Temporal shifts in diversity and quantity of nirS and nirK in a rice paddy field soil

Denitrification is an important part of the nitrogen cycle in the environment, and diverse bacteria, archaea, and fungi are known to have denitrifying ability. Rice paddy field soils have been known to have strong denitrifying activity, but the microbes responsible for denitrification in rice paddy field soils are not well known. Present study analyzed the diversity and quantity of the nitrite reductase genes (nirS and nirK) in a rice paddy field soil, sampled four times in one rice-growing season. Clone library analyses suggested that the denitrifier community composition varied over sampling time. Although many clones were distantly related to the known NirS or NirK, some clones were related to the NirS from Burkholderiales and Rhodocyclales bacteria, and some were related to the NirK from Rhizobiales bacteria. These denitrifiers may play an important role in denitrification in the rice paddy field soil. The quantitative PCR results showed that nirK was more abundant than nirS in all soil samples, but the nirK/nirS ratio decreased after water logging. These results suggest that both diversity and quantity changed over time in the rice paddy field soil, in response to the soil condition.     

Identifying response groups of soil nitrifiers and denitrifiers to grazing and associated soil environmental drivers in Tibetan alpine meadows

Defining response groups within N-related microbial communities is needed to predict land management effect on soil N dynamics, but information on such response groups and associated environmental drivers is scarce. We investigated the abundance and major populations of ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nirS- and nirK-harboring denitrifiers under different grazing managements in Tibetan alpine meadow soils. Grazing increased AOB and AOA abundances up to 42 fold and 3.7 fold, respectively, and increased the percentage of AOB within total ammonia oxidizers from 3.1% to 10.8%. The abundance of nirK-like denitrifiers increased with grazing intensity, while the abundance of nirS-like denitrifiers tended to decrease. However, sub-groups within each of these broad groups of (de)nitrifiers responded differently to grazing. Soil nitrate was the main driver of the abundance of denitrifier sub-groups (nirK or nirS) positively responding to grazing, while soil moisture and carbon concentration were the main drivers of the abundance of denitrifier sub-groups negatively responding to grazing. AOB and nirK-harboring denitrifiers thus generally responded more positively to grazing than AOA and nirS-harboring denitrifiers, but significant functional diversity existed within each group. Our approach demonstrates the usefulness of the concept of response groups to better characterize and understand (de)nitrifier response to grazing.     

Spatial patterns of microbial denitrification genes change in response to poultry litter placement and cover crop species in an agricultural soil

Subsurface-banding manure and winter cover cropping are farming techniques designed to reduce N loss. Little is known, however, about the effects of these management tools on denitrifying microbial communities and the greenhouse gases they produce. Abundances of bacterial (16S), fungal (ITS), and denitrification genes (nirK, nirS, nosZ-I, and nosZ-II) were measured in soil samples collected from a field experiment testing the combination of cereal rye and hairy vetch cover cropping with either surface-broadcasted or subsurface-banded poultry litter. The spatial distribution of genes was mapped to identify potential denitrifier hotspots. Spatial distribution maps showed increased 16S rRNA genes around the manure band, but no denitrifier hotspots. Soil depth and nitrate concentration were the strongest drivers of gene abundance, but bacterial gene abundance also differed by gene, soil characteristics, and management methods. Gene copy number of nirK was higher under cereal rye than hairy vetch and positively associated with soil moisture, while nirS gene copies did not differ between cover crop species. The nirS gene copies increased when manure was surface broadcasted compared to subsurface banded and was positively associated with pH. Soil moisture and pH were positively correlated to nosZ-II but not to nosZ-I gene copy numbers. We observed stronger correlations between nosZ-I and nirS, and nosZ-II and nirK gene copies compared to the reverse pairings. Agricultural management practices differentially affect spatial distributions of genes coding for denitrification enzymes, leading to changes in the composition of the denitrifying community.     

