Effect of common bean (Phaseolus vulgaris L.) on the community composition of ammonia-oxidizing bacteria in soil previously cultivated with Medicago sativa

The community composition of ammonia-oxidizing bacteria (AOB) was studied during four stages of plant development in soil cultivated with Phaseolus vulgaris in comparison to unplanted soil, using an alfisol previously harboring the legume Medicago sativa. Denaturing gradient gel electrophoresis (DGGE) patterns of 16S rRNA gene and clone libraries of the same gene suggested that bacteria related to Nitrosospira cluster 3 were dominant in both planted and unplanted soil. Bacteria related to Nitrosomonas cluster 8 (Nitrosomonas communis cluster) were found at all times in planted soil, but appeared only randomly in unplanted soil. Analysis of PCR products of the gene encoding the alpha-subunit of ammonia monooxygenase (amoA) by DGGE and clone libraries only detected Nitrosospira cluster 3-like organisms, but failed to detect sequences related to Nitrosomonas. The results suggest that P. vulgaris does not affect the dominant members of AOB communities (Nitrosospira cluster 3), but could have an effect on the prevalence of Nitrosomonas cluster 8 in this type of legume-planted alfisol.     

Molecular analysis of β-proteobacterial ammonia oxidizer populations in surface layers of a submerged paddy soil microcosm

The structure of the β-proteobacterial autotrophic ammonia-oxidizing bacterial (AOB) communities in a microcosm of submerged paddy soil was determined by denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments amplified using AOB-selective primers. Shift in the community composition was observed 4 weeks after submergence. The communities from the surface layers (0–1, 2–3 mm) of the soil microcosm were different from those of the subsurface layers (6–9, > 15 mm) and DGGE bands specific to each layer were detected. The majority of the retrieved sequences were Nitrosospira-like, whereas no Nitrosomonas-like sequences were obtained. The 16S rDNA primer set also amplified sequences that were not related to the known Nitrosospira-Nitrosomonas group, although they showed a close relationship with other groups of β-proteobacteria. The results suggest that Nitrosospira-like populations are dominant AOB populations in the submerged paddy soil, and that the oxic layer of submerged paddy soil harbours the specific AOB.     

Net nitrification rate and presence of Nitrosospira cluster 2 in acid coniferous forest soils appear to be tree species specific

The impact of four coniferous tree species and their corresponding soil factors on N transformation rates and presence of ammonia-oxidising bacteria (AOB) was studied in an acid pine forest soil (Appelscha, The Netherlands). Pine soil had a relatively low net nitrification rate, while spruce, fir and larch soils showed high net nitrification rates. 16S rRNA and amoA sequences were only found in soils with high nitrification rates and belonged solely to Nitrosospira cluster 2. We conclude that tree species, possibly through their effects on soil C/N ratios, determines the presence of Nitrosospira cluster 2. Whenever AOB are present, however, the AOB community composition appears to be similar.     

Clear-cutting affects the ammonia-oxidising community differently in limed and non-limed coniferous forest soils

The effects of clear-cutting on the ammonia-oxidising bacterial community were studied in the soil of limed and non-limed spruce forest plots located in the central part of southern Sweden. The communities were studied using denaturing gradient gel electrophoresis (DGGE) profiling after polymerase chain reaction (PCR) amplification from total DNA with primers reported to be specific for -subgroup ammonia-oxidising bacteria. The bands on the DGGE were sequenced and each unique sequence was interpreted as representing one ammonia-oxidising population. The relative abundance of each population was determined by measuring the fluorescence of the respective DGGE bands. In both limed and non-limed soil, the same two Nitrosospira populations were found, one belonging to cluster 2 (NScl2) and one to cluster 4 (NScl4). However, while NScl4 first appeared a year after the clear-cutting in the non-limed plot, it was present both before and after the cutting in the limed plot. Irrespective of previous liming, clear-cutting caused a shift in the ammonia-oxidiser community, from dominance by the NScl2 population to a community with approximately equal relative abundance of NScl2 and NScl4. In both plots the total size of the community increased after clear-cutting (based on increased DGGE band intensity), most likely due to increased NH₄⁺ availability, but the growth response was faster in the limed plot. Hence, the prior liming increased the responsiveness of the ammonia-oxidisers to the changes caused by cutting. This is the first study to report the effects of clear-cutting on the ammonia-oxidising community, and the results show a clear correlation between increased potential nitrification and a shift in the ammonia-oxidiser community.     

