbial community structures and environmental factors.

Results and discussion

N fertilization significantly increased ammonia-oxidizing bacteria (AOB) abundance. Ammonia-oxidizing archaea (AOA) community structure was markedly changed in N fertilizer treatment and strongly affected by soil pH, while soil nitrate and water content correlated with AOB community structure. Soil nitrate was the key factor influencing nirK gene community structure, while soil pH and water content explained much of the variations of nosZ gene community. AOB-amoA and nosZ gene community diversities were influenced by precipitation regimes and interaction of N fertilization and precipitation regimes, respectively.

Conclusions

N fertilization and precipitation regimes had significant influences on the changes of soil properties and microbial functional communities. Soil nitrification was mainly driven by AOB in the semi-arid grassland. Changes of substrate content and soil pH were the key factors in shifting functional microbial communities. The non-synergistic effects of N fertilization and precipitation regimes on the microbial functional groups indicated that the negative effect of lower pH induced by N fertilization would be alleviated by precipitation regimes, which should be well considered in grassland restoration.
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2.

Purpose

Nitrogen (N) application in excess of assimilatory capacity for aquaculture ponds can lead to water-quality deterioration through ammonia accumulation with toxicity to fish. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) potentially process extra ammonium, so their abundance and diversity are of great ecological significance. This study aimed to reveal variations in communities of AOA and AOB as affected by aquaculture activities.

Materials and methods

From June to September 2012, water and sediments were sampled monthly in three ponds feeding Mandarin fish in a suburb of Wuhan City, China. Molecular methods based on ammonia monooxygenase (amoA) gene were used to determine abundance and diversity of AOA and AOB in the sediments.

Results and discussion

The pond with the highest fish stock had the highest nutrient loadings in terms of different forms of N and carbon (C) in both sediment and water. The abundance and diversity of AOB were significantly higher than those of AOA in the sediment. The AOB abundance showed a significantly positive relationship to concentration of soluble reactive phosphorus (SRP) in interstitial water, and both abundance and diversity of AOA were significantly negative to concentration of ammonium in interstitial water. Furthermore, AOA species affiliated to Nitrososphaera-like and Nitrosophaera Cluster was distinguishable from those observed in other aquaculture environments.

Conclusions

Nutrients in sediment were enriched by intensive aquaculture activity, among which organic N and C, together with ammonium and SRP, shaped the communities of ammonia oxidizers, with AOB dominating over AOA in terms of abundance and diversity.
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3.

Purpose

Sampling and analysis of greenhouse soils were conducted in Shouguang, China, to study continuous excessive fertilization effect on nitrifying microbial community dynamics in greenhouse environment.

Materials and methods

Potential nitrification activity (PNA), abundance, and structure of nitrifying microbial communities as well as the correlations with soil properties were investigated.

Results and discussion

Short-term excessive fertilization increased soil nutrient contents and the diversity of nitrifying microbial communities under greenhouse cultivation. However, the abundance and diversity of nitrifying communities decreased greatly due to the increase of soil acidity and salinity after 14 years of high fertilization in greenhouse. There was a significant positive correlation between soil PNA and the abundance of ammonia-oxidizing bacteria (AOB) but not that of ammonia-oxidizing archaea (AOA) in topsoil (0–20 cm) when pH ≥7. Soil PNA and AOB were strongly influenced by soil pH. The groups of Nitrososphaeraceae, Nitrosomonadaceae, and Nitrospiraceae were predominant in the AOA, AOB, and nitrite-oxidizing bacteria (NOB) communities, respectively. Nitrifying community structure was significantly correlated with soil electrical salinity (EC), organic carbon (OC), and nitrate nitrogen (NO3 ?–N) content by redundancy analysis (RDA).

Conclusions

Nitrification was predominated by AOB in greenhouse topsoil with high fertilizer loads. Soil salinity, OC, NO3 ?–N content, and pH affected by continuous excessive fertilization were the major edaphic factors in shaping nitrifying community structure in greenhouse soils.
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4.

