Submerged plants make an important contribution to nitrogen cycling in lakes including in the rhizosphere microenvironment through microbial activities. The main objective of this study was to investigate the abundance of functional genes for nitrogen cycling and the ecological relationship between these genes in the rhizosphere sediment of a freshwater lake in summer.
Materials and methods
Sediment from the rhizosphere of four submerged macrophytes (Ceratophyllum demersum, Hydrilla verticillata, Potamogeton maackianus, and Vallisneria spiralis) was sampled in Lake Liangzi, China, in summer. The anammox bacteria community structure and abundance of five functional genes for nitrogen cycling, ammonia monooxygenase (amoA) of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), anammox 16S rRNA, and nitrite reductase genes (nirK and nirS) in the sampled sediment, were determined.
Results and discussion
A total of 100 anammox gene sequences were grouped into eight operational taxonomic units (OTUs) and genus Ca. Kuenenia was the dominant species in Lake Liangzi in summer. Quantitative polymerase chain reaction (qPCR) revealed that gene copies of AOA amoA (2.42?×?106 copies g?1) were more than one order of magnitude higher than those of AOB amoA (1.98?×?105 copies g?1). The nirS gene (4.13?×?108 copies g?1) was more abundant than the nirK gene (7.28?×?107 copies g?1). There was no significant difference in the abundance of the AOB amoA gene among the rhizosphere of the four macrophytes. Redundancy analysis (RDA) showed a positive correlation between the abundance of the anammox 16S rRNA gene, AOA amoA and AOB amoA, which suggested two of these microbes may have provided a substrate for anammox bacteria in summer.
Conclusions
The diversity of anammox in the rhizosphere of submerged macrophytes of the freshwater lake in summer was very low, but the plant species could affect the abundance of most nitrogen circulating bacteria, especially for anammox bacteria. Anammox 16S rRNA gene was positively correlated with four other functional genes, indicating that all four genes had significant effects on anammox bacteria.
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
Nitrogen is a critical nutrient in plant-based primary production systems, therefore measurements of N cycling by microorganisms may add value to agricultural soil monitoring programs. Bacterial-mediated nitrogen cycling was investigated in soils from two broad land-uses (managed and remnant vegetation) across different Soil Orders from three geomorphic zones in Victoria, Australia, by examining the abundance of the genes amoA and nifH using quantitative polymerase chain reaction (qPCR). The aim of the study was to identify parameters influencing bacterial populations possessing the genes nifH and amoA, and examine their distribution at a regional scale across different management treatments. The gene amoA was most abundant in the neutral to slightly alkaline surface soils from Calcarosols in North-West Victoria. There was a highly significant (P < 0.001) interaction between land-use and geomorphic zones in terms of the abundance of amoA. Detection of the gene nifH was site specific with low copy number (less than 100 copies per nanogram of DNA) observed for some strongly acidic surface soil sites in North-East Victoria (Dermosols) and South-West Victoria (Sodosols/Chromosols), while nifH was more abundant in selected Calcarosols of North-West Victoria. The gene amoA was detected across more sites than nifH and was strongly influenced by land-use, with almost consistently greater abundance in managed compared to remnant sites, particularly for North-West and South-West Victoria. The abundance of nifH was not related to land-use, with similar copy numbers observed for both managed and remnant sites at some locations. For the gene nifH, there was no significant interaction between land-use and geomorphic zones, between managed and remnant sites or between the three geomorphic zones. Regression tree analysis revealed a number of likely soil chemical and microbial variables which may act as drivers of gene abundance of amoA and nifH. Variables identified as drivers for amoA included pH, Olsen P, microbial biomass carbon, nitrate and total nitrogen while for nifH the variables were microbial biomass carbon, electrical conductivity, microbial biomass nitrogen, total nitrogen and total potassium. Measures of N cycling genes could be used as an additional indicator of soil health to assess potential ecosystem functions. The spatial scale of the current study demonstrates that a landscape approach may assist soil health monitoring programs by evaluating N cycle gene abundance in the context of the different microbial and chemical conditions related to Soil Order and land-use management. 相似文献
Previous studies have shown that phosphorus addition to P-limited soils increases gaseous N loss. A possible explanation for this phenomenon is element stoichiometry (specifically of C:N:P) modifying linked nutrient cycling, leading to enhanced nitrification and denitrification. In this study, we investigated how P stoichiometry influenced the dynamics of soil N-cycle functional genes. Rice seedlings were planted in P-poor soils and incubated with or without P application. Quantitative PCR was then applied to analyze the abundance of ammonia-oxidizing (amoA) and denitrifying (narG nirK, nirS, nosZ) genes in soil. P addition reduced bacterial amoA abundance but increased denitrifying gene abundance. We suggest this outcome is due to P-induced shifts in soil C:P and N:P ratios that limited ammonia oxidization while enhancing P availability for denitrification. Under P application, the rhizosphere effect raised ammonia-oxidizing bacterial abundance (amoA gene) and reduced nirK, nirS, and nosZ in rhizosphere soils. The change likely occurred through greater C input and O2 release from roots, thus altering C availability and redox conditions for microbes. Our results show that P application enhances gaseous N loss potential in paddy fields mainly through stimulating denitrifier growth. We conclude that nutrient availability and elemental stoichiometry are important in regulating microbial gene responses, thereby influencing key ecosystem processes such as denitrification.