Management practices have a major impact on nitrifier and denitrifier communities in a semiarid grassland ecosystem

Purpose

Nitrification and denitrification, two of the key nitrogen (N) transformation processes in the soil, are carried out by a diverse range of microorganisms and catalyzed by a series of enzymes. Different management practices, such as continuous grazing, mowing, and periodic fencing off from grazing, dramatically influenced grassland ecosystems. This study aimed to examine the effects of management practices on the abundance and community structure of nitrifier and denitrifier communities in grassland ecosystems.

Materials and methods

Soil samples were collected from a semiarid grassland ecosystem in Xilingol region, Inner Mongolia, where long-term management practices including free-grazing, different periods of enclosure from grazing, and different frequencies of mowing were conducted. Real-time quantitative polymerase chain reaction (Q-PCR), denaturing gradient gel electrophoresis (DGGE), sequencing, and phylogenetic analysis were applied to estimate the abundance and composition of amoA, nirS, nirK, and nosZ genes.

Results and discussion

The ammonia-oxidizing archaea (AOA) amoA copies were in the range 5.99?×?10⁸ to 8.60?×?10⁸, while those of ammonia-oxidizing bacteria (AOB) varied from 3.02?×?10⁷ to 4.61?×?10⁷. The abundance of AOA was substantially higher in the light grazing treatment (LG) than in the mowing treatments. The quantity and intensity of DGGE bands of AOA varied with pasture management. In stark contrast, AOB population abundance and community structure remained largely unchanged in all the soils irrespective of the management practices. All these results suggested that ammonia oxidizers were dominated by AOA. The higher gene abundance and greater intensity of DGGE bands of nirS and nosZ under the enclosure treatments would suggest greater stimulated denitrification. The ratio of nosZ/(nirS?+?nirK) was higher in mowing treatments than in the free-grazing and enclosure treatments, possibly leading to more complete denitrification. Correlation analysis indicated that soil moisture and inorganic nitrogen content were the two main soil environmental variables that influence the community structure of nitrifiers and denitrifiers.

Conclusions

In this semiarid neutral to alkaline grassland ecosystem under low temperature conditions, AOA mainly affiliated with Nitrososphaera dominated nitrification. These results clearly demonstrate that grassland management practices can have a major impact on nitrifier and denitrifier communities in this semiarid grassland ecosystem, under low temperature conditions.

     

Biogeography and biophysicochemical traits link N2O emissions,N2O emission potential and microbial communities across New Zealand pasture soils

The process of denitrification has been studied for decades, with current evidence suggesting that an ecosystem's ability to produce and emit N₂O is controlled both by transient ‘proximal’ regulators (e.g. temperature, moisture, N availability) as well as distal regulators (e.g. soil type, microbial functional diversity, geography). In this study we use New Zealand soils as a model system to test the impact of distal regulators (i.e. geography) on microbial communities and their N₂O emission potential. Using gas chromatography, soil chemical analyses, 16S amplicon sequencing, terminal restriction fragment length polymorphism (T-RFLP) and quantitative PCR (qPCR) on three denitrifier functional genes (nirS, nirK and nosZ), we assessed the factors linked to N₂O emissions across a latitudinal gradient. Results show that soil drainage class, soil texture class, and latitude were powerful regulators of both emissions and emission end products (N₂ vs. N₂O). Mixed models demonstrate that a few variables (including latitude, texture class, drainage class and denitrifier community data [abundance and diversity] amongst others) were enough to predict both the amount and type of gas emitted. In addition we show that microbial community composition (based on 16S rRNA gene sequencing) can also be used to predict both the gas species and quantity emitted.     

The effects of silicon fertilizer on denitrification potential and associated genes abundance in paddy soil

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.     

