不同类型秸秆还田对稻田土壤nirK型反硝化细菌群落结构的影响

为探明油菜、蚕豆、小麦秸秆还田对稻田土壤nirK型反硝化细菌群落结构的影响,采用IlluminaMiseq高通量测序法,研究了盆栽试验条件下单施化肥(NS)、油菜秸秆+化肥(RS)、蚕豆秸秆+化肥(BS)和小麦秸秆+化肥(WS)4个处理对稻田土壤nirK型反硝化细菌群落多样性及群落结构的影响。结果表明,相比NS处理,秸秆还田(RS、BS和WS处理)对nirK基因微生物的多样性指数没有显著影响(P 0.05),而RS处理的微生物多样性指数显著高于BS和WS处理(P 0.05)。Venn分析结果显示,相比NS处理,秸秆还田增加了红螺菌目(Rhodospirillales)。此外,RS处理增加了unclassified_Proteobacteria_miscellaneous,BS和WS处理增加了红细菌目(Rhodobacterales)。相比NS处理,秸秆还田改变了nirK基因微生物的共有目群落组成,而秸秆类型显著改变了共有目的相对丰度。综上所述,还田秸秆类型对nirK基因微生物的多样性和目水平微生物的群落结构均有显著影响,其中油菜秸秆还田的影响强于蚕豆和小麦秸秆。     

作物茬口对黑土农田土壤反硝化细菌数量及群落结构的影响

  【目的】  反硝化作用导致农田土壤氮素损失和温室气体N₂O的排放。研究不同作物茬口对土壤反硝化细菌群落结构的影响,旨在揭示作物茬口影响N₂O排放的相关机制。  【方法】  定位试验位于黑龙江省海伦市前进乡光荣村(47°23′N,126°51′E),种植方式包括玉米连作(CC)、大豆连作(SS)以及玉米–大豆轮作,每年一季。取样时,轮作体系玉米已倒茬三次、大豆两次。采集CC、SS以及轮作体系中的大豆茬口(SSC)和玉米茬口(CSC)的表层土壤(0—15 cm)样品,利用实时定量PCR (qPCR)和高通量测序技术,分析土壤中的nirS和nirK型反硝化细菌丰度和群落组成。  【结果】  在4个作物茬口土壤中,CC处理的反硝化速率最高,玉米–大豆轮作体系中SSC和CSC处理的反硝化速率显著高于SS处理。轮作体系两个茬口SSC和CSC处理的nirS和nirK型反硝化细菌基因丰度多显著高于SS处理,而与CC处理多差异不显著。PCoA结果显示,SSC和CSC处理的nirS型反硝化细菌群落间差异显著,而CC和SS处理的nirK型反硝化细菌群落间存在显著差异。RDA分析结果表明,NO₃–-N和C/N分别是nirS和nirK型反硝化细菌群落分异的最主要驱动因子。SEM分析结果显示,nirS型反硝化细菌群落与反硝化速率呈显著正相关(R2=0.92),而nirS和nirK型基因丰度与土壤反硝化速率无显著相关关系。  【结论】  作物茬口显著影响黑土农田土壤反硝化细菌群落和丰度组成。反硝化细菌群落组成而非反硝化细菌丰度是反硝化速率变化的决定性因素,nirS型反硝化细菌对土壤反硝化作用贡献更大。     

长期施用有机肥对红壤旱地土壤线虫群落的影响

基于红壤旱地(玉米)的长期施肥试验,研究长期施用有机肥对土壤线虫分布特征及群落结构的影响。田间试验处理包括:CK(对照)、ON1(低量有机肥)、ON2(高量有机肥)和ON2L(高量改良有机肥)。结果表明,施肥8a后,红壤旱地中共鉴定出15科、29属土壤线虫,包括8属植物寄生线虫、9属食细菌线虫、3属食真菌性线虫和9属捕食杂食性线虫,短体属(Pratylenchus)、小杆属(Rhabditis)和原杆属(Pro-torhabditis)为优势属。不同施肥处理中,土壤线虫总数的大小顺序为ON2>ON1>ON2L>CK。线虫群落生态指数对于施用有机肥有不同的响应:除SI外,其他虫群落生态指数均有显著差异,通过线虫群落结构的变化很好地反映了土壤的肥力变化状况,土壤线虫可以作为施有机肥过程中指示土壤健康质量的一个重要的生物学指标。     

