Changes in the activities of key enzymes and the abundance of functional genes involved in nitrogen transformation in rice rhizosphere soil under different aerated conditions

Soil microorganisms play important roles in nitrogen transformation. The aim of this study was to characterize changes in the activity of nitrogen transformation enzymes and the abundance of nitrogen function genes in rhizosphere soil aerated using three different methods(continuous flooding(CF), continuous flooding and aeration(CFA), and alternate wetting and drying(AWD)). The abundances of amoA ammonia-oxidizing archaea(AOA) and ammonia-oxidizing bacteria(AOB), nirS, nirK, and nifH genes, and the activities of urease, protease, ammonia oxidase, nitrate reductase, and nitrite reductase were measured at the tillering(S1), heading(S2), and ripening(S3) stages. We analyzed the relationships of the aforementioned microbial activity indices, in addition to soil microbial biomass carbon(MBC) and soil microbial biomass nitrogen(MBN), with the concentration of soil nitrate and ammonium nitrogen. The abundance of nitrogen function genes and the activities of nitrogen invertase in rice rhizosphere soil were higher at S2 compared with S1 and S3 in all treatments. AWD and CFA increased the abundance of amoA and nifH genes, and the activities of urease, protease, and ammonia oxidase, and decreased the abundance of nirS and nirK genes and the activities of nitrate reductase and nitrite reductase, with the effect of AWD being particularly strong. During the entire growth period, the mean abundances of the AOA amoA, AOB amoA, and nifH genes were 2.9, 5.8, and 3.0 higher in the AWD treatment than in the CF treatment, respectively, and the activities of urease, protease, and ammonia oxidase were 1.1, 0.5, and 0.7 higher in the AWD treatment than in the CF treatment, respectively. The abundances of the nirS and nirK genes, and the activities of nitrate reductase and nitrite reductase were 73.6, 84.8, 10.3 and 36.5% lower in the AWD treatment than in the CF treatment, respectively. The abundances of the AOA amoA, AOB amoA, and nifH genes were significantly and positively correlated with the activities of urease, protease, and ammonia oxidase, and the abundances of the nirS and nirK genes were significantly positively correlated with the activities of nitrate reductase. All the above indicators were positively correlated with soil MBC and MBN. In sum, microbial activity related to nitrogen transformation in rice rhizosphere soil was highest at S2. Aeration can effectively increase the activity of most nitrogen-converting microorganisms and MBN, and thus promote soil nitrogen transformation.

Nitrogen transformation processes in soil along a High Arctic tundra transect

Soil nitrogen(N)transformation processes in the High Arctic tundra are poorly understood even though nitrogen is one of the main limiting nutrients.We analyzed soil samples collected along a High Arctic tundra transect to investigate spatial variability in key nitrogen transformation processes,functional gene abundances,ammonia-oxidizing archaea(AOA)community structures,and key nitrogen transformation regulators.The potential denitrification rates were higher than the nitrification rates in the soil samples,although nitrification may still regulate N2O emissions from tundra soil.The nutrient(total carbon,total organic carbon,total nitrogen,and NH_(4)^(+)-N)contents were important determinants of spatial variability in the potential denitrification rates of soil along the tundra transect.The total sulfurcontent was the main variable controlling potential nitrification processes,probably in association with sulfate-reducing bacteria.The nitrate content was the main variable affecting potential dissimilatory nitrate reduction to ammonium.AOA and ammonia-oxidizing bacteria amoA,nirS,and anammox 16S rRNA genes were found in all of the soil samples.AOA play more important roles than ammonia-oxidizing bacteria in soilnitrification.Anammox bacteria may utilize NO_(2)^(-)produced through nitrification.Phylogenetic analysis indicated that the AOA amoA sequences could be grouped into eight unique operational taxonomic units(OTUs)with a 97%sequence similarity and were affiliated with three group 1.1b Nitrososphaeraclusters.The results indicated that heterogeneous environmental factors(e.g.,the carbon and nitrogen contents of soil)along the High Arctic tundra transect strongly affected the nitrogen transformation rate and relevant functional gene abundances in soil.