Purpose

Nitrification and denitrification processes dominate nitrous oxide (N2O) emission in grassland ecosystems, but their relative contribution as well as the abiotic factors are still not well understood.

Materials and methods

Two grassland soils from Duolun in Inner Mongolia, China, and Canterbury in New Zealand were used to quantitatively compare N2O production and the abundance of bacterial and archaeal amoA, denitrifying nirK and nirS genes in response to N additions (0 and 100 μg NH4 +–N g?1 dry soil) and two soil moisture levels (40 and 80 % water holding capacity) using microcosms.

Results and discussion

Soil moisture rather than N availability significantly increased the nitrification rate in the Duolun soil but not in the Canterbury soil. Moreover, N addition promoted denitrification enzyme activities in the Canterbury soil but not in the Duolun soil. The abundance of bacterial and archaeal amoA genes significantly increased as soil moisture increased in the Duolun soil, whereas in the Canterbury soil, only the abundance of bacterial amoA gene increased. The increase in N2O flux induced by N addition was significantly greater in the Duolun soil than in the Canterbury soil, suggesting that nitrification may have a dominant role in N2O emission for the Duolun soil, while denitrification for the Canterbury soil.

Conclusions

Microbial processes controlling N2O emission differed in grassland soils, thus providing important baseline data in terms of global change.
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5.

Purpose

Organic matter amendment is usually used to improve soil physicochemical properties and to sequester carbon for counteracting climate change. There is no doubt that such amendment will change microbial activity and soil nitrogen transformation processes. However, the effects of straw and biochar amendment on anammox and denitrification activity and on community structure in paddy soil are unclear.

Materials and methods

We conducted a 30-day pot experiment using rice straw and rice straw biochar to deepen our understanding about the activity, microbial abundance, and community structure associated with soil nitrogen cycling during rice growth.

Results and discussion

Regarding activity, anammox contributed 3.1–8.1% of N2 production and denitrification contributed 91.9–96.9% of N2 production; straw amendment resulted in the highest denitrification rate (38.9 nmol N g?1 h?1), while biochar amendment resulted in the highest anammox rate (1.60 nmol N g?1 h?1). Both straw and biochar amendments significantly increased the hzsB and nosZ gene abundance (p < 0.05). Straw amendment showed the highest nosZ gene abundance, while biochar amendment showed the highest hzsB gene abundance. Phylogenetic analysis of the anammox bacteria 16S rRNA genes indicated that Candidatus Brocadia and Kuenenia were the dominant genera detected in all treatments.

Conclusions

Straw and biochar amendments have different influences on anaerobic ammonia oxidation and denitrification within paddy soil. Our results suggested that the changes in denitrification and anammox rates in the biochar and straw treatments were mainly linked to functional gene abundance rather than microbial community structure and that denitrification played the more major role in N2 production in paddy soil.
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6.

Purpose

The nitrification inhibitor 3,4-dimethylpyrazol-phosphate (DMPP) and the urease inhibitor N-(n-butyl) thiophosphoric triamide (nBTPT) can mitigate N losses through reducing nitrification and ammonia volatilization, respectively. However, the impact of repeated applications of these inhibitors on nitrogen cycling microorganisms is not well documented. This study aimed to investigate the changes in the abundance and community structure of the functional microorganisms involved in nitrification and denitrification in Australian pasture soils after repeated applications of DMPP and nBTPT.

Materials and methods

Soil was collected in autumn and spring, 2014 from two pasture sites where control, urea, urea ammonium nitrate, and urea-coated inhibitors had been repeatedly applied over 2 year. Soil samples were analyzed to determine the potential nitrification rates (PNRs), the abundances of amoA, narG, nirK and bacterial 16S rRNA genes, and the community structure of ammonia oxidizers.