土地利用方式和施肥对潮棕壤氨氧化细菌活性和群落组成的影响

The effects of long-term (19 years) different land use and fertilization on activity and composition of ammonia-oxidizing bacteria (AOB) in an aquic brown soil were investigated in a field experiment in Liaoning Province, China. The 19-year experiment conducted from 1990 to 2008 involved seven treatments designed: cropping rotation of soybean-corn-corn with no fertilizer (control, CK), recycled manure (RM), fertilizer nitrogen (N), phosphorous (P) and potassium (K) (NPK), NPK+RM, and no-crop bare land, mowed fallow, and non-mowed fallow. The results showed that the potential nitrification rates of the RM, NPK+RM, mowed fallow, and non-mowed fallow treatments were significantly higher (P < 0.05) than those of the CK and NPK treatments, indicating that the long-term applications of recycled manure and return of plant residues both significantly increased the activity of AOB. Although the application of NPK did not enhance soil potential nitrification because of decreased pH, available K had an important effect on potential nitrification. Denaturing gradient gel electrophoresis (DGGE) fingerprint profiles showed that no-crop treatments had an increase in the diversity of the AOB community compared to the CK, RM, and NPK treatments, implying that agricultural practices, especially tillage, had an adverse effect on the soil AOB community. The NPK+RM treatment had the most diverse DGGE patterns possibly because of the increased available P in this treatment. A phylogenetic analysis showed that most of the DGGE bands derived belonged to Nitrosospira cluster 3, not Nitrosospira cluster 2. These demonstrated that different land use and fertilization significantly influenced the activity and composition of the AOB community by altering the soil properties, mainly including pH, total C, available K, and available P.     

Diversity–function relationship of ammonia-oxidizing bacteria in soils among functional groups of grassland species under climate warming

Although warming and plant diversity losses have important effects on aboveground ecosystem functioning, their belowground effects remain largely unknown. We studied the impact of a 3 °C warming and of three plant functional groups (forbs, grasses, legumes) on ammonia-oxidizing bacteria (AOB) diversity (polymerase chain reaction-denaturing gradient gel electrophoresis, PCR-DGGE) and their function (potential nitrification) in artificial grasslands. Warming did not influence AOB diversity and function. Sequencing of 16S rRNA gene fragments retrieved from DGGE gel revealed that they were all related to Nitrosospira-like sequences. Clustering analysis of DGGE profiles resulted in two nodes, separating AOB community structure under legumes from all other samples. Decreased AOB richness (number of DGGE bands) and concurrent increased potential nitrification were also observed under legumes. We hypothesized that ammonium availability was the driving force regulating the link between aboveground and belowground communities, as well as the AOB diversity and function link. The results document that the physiology of AOB might be an important regulator of AOB community structure and function under plant functional groups. This study highlights the major role of the microbial community composition in soil process responses to changes in the functional composition of plant communities.     

Quantification of ammonia-oxidising bacteria in limed and non-limed acidic coniferous forest soil using real-time PCR