Abundance of ammonia oxidizing microbes and denitrifiers in different soil horizons of an agricultural soil in relation to the cultivated crops

The role of subsoils and their microbial communities for the nutrient supply for plants is to a large extent unknown, especially in comparison to well investigated topsoil layers. Therefore, in this study, the influence of three different plant species with different rooting systems and different N uptake strategies on ammonium and nitrate levels and microbial communities involved in ammonia oxidation and denitrification was investigated in different soil horizons. Overall, our results show a higher genetic potential for both processes in topsoils than in subsoils independent of the present plant. Although we found accumulation of N in top and subsoils in plots with legumes, we could not observe an impact of the higher nitrate content on the genetic potential of denitrification and ammonia oxidation. However, differences in the ratios of ammonia oxidizing archaea to bacteria and also between denitrifying bacteria harboring genes for copper- (nirK) or cytochrome- (nirS) dependent nitrite reductase in top and subsoil samples reveal different ecophysiologies of microbes involved in N turnover in top and subsoil habitats.     

Incongruous variation of denitrifying bacterial communities as soil N level rises in Canadian canola fields

Soil N fertilization stimulates the activity of the soil bacterial species specialized in performing the different steps of the denitrification processes. Different responses of these bacterial denitrifiers to soil N management could alter the efficiency of reduction of the greenhouse gas N₂O into N₂ gas in cultivated fields. We used next generation sequencing to show how raising the soil N fertility of Canadian canola fields differentially modifies the diversity and composition of nitrite reductase (nirK and nirS) and nitrous oxide reductase (nosZ) gene-carrying denitrifying bacterial communities, based on a randomized complete blocks field experiment. Raising soil N levels increased up to 60% the ratio of the nirK to nirS genes, the two nitrite reductase coding genes, in the Brown soil and up to 300% in the Black soil, but this ratio was unaffected in the Dark Brown soil. Raising soil N levels also increased the diversity of the bacteria carrying the nitrite reductase gene nirK (Simpson index, P = 0.0417 and Shannon index, 0.0181), and changed the proportions of the six dominant phyla hosting nirK, nirS, and nosZ gene-carrying bacteria. The level of soil copper (Cu) and the abundance of nirK gene, which codes for a Cu-dependent nitrite reductase, were positively related in the Brown (P = 0.0060, R² = 0.48) and Dark Brown (0.0199, R² = 0.59) soils, but not in the Black soil. The level of total diversity of the denitrifying communities tended to remain constant as N fertilization induced shifts in the composition of these denitrifying communities. Together, our results indicate that higher N fertilizer rate increases the potential risk of nitrous oxide (N₂O) emission from canola fields by promoting the proliferation of the mostly adaptive N₂O-producing over the less adaptive N₂O-reducing bacterial community.     

Direct seeding mulch-based cropping increases both the activity and the abundance of denitrifier communities in a tropical soil

This study evaluated the impact of direct seeding mulch-based cropping (DMC), as an alternative to conventional tilling (CT), on a functional community involved in N cycling and emission of greenhouse gas nitrous oxide (N₂O). The study was carried out for annual soybean/rice crop rotation in the Highlands of Madagascar. The differences between the two soil management strategies (direct seeding with mulched crop residues versus tillage without incorporation of crop residues) were studied along a fertilization gradient (no fertilizer, organic fertilizer, organic plus mineral fertilizers). The activity and size of the denitrifier community were determined by denitrification enzyme activity assays and by real-time PCR quantification of the denitrification genes. Denitrification activity and total C and N content in the soil were significantly increased by DMC both years, whereas the fertilization regime and sampling year (crop and mulch types, climatic conditions) had very little effect. Similar results were also observed for denitrification gene densities. Denitrification enzyme activity was more closely correlated with C content than with N content in the soil and denitrification gene densities. Principal component analysis confirmed that soil management had the strongest impact on the soil denitrifier community and total C and N content for both years and further indicated that changes in microbial and chemical soil parameters induced by the use of fertilizer were favored in DMC plots. Overall, the alternative DMC system had a significant positive effect on denitrifier densities and potential activities, which was not altered by crop rotation and the level of fertilization. These data also suggest that in these clayey soils, the DMC system simultaneously increased the size of the soil N pool and accelerated the N cycle, by stimulating the denitrifier community. Complementary investigations should further determine in greater detail the influence of DMC on in situ N-fluxes caused by denitrification.     