Results and discussion

Two years of urea application resulted in a significantly lower soil pH at Terang and a significant decrease in total bacterial 16S rRNA gene abundance at Glenormiston and led to significantly higher PNRs and abundances of ammonia oxidizers compared to the control. Amendment with either DMPP or nBTPT significantly decreased PNRs and the abundance of amoA and narG genes. However, there was no fertilizer- or inhibitor-induced change in the community structure of ammonia oxidizers.

Conclusions

These results suggest that there were inhibitory effects of DMPP and nBTPT on the functional groups mediating nitrification and denitrification, while no significant impact on the community structure of ammonia oxidizers was observed. The application of nitrification or urease inhibitor appears to be an effective approach targeting specific microbial groups with minimal effects on soil pH and the total bacterial abundance.
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7.
Agricultural management significantly affects methane (CH4) and nitrous oxide (N2O) emissions from paddy fields. However, little is known about the underlying microbiological mechanism. Field experiment was conducted to investigate the effect of the water regime and straw incorporation on CH4 and N2O emissions and soil properties. Quantitative PCR was applied to measure the abundance of soil methanogens, methane-oxidising bacteria, nitrifiers, and denitrifiers according to DNA and mRNA expression levels of microbial genes, including mcrA, pmoA, amoA, and nirK/nirS/nosZ. Field trials showed that the CH4 and N2O flux rates were negatively correlated with each other, and N2O emissions were far lower than CH4 emissions. Drainage and straw incorporation affected functional gene abundance through altered soil environment. The present (DNA-level) gene abundances of amoA, nosZ, and mcrA were higher with straw incorporation than those without straw incorporation, and they were positively correlated with high concentrations of soil exchangeable NH4+ and dissolved organic carbon. The active (mRNA-level) gene abundance of mcrA was lower in the drainage treatment than in continuous flooding, which was negatively correlated with soil redox potential (Eh). The CH4 flux rate was significantly and positively correlated with active mcrA abundance but negatively correlated with Eh. The N2O flux rate was significantly and positively correlated with present and active nirS abundance and positively correlated with soil Eh. Thus, we demonstrated that active gene abundance, such as of mcrA for CH4 and nirS for N2O, reflects the contradictory relationship between CH4 and N2O emissions regulated by soil Eh in acidic paddy soils.  相似文献   

8.

Purpose

We attempt to describe the cover and management (C) factor more comprehensively through the use of a simple and efficient method.

Materials and methods

We measure the coverage of each vegetation layer and C factor for 152 sampled plots in the Ansai watershed. We propose four stratified coverage indices (green coverage (V G), total coverage (V T), probability coverage (V P), weight coverage (V W)), derive green and yellow vegetation indices from Landsat 8 OLI images to reflect green and residue cover, and construct and validate C factor estimation models from stratified coverage and remote sensing indices, respectively.

Results and discussion

(1) V T and V P present C factor estimation advantages for grassland and shrub land. V W can better illustrate the C factor due to the relatively complete spatial structuring of woodland and orchard land. For cropland, four stratified coverage indices present the same estimation capacities for the C factor. Except for cropland and grassland, the estimation capabilities of V G are relatively low because the residue layer is ignored. (2) The C factor is more sensitive to yellow vegetation indices, which indicates that senescent fractional cover and litter are important and cannot be ignored. The linear and non-linear models can explain 56.6 and 61.8% of C factor variation, respectively, and the linear model is more accurate than the non-linear model. (3) Compared to traditional indices (projective coverage and single remote sensing indices), stratified coverage indices and a combination of several remote sensing indices can estimate the C factor more effectively.

Conclusions

At the field scale, the C value estimation model can be selected according to the land-use type. At the watershed and regional scales, a linear model is recommended for C factor estimation.
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9.

Purpose

The alpine meadow has received mounting attention due to its degradation resulting from overgrazing on the Tibetan Plateau. However, belowground biotic characteristics under varied grazing stresses in this ecosystem are poorly understood.