Ammonia-oxidising bacteria (AOB) in limed and non-limed acidic coniferous forest soil were investigated using real-time PCR. Two sites in southern Sweden were studied, 244 Åled and Oxafällan. The primers and probe used earlier appeared to be specific to the 16S rRNA gene of AOB belonging to the β-subgroup of the Proteobacteria [Appl. Environ. Microbiol. 67 (2001) 972]. Plots treated with two different doses of lime, 3 or 6 t ha⁻¹, were compared with non-limed control plots on two occasions during a single growing season. Three different soil depths were analysed to elucidate possible differences in the density of their AOB communities. The only clear effect of liming on the AOB was recorded in the beginning of the growing season at 244 Åled. In samples taken in April from this site, the numbers of AOB were higher in the limed plots than in the control plots. At the end of the growing season the AOB communities were all of a similar size in the different plots at both sites, irrespective of liming. The number of AOB, determined using real-time PCR, ranged between 6×10⁶ and 1×10⁹ cells g⁻¹ soil (dw) at the two sites, and generally decreased with increasing soil depth. The results showed no correlation between community density and potential nitrification. This may indicate a partly inactive AOB community. Furthermore, more than 10⁷ cells g⁻¹ soil (dw) were recorded using real-time PCR in the control plot at 244 Åled, although Bäckman et al. [Soil Biol. Biochem. 35 (2003) 1337] detected no AOB like sequences in the same plots using PCR followed by DGGE. Taken together our results strongly suggest that the primers and probe set used are not well suited for quantifying AOB in acidic forest soils, which is probably due to an insufficient specificity. This shows that it is extremely important to re-evaluate any primers and probe set when used in a new environment. Consideration should be given to the specificity and sensitivity, both empirically and using bioinformatic tools.     

两种农田土壤中的氨氧化细菌和氨氧化古菌对硝化抑制剂DCD和DMPP的响应-盆栽试验

Taking two important agricultural soils with different pH, brown soil （Hap-Udic Luvisol） and cinnamon soil （Hap-Ustic Luvisol）, from Northeast China, a pot culture experiment with spring maize （Zea mays L.） was conducted to study the dynamic changes in the abundance and diversity of soil ammonia-oxidizing bacteria （AOB） and ammonia-oxidizing archaea （AOA） populations during maize growth period in response to the additions of nitrification inhibitors dicyandiamide （DCD） and 3,4-dimethylpyrazole phosphate （DMPP） by the methods of real-time polymerase chain reaction （PCR） assay, PCR-denaturing gradient gel electrophoresis （DGGE）, and construction of clone library targeting the amoA gene. Four treatments were established, i.e., no urea （control）, urea, urea plus DCD, and urea plus DMPP. Both DCD and DMPP inhibited growth of AOB significantly, compared to applying urea alone. Soil bacterial amoA gene copies had a significant positive linear correlation with soil nitrate content, but soil archaeal amoA gene copies did not. In both soils, all AOB sequences fell within Nitrosospira or Nitrosospira-like groups, and all AOA sequences belonged to group 1.1b crenaxchaea. With the application of DCD or DMPP, community composition of AOB and AOA in the two soils had less change except that the AOB community composition in Hap-Udic Luvisol changed at the last two growth stages of maize under the application of DCD. AOB rather than AOA likely dominated soil ammonia oxidation in these two agricultural soils.     

Traceability of ammonia-oxidizing bacteria in compost-treated soils

Composts are increasingly used as environmentally safe biofertilizers in sustainable agriculture all over the world. Although it is well known that composts may contribute to soil vitality and sustainability, and in the enhancement of various soil microbiological processes, little is known about their direct or indirect effects on a microbial-community or population level. Ammonia oxidation by autotrophic ammonia-oxidizing bacteria (AOB) is a key process in agricultural and natural ecosystems and plays an important role in the global nitrogen cycle. Here, we studied the diversity and community composition of ammonia oxidizers in a long-term crop rotation field experiment (>10 years) where four major types of compost (from organic waste, cattle manure, green waste and sewage sludge) had been applied annually. The methods used ranged from PCR-DGGE (denaturing gradient gel electrophoresis) and cloning of 16S rDNA fragments to quantitative real-time PCR. Cluster analysis of DGGE profiles differentiated between the microbial communities of composts, compost-treated soils and mineral-fertilized soils. The community composition of the composts was not reflected in the community composition of the compost-treated soils. Sequencing of screened clones revealed a characteristic AOB community structure for the representative soil sample and the four composts. All AOB-like sequences grouped within the Nitrosospira cluster 3 and 4 and within the Nitrosomonas cluster 6 and 7. The average AOB abundance in compost-treated soils was two times higher than in mineral-fertilized soils (4.3×10⁷ and 1.9×10⁷, respectively). Our data suggest that composts do not leave direct microbial imprints in soils after long-term amendment, but an indirect effect on the AOB community was evident.     