Response of microbial biomass and bacterial community composition to fertilization in a salt marsh in China

The effects of nitrogen （N） addition on microbial biomass, bacterial abundance, and community composition in sediment colonized by Suaeda heteroptera were examined by chloroform fumigation extraction method, real-time quantitative polymerase chain reaction, and denaturing gradient gel electrophoresis （DGGE） in a salt marsh located in Shuangtai Estuary, China. The sediment samples were collected from plots treated with different amounts of a single N fertilizer （urea supplied at 0.1, 0.2, 0.4 and 0.8 g/kg （nitrogen content in sediment） and different forms of N fertilizers （urea, （NH4）2SO4, and NH4NO3, each supplied at 0.2 g/kg （calculated by nitrogen）. The fertilizers were applied 1-4 times during the plant-growing season in May, luly, August, and September of 2013. Untreated plots were included as a control. The results showed that both the amount and form of N positively influenced microbial biomass carbon, microbial biomass nitrogen, and bacterial abundance. The DGGE profiles revealed that the bacterial community composition was also affected by the amount and form of N. Thus, our findings indicate that short-term N amendment increases microbial biomass and bacterial abundance, and alters the structure of bacterial community.

Integrated management of crop residue and nutrient enhances new carbon formation by regulating microbial taxa and enzymes

Although returning crop residue to fields is a recommended measure for improving soil carbon(C)stocks in agroecosystems,the response of newly formed soil C(NFC)to the integrated supply of residue and nutrients and the microbial mechanisms involved in NFC are not fully understood.Therefore,an 84-day incubation experiment was conducted to ascertain the microbial mechanisms that underpin the NFC response to inputs of residue and nitrogen(N),phosphorus(P),and sulfur(S)in two black(Phaeozem)soils from experimental plots at Gongzhuling,Jilin Province and Hailun,Heilongjiang Province,China.The results showed that adding residue alone accelerated microbial nutrient mining,which was supported by decreases of 8^(-1)6%in the ratios of C:N and C:P enzyme activities,relative to soils with nutrient inputs.The NFC amounts increased from 1156 to 1722 mg kg^(−1) in Gongzhuling soil and from 725 to 1067 mg kg^(−1) in Hailun soil as the levels of nutrient supplementation increased.Boosted regression tree analysis suggested thatβ-glucosidase(BG),acid phosphatase(AP),microbial biomass C(MBC),and Acidobacteria accounted for 27.8,18.5,14.7,and 8.1%,respectively,of the NFC in Gongzhuling soil and for 25.9,29.5,10.1,and 13.9%,respectively,of the NFC in Hailun soil.Path analysis determined that Acidobacteria positively influenced NFC both directly and indirectly by regulating BG,AP,and MBC,in which MBC acquisition was regulated more by AP.The amount of NFC was lower in Hailun soil than in Gongzhuling soil and was directly affected by AP,indicating the importance of soil properties such as SOC and pH in determining NFC.Overall,our results reveal the response of NFC to supplementation by N,P,and S,which depends on Acidobacteria and Proteobacteria,and their investment in BG and AP in residue-amended soil.

DMPP mitigates N_(2)O and NO productions by inhibiting ammonia-oxidizing bacteria in an intensified vegetable field under different temperature and moisture regimes

Vegetable soils with high nitrogen input are major sources of nitrous oxide(N_(2)O)and nitric oxide(NO),and incorporation of the nitrification inhibitor 3,4-dimethylpyrazole phosphate(DMPP)into soils has been documented to effectively reduce emissions.However,the efficiency of DMPP in terms of soil N_(2)O and NO mitigations varies greatly depending on soil temperature and moisture levels.Thus,further evaluations of DMPP efficiency in diverse environments are required to encourage widespread application.A laboratory incubation study(28 d)was established to investigate the interactive effects of DMPP,temperature(15,25,and 35?C),and soil moisture(55% and 80% of water-holding capacity(WHC))on net nitrification rate,N_(2)O and NO productions,and gene abundances of nitrifiers and denitrifiers in an intensive vegetable soil.Results showed that incubating soil with 1%DMPP led to partial inhibition of the net nitrification rate and N_(2)O and NO productions,and the reduction percentage of N_(2)O production was higher than that of NO production(69.3%vs.38.2%)regardless of temperature and soil moisture conditions.The increased temperatures promoted the net nitrification rate but decreased soil N_(2)O and NO productions.Soil moisture influenced NO production more than N_(2)O production,decreasing with the increased moisture level(80%).The inhibitory effect of DMPP on cumulative N_(2)O and NO productions decreased with increased temperatures at 55%WHC.Conversely,the inhibitory effect of DMPP on cumulative N_(2)O production increased with increased temperatures at 80%WHC.Based on the correlation analyses and automatic linear modeling,the mitigation of both N_(2)O and NO productions from the soil induced by DMPP was attributed to the decreases in ammonia-oxidizing bacteria(AOB)amoA gene abundance and NO_(2)^(-)-N concentration.Overall,our study indicated that DMPP reduced both N_(2)O and NO productions by regulating the associated AOB amoA gene abundance and NO_(2)^(-)-N concentration.These findings improve our insights regarding the implications of DMPP for N_(2)O and NO mitigations in vegetable soils under various climate scenarios.