The nitrous oxide and molecular N emissions from 5-cm length subsamples taken from 20-cm length sample corers containing eutric Cambisol soil fertilised either with urea, ammonium or nitrate for 1 year have been examined using gas chromatography. At the beginning of the incubation, the same N rate (260 kg N/ha) was added to the soil and kept constant during the experiment. The total abundance of the soil Bacteria and Archaea and that of nitrifiers and denitrifiers was estimated by quantitative PCR of the corresponding biotic variables 16S rRNA, amoA and napA, narG, nirK, nirS, norB, nosZI and nosZII genes. The abiotic variables dissolved oxygen, pH, exchangeable NH4+-N and NO3?-N contents and total C and total N were also analysed. None of the three fertilisers affected the total abundance of Bacteria and Archaea and nitrification was the main driver of nitrous oxide production in the 0- to 5-cm and 5- to 10-cm soil layers while denitrification was in the 10- to 15-cm and 15- to 20-cm soil horizons. Parallel to the reduction in the content of dissolved oxygen along the soil profile, there was a decrease in the total and relative abundance of the bacterial and archaeal amoA gene and an increase in the abundances of the denitrification genes, mainly in the 10- to 15-cm and 15- to 20-cm soil layers. A non-metric multidimensional scaling plot comparing the biotic and abiotic variables examined in each of the four 5-cm soil subsamples and the whole 20-cm sample showed a disparate effect of N fertilisation on N gas emissions and abundance of nitrifiers and denitrifiers bacterial and archaeal communities. 相似文献
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
Bacterial-feeding nematodes represent an important driver of the soil microbial activity and diversity. This study aimed at characterizing the impact of nematode grazing on a model functional bacterial guild involved in N-cycling, the denitrifiers. Bacterial-feeding nematodes (Cephalobus pseudoparvus) were inoculated into soil microcosms whose indigenous nematofauna had previously been removed. The size, genetic structure and activity of the soil denitrifier community were characterized 15 and 45 days after nematodes inoculation using quantitative PCR of the nirK, nirS and nosZ denitrification genes, fingerprinting of the nirK and nirS genes and denitrification enzyme activity measurements, respectively. A significant impact of C. pseudoparvus was observed on genetic structure of the nirK community, mainly due to shifts in the relative abundance of the dominant populations, but not on the nirS community. The grazing pressure also tended to decrease the density of all denitrification genes as well as that of 16S rRNA genes. Despite being non-significant, the extent of this decline in gene copy numbers ranged between 60 and 80% of the control microcosm genes densities. Finally, compared to non-inoculated microcosms, denitrification activity significantly decreased by 8% in response to the nematodes inoculation. The herewith data showed that predation by a single species of bacterial-feeding nematode can affect the soil denitrifier community. 相似文献
Winter forage grazing systems in New Zealand cause compaction of soil by grazing animals, especially when the soil is wet. However, there is little information on the effects of animal trampling on denitrifiers in soil, despite their importance for N2O production. Here, we report a field study of the abundance of the denitrifying genes nirS, nirK, and nosZ and N2O emissions following the application of dairy cow urine in a free‐draining stony soil. Importantly, we found that simulated animal trampling altered some of the denitrifying microbial communities, thus leading to increased N2O emissions. Over the 111 day measurement period, the abundance of nitrite (NO2?)‐reducing nirS gene copy numbers increased significantly by 87% in the trampled soil with urine (P < 0.01) and increased by 40% in the trampled soil without urine (P < 0.05), but the nirS gene abundance did not change significantly in the nontrampled soil. The abundance of NO2? reducing nirK gene copy numbers was not affected by trampling, but increased significantly following urine application. The abundance of N2O‐reducing nosZ clade I and nosZ clade II gene copy numbers increased significantly in the trampled soil, but did not change significantly in the nontrampled soil. N2O emissions from the trampled soil were about twice that from the nontrampled soil without urine (1.20 and 0.62 kg N2O‐N per ha, respectively) and about eight times greater (6.24 kg N2O‐N per ha) than from nontrampled soil (0.80 kg N2O‐N per ha) when urine was applied. These results strongly suggest that animal trampling during winter forage grazing can have a major impact on denitrifying communities in soil, which in turn stimulate greater denitrification with increased N2O emissions. 相似文献
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