Overland flow systems for treatment of landfill leachates—Potential nitrification and structure of the ammonia-oxidising bacterial community during a growing season

Overland flow systems are useful for treating landfill leachates, because they provide favourable conditions for nitrification and they are easy to maintain. However, little is known about the microbial communities in such systems or the nitrification capacity of those microorganisms. In this study, seasonal variations in potential nitrification and in community composition of nitrifying bacteria were investigated in two overland flow areas receiving leachate from landfills at Korslöt and Hagby, Sweden. Samples were collected in the settling ponds sediment and at two depths in the overland flow areas (the macrophyte litter layer and the rhizosphere) in May, August and November 2003. A short-term incubation method was used to measure potential oxidation of ammonia and nitrite (designated PAO and PNO). The ammonia-oxidising bacterial (AOB) community was investigated using a 16S rRNA gene approach that included PCR amplification and analysis of PCR products by denaturing gradient gel electrophoresis (DGGE), followed by nucleotide sequencing and phylogenetic analysis.PAO was determined in the range 5-2700 (NO₂⁻+NO₃⁻)-N g⁻¹ dw d⁻¹ and PNO in the range 60-2000 μg NO₂⁻-N g⁻¹ dw d⁻¹. At Korslöt, PAO and PNO showed similar temporal variation in the different ecosystems, whereas no such relationship was noticed at Hagby. Considering both sites, there was no obvious change in the composition of the AOB community over the growing season. However, the composition did differ between the ecosystems: Nitrosomonas-like sequences were more common in the ponds, and in the litter layers they were found as often as Nitrosospira-like sequences, whereas Nitrosospira-like sequences were more common in the rhizospheres. Altogether, we found nine different AOB sequences, five Nitrosomonas-like and four Nitrosospira-like, which belonged to clusters 0, 2, 3b, 6a, 6b and 7. There was no apparent relationship between the number of AOB populations and the PAO in different soil layers and sediments.     

Lime Residues and Metal Sequestration in Sediments of Excessively Limed Lakes

Sediment profiles from ten excessively limed lakes were used to study the occurrence of lime residues as a result of incomplete lime dissolution and the influence of treatment with very high lime doses on the sequestration of metals in lake sediments. The sediment profiles were subjected to multi-element analysis and compared to sediment profiles from previous studies of lakes limed with normal lime doses and untreated reference lakes. The high lime doses were found to result in large lime residues in the sediment, with lime concentrations of up to 70% of the dry sediment in the studied lakes. Excessive liming, like liming with normal doses, was found to cause increased sequestration in sediments of, e.g. Cd, Co, Ni and Zn, metals where the mobility is known to be highly pH dependent, compared to non-limed reference lakes. No effect of liming on the sequestration of Cu, Cr, Pb and V could be shown. The size of the lime dose did not seem to influence the metal sequestration in the sediment, since no difference between the excessively limed lakes and lakes limed with normal doses was found. On the contrary, the large lime residues were found to cause a dilution of the metal concentrations in the sediments, since lime products used for lake liming generally have lower metal concentrations compared to the sediments.     