Enhanced nitrogen removal of the anaerobic ammonia oxidation process by coupling with an efficient nitrate reducing bacterium(Bacillus velezensis M3-1)

Bacillus velezensis M3-1 strain isolated from the sediment of Myriophyllum aquatium con-structedwetlandswas found to efficiently convert NO_(3)^(-)-N to NO_(2)^(−)-N,and the requirements for carbon source additionwere not very rigorous.Thiswork demonstrates,for the first time,the feasibility of using the synergy of anammox and Bacillus velezensis M3-1 microorganisms for nitrogen removal.In this study,the possibility of M3-1 that converted NO_(3)^(−)-N produced by anammox to NO_(2)^(−)-N was verified in an anaerobic reactor.The NO_(3)^(−)-N reduction ability of M3-1 and denitrifying bacteria in coupling system was investigated under different C/N conditions,and it was found that M3-1 used carbon sources preferentially over denitrifying bacteria.By adjusting the ratio of NH4+-N to NO_(2)^(−)-N,it was found that the NO_(2)^(−)-N con-verted from NO_(3)^(−)-N by M3-1 participated in the original anammox.The nitrogen removal efficacy(NRE)of the coupled system was increased by 12.1%,compared to the control group anammox system at C/N=2:1.Functional gene indicated that itmight be a nitrate reducing bacterium.This study shows that the nitrate reduction rate achieved by the Bacillus velezensis M3-1 can be high enough for removing nitrate produced by anammox process,which would enable improve nitrogen removal from wastewater.

Decreased nitrous oxide emissions associated with functional microbial genes under bio-organic fertilizer application in vegetable fields

Bio-organic fertilizers enriched with plant growth-promoting microbes(PGPMs)have been widely used in crop fields to promote plant growth and maintain soil microbiome functions.However,their potential effects on N_(2)O emissions are of increasing concern.In this study,an in situ measurement experiment was conducted to investigate the effect of organic fertilizer containing Trichoderma guizhouense(a plant growth-promoting fungus)on soil N_(2)O emissions from a greenhouse vegetable field.The following four treatments were used:no fertilizer(control),chemical fertilizer(NPK),organic fertilizer derived from cattle manure(O),and organic fertilizer containing T.guizhouense(O+T,referring to bio-organic fertilizer).The abundances of soil N cycling-related functional genes(amoA)from ammonium-oxidizing bacteria(AOB)and archaea(AOA),as well as nirS,nirK,and nosZ,were simultaneously determined using quantitative PCR(qPCR).Compared to the NPK plot,seasonal total N_(2)O emissions decreased by 11.7%and 18.7%in the O and O+T plots,respectively,which was attributed to lower NH_(4)^(+)-N content and AOB amoA abundance in the O and O+T plots.The nosZ abundance was significantly greater in the O+T plot,whilst the AOB amoA abundance was significantly lower in the O+T plot than in the O plot.Relative to the organic fertilizer,bio-organic fertilizer application tended to decrease N_(2)O emissions by 7.9%and enhanced vegetable yield,resulting in a significant decrease in yield-scaled N_(2)O emissions.Overall,the results of this study suggested that,compared to organic and chemical fertilizers,bio-organic fertilizers containing PGPMs could benefit crop yield and mitigate N_(2)O emissions in vegetable fields.

Effects of Inoculum Density on Plant Growth and Hydrocarbon Degradation

The combined use of plants and bacteria is a promising approach for the remediation of soil contaminated with organic pollutants. Different biotic and abiotie factors can affect the survival and activity of the applied bacteria and consequently plant growth and phy- toremediation efficiency. The effect of inoculum density on the abundance and expression of alkune-degrading genes in the rhizosphere of plant vegetated in hydrocarbon-contaminated soil has been rarely observed. In this study, an alkane-degrading bacterium （Pantoea sp. strain BTRH79）, at different inoculum densities （10^5 to 10^8 cells cm^-3 soil）, was inoculated to ryegrass （Lolium perenne） vegetated in diesel-contaminated soil to find the optimum inoculum density needed for its efficient colonization and hydrocarbon degradation activity. Bacterial inoculation improved plant growth and hydrocarbon degradation. Maximum plant growth and hydrocarbon degra- dation were observed with the inoculum having the highest cell density （10^8 cells cm^-3 soil）. Moreover, the inoculum with higher cell density exhibited more abundance and expression of alkane hydroxylase gene, CYP153. This study suggests that the inoculum density is one of the main factors that can affect bacterial colonization and activity during phytoremediation.