Overwintering management on upland pasture causes shifts in an abundance of denitrifying microbial communities, their activity and N2O-reducing ability

Pasture soils used for cattle overwintering may represent significant sources of N₂O emissions from soils. Therefore, the long-term effect of cattle overwintering on the abundance and activity of a denitrifying community was explored. The study was performed at a cattle overwintering area in South Bohemia (Czech Republic), where three sites differing in the degree of animal impact were selected: severely impacted (SI) and moderately impacted (MI), as well as a control site with no impact (NI). N₂O flux measurement and soil sampling were performed in spring and fall of 2005. The activity was measured in terms of potential denitrification activity. Bacterial nirK, nirS and nosZ genes were used as functional markers of the denitrifying communities; abundance was analyzed using a real-time PCR assay. Surprisingly, in situ N₂O emissions were the highest in spring at MI and significantly differed from those at SI and NI, while in autumn, rates of emissions generally decreased. In contrast potential denitrification rates were highest at SI, followed by MI, and the lowest at NI. An overall significant shift in N₂O/N₂ molar ratio was shown in cattle impacted sites. The highest abundance of all genes measured at both sampling times was found at site SI, whereas at site MI increased numbers were observed only in spring. Our results indicate a strong influence of cattle on the abundance as well as the activity of microbes involved in denitrification.     

Influence of bacterial-feeding nematodes (Cephalobidae) on soil microbial communities during maize growth

The effect of several bacterial-feeding nematodes of the Cephalobidae family (Zeldia punctata, Acrobeloides nanus and Cephalobus pseudoparvus) on the microbial community of a Sahelian soil (Senegal) was investigated in microcosm. The consequences of the activity of these nematodes on the growth and nitrogen nutrition of young maize plants (aerial biomass, root biomass and nitrogen content) were also estimated. Laboratory-cultured nematodes were inoculated into soil containing maize seedlings where the natural nematofauna had been previously eliminated by alternately freezing and defrosting (five cycles). The microbial compartment of the soil community was characterised through total microbial biomass (using fumigation-extraction), density of bacteria (using colony forming units counts), microbial activity (using alkaline phosphatase) and genetic structure of soil microbial community (using denaturing gradient gel electrophoresis) at sowing and at 12, 26 and 47 days after planting. Final nematode densities in the different treatments (between 4 and 20 Ind g⁻¹ dry soil) demonstrated a high level of reproduction. The different types of nematodes tested induced similar trends in changes in the microbial pool of the soil and in maize seedling growth. Compared to control soils, the presence of nematodes led to an increase (+12%) in plant biomass and reduced concentrations of soil ammonium but had no effect on concentrations of nitrate by the end of the experiment. Sixty-three percent of the inorganic nitrogen initially present in the soil was incorporated into the maize plants with nematodes whereas only 47% was incorporated without nematodes. Nematode activity led to a significant decrease in microbial biomass (−28%) and density of cultivable bacteria (−55%), however, nematodes stimulated bacterial activity (+18%). The effects of Z. punctata were weakest compared to A. nanus and C. pseudoparvus. The presence of nematodes modified the genetic structure of the microbial community essentially by changing the relative abundance of dominant bacterial populations. Among nematode species tested, A. nanus modified the structure of the microbial communities the most compared with control soils without nematodes. Overall, results from this study provide evidence for the ability of microbial feeding nematodes to alter microbial activity, microbial community structure, nitrogen mineralisation and growth of maize seedlings in a Sahelian soil from Senegal, West Africa.     

Season and management related changes in the diversity of nitrifying and denitrifying bacteria over winter and spring