Materials and methods

Here, the responses of soil protozoan abundance, community composition, microbial biomass, and enzyme activity to five grazing patterns including (1) artificial grassland without grazing (AG), (2) winter grazing (WG), (3) grazing for 7 months within a fence (GF), (4) continuous grazing for a whole year (CG), and (5) natural heavy grazing (HG) were investigated for two continuous years. Soil protozoan community composition was investigated using the most possible number (MPN) method, and soil microbial biomass and enzyme activity were analyzed using chloroform fumigation extraction and substrate utilization methods, respectively. Multivariate statistical analysis, the analysis of variance (ANOVA), multiple comparisons, and correlation analysis were together performed.

Results and discussion

The WG treatment had the highest abundance of total protozoa (2342–2524 cell g?1). Compared with AG treatment, HG treatment significantly reduced the abundance of soil total, flagellate and ciliate protozoa, and protease activities in 2012 and 2013. Significantly, lower soil microbial biomass nitrogen (MBN) was also observed in the HG (6.60 and 14.6 mg N kg?1) than those in other four treatments (22.3–82.9 mg N kg?1) both in 2012 and 2013, whereas significantly higher microbial biomass carbon (MBC) was observed in HG than that in AG treatment in 2012. Moreover, significantly positive correlations were detected between the abundance of soil protozoa and soil moisture, pH, organic C, total N, and MBN. Our results indicated that soil protozoa showed a negative response to increasing grazing intensities and therefore, suggesting that aboveground grazing practices also exerted strong impact on belowground protozoa, not only on soil microbial characteristics.

Conclusions

Soil protozoan community composition was apparently different between the HG treatment and other four grazing patterns and was potentially impacted by altered soil properties and MBC and/or MBN. Our results suggested that moderate grazing may sustain better belowground biotic diversity and ecosystem functioning in this alpine meadow on the Tibetan Plateau.
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10.
This study evaluated the effect of silicate fertilizer on denitrification and associated gene abundance in a paddy soil. A consecutive trial from 2013 to 2015 was conducted including the following treatments: control (CK), mineral fertilizer (NPK), NPK plus sodium metasilicate (NPK + MSF), and NPK plus slag-based silicate fertilizer (NPK + SSF). Real-time quantitative PCR (qPCR) was used to analyze the abundances of nirS, nirK, and nosZ genes. Potential N2O emissions and ammonium and nitrate concentrations were related to the nirS and nirK gene abundance. Compared with the NPK treatments, the addition of a Si fertilizer decreased N2O emission rates and denitrification potential by 32.4–66.6 and 22.0–59.2%, respectively, which were probably related to increased rice productivity, soil Fe availability, and soil N depletion. The abundances of nirS and nirK genes were decreased by 17.7–35.8% and 21.1–43.5% with addition of silicate fertilizers, respectively. Rates of total N2O and N2O from denitrification (DeN2O) emission were positively correlated with the nirS and nirK gene abundance. Nitrate, exchangeable NH4 +, and Fe concentrations were the main factors regulating the nirS and nirK gene abundance. Silicate fertilization during rice growth may serve as an effective approach to decreasing N2O emissions.  相似文献   

11.

Purpose

The purpose of this study was to determine the first-order rate constants and half-lives of aerobic and anaerobic biomineralization of atrazine in soil samples from an agricultural farm site that had been previously used for mixing pesticide formulations and washing application equipment. Atrazine catabolic genes and atrazine-degrading bacteria in the soil samples were analyzed by molecular methods.

Materials and methods

Biomineralization of atrazine was measured in soil samples with a [U-ring-14C]-atrazine biometer technique in soil samples. Enrichment cultures growing with atrazine were derived from soil samples and they were analyzed for bacterial diversity by constructing 16S rDNA clone libraries and sequencing. Bacterial isolates were also obtained and they were screened for atrazine catabolic genes.