桂西北不同植被恢复阶段土壤氨氧化细菌遗传多样性研究

以桂西北喀斯特不同植被恢复阶段(草丛、灌木林、次生林、原生林)生态系统为研究对象,运用分子生物学技术分析了土壤氨氧化细菌amoA功能基因多样性,探讨了其与脲酶活性和土壤理化性质的关系.结果显示,随着植被的恢复,土壤氨氧化细菌多样性指数与均匀度指数呈增大趋势(灌木林例外),且土壤中氨氧化细菌群落结构发生了改变:主要表现在因Nitrosospira3簇种群对铵态氮浓度敏感度差异导致其在3a、3b簇中分布不一致;相关分析表明;土壤脲酶活性与铵态氮浓度呈正相关关系,土壤脲酶可能通过影响铵态氮浓度改变氨氧化细菌多样性,但植被恢复后期土壤铵态氮浓度减少并未降低土壤氨氧化细菌多样性.LIBSHUFF和RDA分析揭示,植被类型和土壤脲酶活性及pH与氨氧化细菌群落结构紧密相关,说明植被和土壤氮素有效性以及pH可能是决定土壤氨氧化细菌多样性的主要因子,为深入理解喀斯特地区土壤氮素循环提供了一定的科学依据.     

Earthworm communities in temperate beech wood forest soils affected by liming

To monitor the effects of liming on forest ecosystems, experimental plots were installed in forests in mid-western Germany. In addition to soil chemical indices, earthworm communities were investigated on these plots about 15 years after first lime applications took place. As a “natural reference”, communities were compared to earthworm records that derived from a beech forest on limestone. In the non-acidified plots that had never been limed only epigeic earthworms were detected in small numbers and low species richness. Forest liming caused higher pH and a higher base saturation in the mineral topsoils. To a large extent, epigeic earthworm species seemed to benefit from this and had increased in number and biomass at all three different locations selected for the investigations. The epigeic dominated communities were completed by anecic Lumbricus terrestris that was rarely found in some of the samples from one location and a number of endogeic species that showed a very patchy distribution in limed plots. In contrast to this, the soil of the beech forest on limestone showed a different community composition. It was dominated by endogeic species in abundance and by anecic species in biomass. On limestone the total biomass of earthworms clearly exceeded the biomass values from all other plots. In conclusion, a long-term support of forest earthworm fauna due to liming was detected. This support was mainly effective for epigeic species, but in some cases for endogeic and anecic species, too.     

Influence of bacterial-feeding nematodes on nitrification and the ammonia-oxidizing bacteria (AOB) community composition

The effects of bacterial-feeding nematodes on nitrification and the ammonia-oxidizing bacteria (AOB) community composition were studied in soil microcosms. Sterilized soils were inoculated with mixed soil bacteria (obtained by filtering) or with bacteria and bacterial-feeding nematodes, after which the dynamic inorganic nitrogen concentration was measured weekly. After 28 days of incubation, denaturing gradient gel electrophoresis (DGGE) based on PCR amplification of the amoA gene was used to analyze the AOB community composition. In addition, a clone library from the amoA gene fragments was established using clones randomly selected and sequenced from the two treatments. The results showed that the presence of bacterial-feeding nematodes led to significantly greater NH₄⁺ and NO₃⁻ contents over the entire incubation period, indicating that bacterial-feeding nematodes promoted both N mineralization and nitrification. The results of DGGE showed that the AOB community composition was significantly changed in the presence of bacterial-feeding nematodes. Furthermore, the sequencing results suggested that Nitrosospira sp. was the dominant species in the treatment without nematodes, while Nitrosomonas sp. and Nitrosospira sp. were the dominant species in the treatment with nematodes. Such changes in the AOB community may be one of explanation of the important role that nematodes play in promoting nitrification.     

Characterization of ammonia oxidizing bacteria associated with weeds in a Japanese paddy field using amoA gene fragments

Abstract

Ammonia oxidizing bacteria (AOB) are important microorganisms in rice paddy field ecosystems because they play a key role in the nitrogen (N) cycle by converting ammonia (NH₃) to nitrite (NO^? ₂). In this study, we investigated AOB associated with three types of weeds in a Japanese paddy field (semi-aquatic Echinochloa oryzicola Vasing, floating Lemna paucicostata Hegelm and submerged Najas graminea Delile) using molecular techniques polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and DNA sequencing targeting ammonia monooxygenase (amoA) gene. This work confirmed that rice paddy weeds harbor AOB and that the community composition is different for each type of weed. However, all AOB sequences associated with the tested weeds were closely related to known species of Nitrosospira-like AOB isolated from soil, suggesting that AOB associated with weeds were not specific to weeds and can also be found in the soil. Nitosomanas-like AOB were not detected on any of the weeds tested. In addition, the most dominant AOB strains present in the tested weeds were closely related to Nitrosospira sp. Ka3 and Nitrosospira sp. CT2F. The phylogenetic tree revealed that most of the AOB detected in the present study belonged to amoA cluster 1.     