This study assessed the effects that season and tillage practices have on the diversity of nitrous oxide producing bacteria (nitrifiers and denitrifiers) and to relate this to measured N₂O fluxes at our field site. Large-scale field plots (1.5 ha) were established in Elora, Ontario in 2000, and managed using conventional tillage (CT) or no-tillage (NT). Each field plot was instrumented with micrometeorological equipment to determine N₂O fluxes on a field scale. Soil samples were taken at four time points between the fall of 2005 and the spring of 2006. The diversity of the nitrifier and denitrifier communities was assessed by PCR–denaturing gradient gel electrophoresis (DGGE) using primer pairs targeting the amoA, nirS and nirK gene. Seasonal variation (a combination of soil temperature, available soil moisture, nutrient levels and other potential factors) had the largest influence on the diversity of nitrifier and denitrifier populations; while tillage practice also influenced the diversity of the microbial community at certain time periods. Tillage significantly affected all communities in March and affected denitrifiers on all other dates except for the nirS community in February. Further statistical analysis revealed that diversity of the nitrifying and denitrifying populations was the lowest in February, in frozen soils, and rapidly increased in March, corresponding with spring thaw N₂O emissions. Long-term soil nutrient, temperature and N₂O data taken at this site added additional information on the dynamics of the nitrogen cycle.     

Nutrition on bacteria by bacterial-feeding nematodes and consequences on the structure of soil bacterial community

Bacterial-feeding nematodes are, with protozoa, the main grazers of soil bacteria. Interactions between bacteria and nematodes have important repercussions on soil functioning and particularly on nutrient availability. We assessed the influence of the bacterial strains ingested on bacterial-feeding nematodes population development and also the consequences of nematode feeding behaviour on the structure of the soil microbial community with a special attention to different soil micro-habitats for nematode and bacteria. In vivo studies conducted in the presence of single bacterial strains showed that the type of ingested bacteria conditioned the development of the different bacterial-feeding Cephalobidae nematode species tested and that the effect of bacteria differed between nematode species. The spatial distribution of soil nematodes between three soil habitats (fresh organic matter, inter-aggregates pores and aggregates) depended of the trophic behaviour of nematodes. Bacterial-feeding nematodes and fungal-feeding nematodes showed comparable distribution: being preferentially located in the fresh organic matter and in the inter-aggregate pores. Besides, the activity of inoculated bacterial-feeding nematodes modified the genetic structure of the soil microbial community. Bacterial community of the macroporosity was significantly influenced by the nematodes. On the contrary, no modification of the structure of the bacterial community linked with nematode activity was measured in the bulk soil.     

氮肥对稻田土壤反硝化细菌群落结构和丰度的影响

以氮肥田间定位试验为研究对象,利用PCR-DGGE(聚合酶链反应变性梯度凝胶电泳)和荧光定量PCR(real-time PCR)技术,通过对反硝化细菌nirS基因的检测,分析了定位试验第2年稻田反硝化细菌群落结构和丰度的变化。DGGE图谱及依据其条带位置和亮度数字化数值进行的主成分分析(PCA)结果均显示:在氮肥定位试验第2年,与不施肥对照(CK)比较,在水稻各个生育期(分蘖期、齐穗期和成熟期)内,施用氮肥[150kg(N)·hm-2]的稻田根层土或表土中的反硝化细菌群落结构均无明显变化;且稻田根层土或表土中的反硝化细菌群落结构在水稻各个生育期间也均无明显差异。荧光定量PCR结果显示,在水稻生长发育过程中,施用氮肥的稻田根层土或表土中的反硝化细菌nirS基因拷贝数始终显著(P<0.05)高于其对应的不施肥对照。此外,无论施用氮肥与否,根层土中的反硝化细菌nirS基因拷贝数在水稻成熟期时都会显著(P<0.05)降低;但表土中的nirS基因拷贝数在水稻各生育期间无明显变化;且水稻成熟期时施用氮肥和不施肥的稻田表土中nirS基因拷贝数都显著(P<0.05)高于根层土。同时,与对照比较施用氮肥可促进水稻增产44%。研究表明,短期定位试验中施用氮肥能够显著提高稻田土壤反硝化细菌的丰度,但对其群落结构没有明显影响。     

Simulated animal trampling of a free‐draining stony soil stimulated denitrifier growth and increased nitrous oxide emissions

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.     