Results and discussion

The soils contained active atrazine-metabolizing microbial communities and both aerobic and anaerobic biomineralization of [U-ring-14C]-atrazine to 14CO2 was demonstrated. In contrast to aerobic incubations, anaerobic biometers displayed considerable differences in the kinetics of atrazine mineralization between duplicates. Sequence analysis of 16S rDNA clone libraries constructed from the enrichment cultures revealed a preponderance of Variovorax spp. (51 %) and Schlesneria (16 %). Analysis of 16S rRNA gene sequences from pure cultures (n?=?12) isolated from enrichment cultures yielded almost exclusively Arthrobacter spp. (83 %; 10/12 isolates). PCR screening of pure culture isolates for atrazine catabolic genes detected atzB, atzC, trzD, trzN, and possibly atzA. The presence of a complete metabolic pathway was not demonstrated by the amplification of catabolic genes among these isolates.

Conclusions

The soils contained active atrazine-metabolizing microbial communities. The anaerobic biometer data showed variable response of atrazine biomineralization to external electron acceptor conditions. Partial pathways are inevitable in soil microbial communities, with metabolites linking into other catabolic and assimilative pathways of carbon and nitrogen. There was no evidence for the complete set of functional genes of the known pathways of atrazine biomineralization among the isolates.
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12.

Purpose

Soil water overconsumption is threatening the sustainability of regional vegetation rehabilitation in the Loess Plateau of China. In this study, two typical natural and artificial grasslands under different precipitation regimes were selected and the spatial variations in and the factors that impact the soil water content were investigated to provide support for vegetation restoration and sustainability management in the Loess Plateau.

Materials and methods

Soil samples were collected in May and September. Medicago sativa L. and Stipa bungeana Trin. were selected as representatives of natural and artificial grasslands, respectively. Soil measurements were conducted at the beginning and end of the rainy seasons at soil depths of 0 to 3 m in 0.2-m increments, and 147 undisturbed and 2205 disturbed soil samples were collected at 27 sampling sites with different precipitation gradients across the Loess Plateau. The plant height, the field capacity, the saturated hydraulic conductivity, the bulk density, and the slope gradient were considered as impact factors. Statistic methods included one-way ANOVA, correlation tests, significance tests, and redundancy analyses.

Results and discussion

Spatial variation trends indicated that the mean soil water content increased as the multi-year mean precipitation increased, and the soil water content was higher in the natural grassland of Stipa bungeana Trin. than in the artificial grassland of Medicago sativa L. in the same precipitation gradient zone. Vertical spatial variation trends indicated that the soil water content was higher in most surface layers than in the deep layer and lower at the end of the rainy season than at the beginning of the rainy season, when the mean annual precipitation was less than 510 mm. The soil water content of the Stipa bungeana Trin. grassland was significantly correlated with precipitation and plant height, whereas the soil water content of the Medicago sativa L. grassland only exhibited a significant correlation with precipitation. Thus, grasses with fine palatability, good adaptability, and low water consumption should be cultivated in the Loess Plateau.

Conclusions

The decreased soil water content is more obvious in the soil layers with active vegetation roots. In the areas with multi-year precipitation at 370–440 mm, natural grasslands are more suitable for restoration and these areas should be treated as key areas for vegetation restoration. With regard to the spatial distribution of vegetation restoration, the economic and ecological benefits must be balanced so that the ratio of artificial vegetation and natural restoration can be optimized to realize the continued sustainability of vegetation restorations.
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13.

Purpose

Knowledge of archaeal communities is essential for understanding of the mechanism of carbon and nitrogen cycle in the mangrove sediment ecosystem. Presently, little is known about archaeal communities in the Dongzhaigang mangrove sediments. This study aimed to characterize the archaeal communities in sediments of different mangrove stands and to find out the correlations between archaeal communities and the environmental factors of sediments.

Materials and methods

Sediment samples were collected from the Dongzhaigang mangrove forest for analysis of soil properties and archaeal communities, by national standard methods and Illumina Miseq archaeal 16S ribosomal RNA (rRNA) gene sequencing, respectively.