浙江中部红壤施用石灰对土壤交换性钙、镁及土壤酸度的影响

为了确定红壤施用石灰后钙、镁移动和土壤酸化速率,监测了耕层（10～20ｃｍ）和底土（20～60ｃｍ）的ｐＨ和交换性Ca2+、Mg2+、Al2+的长期变化。结果表明,耕层交换性Ca2+在施用石灰后的一年半时间达到最高值,此后随着时间的推移而急剧减少;而底土的交换性Ca2+随石灰用量的增加和施用石灰后时间的推移而增加。镁在土壤剖面中的移动比钙快;施用石灰后耕层和底土酸度的降低与交换性Ca2+的增加基本同步。在本试验条件下,不论施用石灰与否都存在着复酸化过程,但施用石灰后复酸化作用更强。     

The response of soil microbial biomass and activity of a Norway spruce forest to liming and drought

Long-term effects of liming and short-term effects of an experimentally induced drought on microbial biomass and activity were investigated in samples from the O-layer (Of/Oh) and uppermost mineral soil (0—10 cm) in a spruce forest near Schluchsee (Black Forest, South-West Germany). Seven years after lime application a marked increase of pH values was restricted to the O-layer. The contents of C and N in the O-layer of the limed plot appeared to be lower, whereas in the A-horizon from the limed plot the contents of C and N appeared to be higher than on the control. However, these differences were statistically not significant due to a distinct spatial variability of topsoil conditions. On the limed plots C_mic, N_mic, and P_mic in the O-layer were lower in comparison to the control whereas differences in the A-horizon were negligible. In both sampling depths of the limed plot protease activity was higher while N-mineralization was lower. The other microbial activities studied (basal respiration, catalase activity) followed no consistent pattern after liming. Drought and drought in combination with liming, respectively, had no clear effects on microbial biomass and activity. Only in the A-horizon of the control, there is some evidence for drought stress for microorganisms. The high variability of results from the drought experiment (roof installation) is likely due to the marked spatial variability of top soil properties as well as imperfect and uneven achievement of experimental drought. Nevertheless, our study indicates that long-term effects of liming on microorganisms highly depend on site conditions. Thus, liming operations which currently affect vast areas of forest land should be accompanied by monitoring of soil organisms and their activities to reduce the possibility of a loss in functional diversity of soil organisms.     

The short-term effects of liming on organic carbon mineralisation in two acidic soils as affected by different rates and application depths of lime

Two acidic soils (initial pH, 4.6) with contrasting soil organic C (SOC) contents (11.5 and 40 g C kg^?1) were incubated with ¹³C-labelled lime (Ca¹³CO₃) at four different rates (nil, target pH 5, 5.8 and 6.5) and three application depths (0–10, 20–30 and 0–30 cm). We hypothesised that liming would stimulate SOC mineralisation by removing pH constraints on soil microbes and that the increase in mineralisation in limed soil would be greatest in the high-C soil and lowest when the lime was applied in the subsoil. While greater SOC mineralisation was observed during the first 3 days, likely due to lime-induced increases in SOC solubility, this effect was transient. In contrast, SOC mineralisation was lower in limed than in non-limed soils over the 87-day study, although only significant in the Tenosol (70 μg C g^?1 soil, 9.15%). We propose that the decrease in SOC mineralisation following liming in the low-C soil was due to increased microbial C-use efficiency, as soil microbial communities used less energy maintaining intracellular pH or community composition changed. A greater reduction in SOC mineralisation in the Tenosol for low rates of lime (0.3 and 0.5 g column^?1) or when the high lime rate (0.8 g column^?1) was mixed through the entire soil column without changes in microbial biomass C (MBC) could indicate a more pronounced stabilising effect of Ca²⁺ in the Tenosol than the Chromosol with higher clay content and pH buffer capacity. Our study suggests that liming to ameliorate soil acidity constraints on crop productivity may also help to reduce soil C mineralisation in some soils.     