Responses of soil nitrous oxide production and abundances and composition of associated microbial communities to nitrogen and water amendment

Soil moisture and nitrogen (N) are two important factors influencing N₂O emissions and the growth of microorganisms. Here, we carried out a microcosm experiment to evaluate effects of soil moisture level and N fertilizer type on N₂O emissions and abundances and composition of associated microbial communities in the two typical arable soils. The abundances and community composition of functional microbes involved in nitrification and denitrification were determined via quantitative PCR (qPCR) and terminal restriction length fragment polymorphism (T-RFLP), respectively. Results showed that N₂O production was higher at 90% water-filled pore (WFPS) than at 50% WFPS. The N₂O emissions in the two soils amended with ammonium were higher than those amended with nitrate, especially at relatively high moisture level. In both soils, increased soil moisture stimulated the growth of ammonia-oxidizing bacteria (AOB) and nitrite reducer (nirK). Ammonium fertilizer treatment increased the population size of AOB and nirK genes in the alluvial soil, while reduced the abundances of ammonia-oxidizing archaea (AOA) and denitrifiers (nirK and nosZ) in the red soil. Nitrate addition had a negative effect on AOA abundance in the red soil. Total N₂O emissions were positively correlated to AOB abundance, but not to other functional genes in the two soils. Changed soil moisture significantly affected AOA rather than AOB community composition in both soils. The way and extent of N fertilizers impacted on nitrifier and denitrifier community composition varied with N form and soil type. These results indicate that N₂O emissions and the succession of nitrifying and denitrifying communities are selectively affected by soil moisture and N fertilizer form in the two contrasting types of soil.     

Chronic effects of different fertilization regimes on nirS-type denitrifier communities across the black soil region of Northeast China

Denitrification is one of the major processes causing nitrogen loss from arable soils.This study aimed to investigate the responses of nir S-type denitrifier communities to different chronic fertilization regimes across the black soil region of Northeast China.Soil samples were collected from sites located in the north(NB),middle(MB),and south(SB)of the black soil region of Northeast China,each with four chronic fertilization regimes:no fertilizer(No F),chemical fertilizer(CF),manure(M),and chemical fertilizer plus manure(CFM).Methods of quantitative polymerase chain reaction(q PCR)and Illumina Mi Seq sequencing were applied to assess the abundance and composition of denitrifier communities by targeting the nir S gene.The results showed that the M and CFM regimes significantly increased the abundances of nir S-type denitrifiers compared with No F at the three locations.The majority of nir S sequences were grouped as unclassified denitrifiers,and the different fertilizers induced little variation in the relative abundance of known nir S-type denitrifier taxa.Over 90%of the sequences were shared among the four fertilization regimes at each location,but none of the abundant operational taxonomic units(OTUs)were shared among the three locations.Principal coordinate analysis(PCo A)revealed that the communities of nir S-type denitrifier were separated into three groups that corresponded with their locations.Although similar fertilization regimes did not induce consistent changes in the nir S-type denitrifier communities,soil p H and NO-3-N content simultaneously and significantly influenced the structure of nir S-type denitrifier communities at the three locations.Our results highlight that geographical separation rather than chronic fertilization was the dominant factor determining the nir S-type denitrifier community structures,and similar chronic fertilization regimes did not induce consistent shifts of nir S-type denitrifier communities in the black soils.     

Effect of P stoichiometry on the abundance of nitrogen-cycle genes in phosphorus-limited paddy soil

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.

Open image in new window

Graphical abstract ?

     

Do bacterial-feeding nematodes stimulate root proliferation through hormonal effects?

We prepared soil with greater populations of bacterial-feeding nematodes either by stimulating the native populations of the soil, adding an additional mixed community of nematodes, or by adding Caenorhabditis elegans, to investigate the effects of bacterial-feeding nematodes on root morphology, soil auxin (indolyl-3-acetic acid—IAA) concentrations and microbial community structure. In the presence of enhanced bacterial-feeding nematode populations, tomato plants had a more highly branched root system with longer and thinner roots. Root system development was greater with native nematodes than C. elegans. The changes of root morphology were accompanied by an increase of soil IAA content and an altered microbial community structure. Bacterial-feeding nematodes may have affected plant growth by stimulating hormone production through grazing-induced changes to the soil microbial community.