Results and discussion

The archaeal community in the Dongzhaigang mangrove forest was constituted by some phyla from “TACK” and “DPANN” supergroups, and dominated by Euryarchaeota. Among sediments of the four mangroves in Dongzhaigang, principal coordinates analysis (PCoA) scatter plot showed a trend of difference in the archaeal community structure in the Bruguiera gymnoihiza and Kandelia candel stands from that in the Laguncularia racemosa and Sonneratia apetala stands. The abundance of the order Methanosarcinales was the highest in the sediments of K. candel mangroves, whereas the order of Methanobacteriales dominated in B. gymnoihiza sediments. The highest richness and diversity values of Archaea occurred in K. candel sediments, while the lowest in B. gymnoihiza. Pearson correlation showed the significant relationships between sediment properties and some dominant genera, with a positive and significant correlation between sediment properties and genus Methanobacterium, coinciding with the maximum values of sediment properties and abundance of Methanobacterium in the sediment of B. gymnoihiza. Such results indicated that the difference of archaeal community structure among mangrove sediments may be caused by the different sediment characteristics. Methanogenic communities in the Dongzhaigang mangrove forest sediments were, at the order level, constituted by Methanobacteriales, Methanomicrobiales, Methanosarcinales, and Methanomassiliicoccales.

Conclusions

The investigation indicated that the Dongzhaigang mangrove sediment ecosystems support diverse archaeal communities and methanogenic communities, and that there was a general trend of difference in the archaeal community structure in the B. gymnoihiza and K. candel mangrove sediments from that in the L. racemosa and S. apetala sediments. Such difference may be caused by the difference in sediment characteristics.
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14.

Purpose

Increasing data have shown that biochar amendment can improve soil fertility and crop production, but there is little knowledge about whether biochar amendment can improve water infiltration in saline soils. We hypothesized that biochar amendment could promote water infiltration in saline soil. The aims of this study were to evaluate the effects of biochar amendment on water infiltration and find the suitable amendment rate and particle size of biochar as a saline soil conditioner.

Materials and methods

We measured water infiltration parameters in a coastal saline soil (silty loam) amended with non-sieved biochar at different rates (0.5, 1, 2, 5, and 10%, w/w) or sieved biochar of different particle sizes (≤?0.25 mm, 0.25–1 mm, and 1–2 mm) at 1 and 10% (w/w).

Results and discussion

Compared with the control, amending non-sieved biochar at 10% significantly decreased water infiltration into the saline soil (P?<?0.05). In contrast, sieved biochar of ≤?0.25 mm significantly improved water infiltration capacity, irrespective of the amendment rate. Sieved biochar of 1–2 mm was less effective to improve soil porosity and when amended at 10%, it even reduced the water infiltration capacity. The Philip model (R2?=?0.983–0.999) had a better goodness-of-fit than the Green-Ampt model (R2?=?0.506–0.923) for simulation of cumulative infiltration.

Conclusions

Amending biochar sieved to a small particle size improved water infiltration capacity of the coastal saline soil compared with non-sieved biochar irrespective of the amendment rate. This study contributes toward improving the hydrological property of coastal saline soil and rationally applying biochar in the field.
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15.

Purpose

This work investigated changes in priming effects and the taxonomy of soil microbial communities after being amended with plant feedstock and its corresponding biochar.

Materials and methods

A soil incubation was conducted for 180 days to monitor the mineralization and evolution of soil-primed C after addition of maize and its biochar pyrolysed at 450 °C. Responses of individual microbial taxa were identified and compared using the next-generation sequencing method.