Responses of bacterial and archaeal ammonia oxidisers of an acidic luvisols soil to different nitrogen fertilization rates after 9?years

It is still not clear which group of ammonia-oxidizing microorganisms plays the most important roles in nitrification in soils. Change in abundances and community compositions of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) under long-term different nitrogen (N) fertilization rates were investigated in an acidic luvisols soil using real-time polymerase chain reaction and denaturing gradient gel electrophoresis, respectively, based on the ammonia monooxygenase a-subunit gene. The experimental plan included the following treatments: control without N fertilization (N_CK), low N fertilization rate, middle N fertilization rate, and high N fertilization rate as 0, 100, 150, and 250?kg urea-N?ha^?1, respectively. Long-term different N fertilization rates did not significantly alter the total C and N contents of soil while it significantly decreased soil pH, which ranged from 5.60 to 5.20. The AOB abundance was more abundant in the N fertilization treatments than the N_CK treatment; the AOA abundance decreased by the increasing N fertilization rates, as did the ratios of AOA/AOB. The large differences in the potential nitrification rates among four treatments depended on the changes in AOA abundance but not to changes in AOB abundance. Phylogenetic analysis showed that the AOB communities were dominated by Nitrosospira clusters 1, 3, and 9 while all AOA sequences were grouped into soil/sediment cluster except for one sequence. Taken together, these results indicated that AOB and AOA preferred different soil N conditions and AOA were functionally more important in the nitrification than AOB in the acidic luvisols soil.     

Shift in abundance and structure of soil ammonia-oxidizing bacteria and archaea communities associated with four typical forest vegetations in subtropical region

Purpose

Nitrogen (N) is one of the most important elements that can limit plant growth in forest ecosystems. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are considered as the key drivers of global N biogeochemical cycling. Soil ammonia-oxidizing microbial communities associated with subtropical vegetation remain poorly characterized. The aim of this study was to determine how AOA and AOB abundance and community structure shift in response to four typical forest vegetations in subtropical region.

Materials and methods

Broad-leaved forest (BF), Chinese fir forest (CF), Pinus massoniana forest (PF), and moso bamboo forest (MB) were widely distributed in the subtropical area of southern China and represented typical vegetation types. Four types of forest stands of more than 30 years grew adjacent to each other on the same soil type, slope, and elevation, were chosen for this experiment. The abundance and community structure of AOA and AOB were characterized by using real-time PCR and denaturing gradient gel electrophoresis (DGGE). The impact of soil properties on communities of AOA and AOB was tested by canonical correspondence analysis (CCA).

Results and discussion

The results indicated that AOB dominated in numbers over AOA in both BF and MB soils, while the AOA/AOB ratio shifted with different forest stands. The highest archaeal and bacterial amoA gene copy numbers were detected in CF and BF soils, respectively. The AOA abundance showed a negative correlation with soil pH and organic C but a positive correlation with NO₃ ^??N concentration. The structures of AOA communities changed with vegetation types, but vegetation types alone would not suffice for shaping AOB community structure among four forest soils. CCA results revealed that NO₃ ^??N concentration and soil pH were the most important environmental gradients on the distribution of AOA community except vegetation type, while NO₃ ^??N concentration, soil pH, and organic C significantly affected the distribution of the AOB communities.

Conclusions

These results revealed the differences in the abundance and structure of AOA and AOB community associated with different tree species, and AOA was more sensitive to vegetation and soil chemical properties than AOB. N bioavailability could be directly linked to AOA and AOB community, and these results are useful for management activities, including forest tree species selection in areas managed to minimize N export to aquatic systems.