Results and discussion

Cumulative CO2 showed similar trends but different magnitudes in soil supplied with feedstock and its biochar. Feedstock addition resulted in a positive priming effect of 1999 mg C kg?1 soil (+253.7 %) while biochar gave negative primed C of ?872.1 mg C kg?1 soil (?254.3 %). Linear relationships between mineralized material and mineralized soil C were detected. Most priming occurred in the first 15 days, indicating co-metabolism. Differences in priming may be explained by differences in properties of plant material, especially the water-extractable organic C. Predominant phyla were affiliated to Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Firmicutes, Planctomycetes, Proteobacteria, Verrucomicrobia, Ascomycota, Basidiomycota, Blastocladiomycota, Chytridiomycota, Zygomycota, Euryarchaeota, and Thaumarchaeota during decomposition. Cluster analysis resulted in separate phylogenetic grouping of feedstock and biochar. Bacteria (Acidobacteria, Firmicutes, Gemmatimonadetes, Planctomycetes), fungi (Ascomycota), and archaea (Euryarchaeota) were closely correlated to primed soil C (R 2?=??0.98, ?0.99, 0.84, 0.81, 0.91, and 0.91, respectively).

Conclusions

Quality of plant materials (especially labile C) shifted microbial community (specific microbial taxa) responses, resulting in a distinctive priming intensity, giving a better understanding of the functional role of soil microbial community as an important driver of priming effect.
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16.

Purpose

Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, is a pivotal component of the biogeochemical nitrogen cycle. Nitrification was conventionally assumed as a two-step process in which ammonia oxidation was thought to be catalyzed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), as well as nitrite oxidation by nitrite-oxidizing bacteria (NOB). This long-held assumption of labour division between the two functional groups, however, was challenged by the recent unexpected discovery of complete ammonia oxidizers within the Nitrospira genus that are capable of converting ammonia to nitrate in a single organism (comammox). This breakthrough raised fundamental questions on the niche specialization and differentiation of comammox organisms with other canonical nitrifying prokaryotes in terrestrial ecosystems.

Materials and methods

This article provides an overview of the recent insights into the genomic analysis, physiological characterization and environmental investigation of the comammox organisms, which have dramatically changed our perspective on the aerobic nitrification process. By using quantitative PCR analysis, we also compared the abundances of comammox Nitrospira clade A and clade B, AOA, AOB and NOB in 300 forest soil samples from China spanning a wide range of soil pH.

Results and discussion

Comammox Nitrospira are environmentally widespread and numerically abundant in natural and engineered habitats. Physiological data, including ammonia oxidation kinetics and metabolic versatility, and comparative genomic analysis revealed that comammox organisms might functionally outcompete other canonical nitrifiers under highly oligotrophic conditions. These findings highlight the necessity in future studies to re-evaluate the niche differentiation between ammonia oxidizers and their relative contribution to nitrification in various terrestrial ecosystems by including comammox Nitrospira in such comparisons.

Conclusions

The discovery of comammox and their broad environmental distribution added a new dimension to our knowledge of the biochemistry and physiology of nitrification and has far-reaching implications for refined strategies to manipulate nitrification in terrestrial ecosystems and to maximize agricultural productivity and sustainability.
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17.

Purpose

The present paper concerns the distribution and mobility of heavy metals (Cu, Pb, Zn and Fe) in the soils of some abandoned mine sites in Italy and their transfer to wild flora.

Materials and methods

Soils and plants were sampled from mixed sulphide mine dumps in different parts of Italy, and the concentrations of heavy metals were determined.

Results and discussion

The phytoremediation ability of Salix species (Salix eleagnos, Salix purpurea and Salix caprea), Taraxacum officinale and P?lantago major for heavy metals and, in particular, zinc was estimated. The results showed that soils affected by mining activities presented total Zn, Cu, Pb and Fe concentrations above the internationally recommended permissible limits. A highly significant correlation occurred between metal concentrations in soils.

Conclusions

The obtained results confirmed the environmental effects of mine waste; exploring wild flora ability to absorb metals, besides metal exploitation, proved a useful tool for planning possible remediation projects.
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18.

Purpose

This study investigated the extent of metal accumulation by plants colonizing a mining area in Yazd Province in Central Iran. It also investigated the suitability of these plants for phytoextraction and phytostabilization as two potential phytoremediation strategies.

Materials and methods

Plants with a high bioconcentration factor (BCF) and low translocation factor (TF) have the potential for phytostabilization, whereas plants with both BCFs and TFs >1 may be appropriate for phytoextraction. In this study, both shoots and roots of 40 plant species and associated soil samples were collected and analyzed for total concentrations of trace elements (Pb, Zn, and Ag). BCFs and TFs were calculated for each element.

Results and discussion

Nonnea persica, Achillea wilhelmsii, Erodium cicutarium, and Mentha longifolia were found to be the most suitable species for phytostabilization of Pb and Zn. Colchicum schimperi, Londesia eriantha, Lallemantia royleana, Bromus tectorum, Hordeum glaucum, and Thuspeinantha persica are the most promising species for element phytoextraction in sites slightly enriched by Ag. Ferula assa-foetida is the most suitable species for phytostabilization of the three studied metals. C. schimperi, L. eriantha, L. royleana, B. tectorum, M. longifolia, and T. persica accumulated Ag, albeit at low level.

Conclusions

Our preliminary study shows that some native plant species growing on this contaminated site may have potential for phytoremediation.
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19.

Purpose

This study aimed to assess the effects of biochar on improving nitrogen (N) pools in mine spoil and examine the effects of elevated CO2 on soil carbon (C) storage.

Materials and methods

The experiment consisted of three plant species (Austrostipa ramossissima, Dichelachne micrantha, and Lomandra longifolia) planted in the N-poor mine spoil with application of biochar produced at three temperatures (650, 750, and 850 °C) under both ambient (400 μL L?1) and elevated (700 μL L?1) CO2. We assessed mine spoil total C and N concentrations and stable C and N isotope compositions (δ13C and δ15N), as well as hot water extractable organic C (HWEOC) and total N (HWETN) concentrations.

Results and discussion

Soil total N significantly increased following biochar application across all species. Elevated CO2 induced soil C loss for A. ramossissima and D. micrantha without biochar application and D. micrantha with the application of biochar produced at 750 °C. In contrast, elevated CO2 exhibited no significant effect on soil total C for A. littoralis, D. micrantha, or L. longifolia under any other biochar treatments.

Conclusions

Biochar application is a promising means to improve N retention and thus, reduce environmentally harmful N fluxes in mine spoil. However, elevated CO2 exhibited no significant effects on increasing soil total C, which indicated that mine spoil has limited potential to store rising atmospheric CO2.
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20.

Purpose

Biochar has been suggested as a soil conditioner to improve soil fertility and crop productivity while simultaneously mitigate global climate change by storing carbon in the soil. This study investigated the effect of pine (Pinus radiata) biochar application on soil water availability, nitrogen (N) and carbon (C) pools and growth of C3 and C4 plants.

Materials and methods

In a glasshouse pot trial, a pine biochar (untreated) and nutrient-enriched pine biochar were applied to a market garden soil with C3 (Spinacia oleracea L.) and C4 (Amaranthus paniculatus L.) plants at rates of 0, 1.0, 2.0, and 4.0 % (w/w). Plant biomass, soil pH, moisture content, water holding capacity (WHC), hot water extractable organic C (HWEOC), and total N (HWETN), total C and N, and their isotope compositions (δ 13C and δ 15N) of soils and plants were measured at the end of the experimentation.

Results and discussion

The soil moisture content increased while plant biomass decreased with increasing untreated biochar application rates. The addition of nutrient-enriched biochar significantly improved plant biomass in comparison to the untreated biochar addition at most application rates. Biochar application also increased the levels of labile organic C and N pools as indicated by HWEOC and HWETN.

Conclusions

The results suggested that the addition of pine biochar significantly improved soil water availability but not plant growth. The application of nutrient-enriched pine biochar demonstrated that the growth of C3 and C4 plants was governed by biochar nutrient availability rather than its water holding capacity under the pot trial condition.
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