饲喂纳豆枯草芽胞杆菌对荷斯坦犊牛瘤胃细菌区系的影响

本研究选取8头(60日龄)犊牛随机分为对照组和处理组,对照组犊牛饲喂开食料,处理组在开食料中添加纳豆枯草芽胞杆菌(Bacillus subtilis)(1×10~6 CFU/g日粮)菌液,于断奶后2个月进行屠宰,采集瘤胃食糜构建16S rDNA克隆文库,随机挑取克隆进行测序,对照组16S rDNA克隆文库共有111个克隆,可分为88个操作分类单元;处理组16S rDNA克隆文库中有142个克隆,可分为131个操作分类单元.序列分析和多样性指数分析表明,两组犊牛瘤胃细菌区系多样性存在显著差异.拟杆菌门(Bacteroidetes)和壁厚菌门(Firmicutes)是两克隆文库中主要的代表菌群.对照组和处理组中的拟杆菌门分别占文库中总克隆数的38%和25%,而壁厚菌门分别占47%和57%.与瘤胃球菌相关的克隆在对照组克隆文库中分别占5%,而在处理组文库中分别占10%.RT-PCR结果显示,处理组中白色瘤胃球菌(R.albus)(log_(10)7.7/mL)和黄色瘤胃球菌(R.flavefaciens)(log_(10)8.1/mL)的数量比对照组(分别为log_(10)7.2/mL和log_(10)7.7/mL)分别增加了3倍和2.4倍.研究结果提示,饲喂纳豆枯草芽胞杆菌有助于促进断奶后犊牛瘤胃中细菌区系的建立,促进纤维分解菌群的定植和生长.     

长期施肥对旱地红壤细菌群落的影响

为探讨长期不同施肥对旱地红壤细菌群落的影响,以中国农业科学院祁阳红壤实验站的冬小麦—夏玉米定位试验为研究对象,选取不施肥(CK)、单施氮肥(N)、施化学氮磷钾肥(NPK)和化学氮磷钾+有机肥配施(NPKM)4个处理,于试验开展25年(2015年)小麦收获后采集各处理0~20 cm的土壤样品,利用Illumina MiSeq高通量测序技术对土壤细菌群落进行测定,并深入揭示影响旱地红壤细菌群落的关键因素。结果表明:(1)长期不同施肥显著改变了旱地红壤的化学性质,N和NPK处理的土壤pH显著降低至4.02和4.15,而NPKM处理的土壤pH显著上升至5.99。NPK和NPKM处理均显著改善土壤肥力,但后者效果明显优于前者,而N处理对土壤肥力的提升效果微弱。(2)长期不同施肥改变了旱地红壤优势菌的相对丰度,非度量多维度分析(NMDS)和相似性分析(ANOSIM)表明不同处理的土壤细菌群落发生显著变化。(3)与CK相比,N处理的4种多样性指数(物种丰富度、Chao1指数、系统发育多样性和香农指数)显著降低了21.4%~49.4%,而NPKM处理显著增加了7.0%~66.9%,NPK处理也会使系统发育多样性和香农指数显著降低10.3%和13.0%。(4)逐步回归分析表明土壤pH是决定优势菌相对丰度及4种多样性指数的首要因素,多元回归树分析(MRT)探明土壤pH共解释了83.1%的细菌群落变异,不同处理间细菌群落转变均由土壤pH驱动。(5)STAMP分析发现,N、NPK和NPKM处理与CK分别有11、14和8个显著差异细菌属。综上所述,长期施肥后旱地红壤细菌群落主要受土壤pH的影响,而土壤肥力的作用相对较弱,长期施用化学氮肥造成的红壤酸化的负面效应已远超肥力改善的正面效应。因此,旱地红壤施肥应以防治土壤酸化为前提,长期化肥有机肥配施是一项适宜的施肥措施。     

红壤荒草地氨氧化细菌富集液16SrDNA文库的RFLP分析

分析红壤荒草地富集液中氨氧化细菌的种群组成,选取氨氧化细菌16S rDNA特异性引物序列,利用PCR技术对从富集液中抽提的细菌总DNA进行扩增,并建立了氨氧化细菌特异性的16S rDNA文库。用酶HhaⅠ和RsaⅠ对该文库特异性片段进行了限制性酶切片断长度多态性分析(Restriction fragment lengthpolymorphism,RFLP),随机挑选的35个特异性克隆片段被分成3个不同的RFLP类型,其中优势型占了所有分析克隆子的94%,另两个型各占3%。从每个RFLP类型中挑取一定的转化子进行测序,测序结果经GenBank检索,发现在该富集液体系文库中存在大量亚硝化单胞菌属(Nitrosomonas)细菌序列,由此推测红壤荒草地中存在氨氧化细菌,Nitrosomonas属细菌能在富集条件下成为优势菌。     

连作年限对设施百合土壤微生物多样性的影响

为探究不同年限连续栽培百合的设施土壤细菌和真菌群落组成变化及其与环境因子间的关系,采用Mi Seq高通量测序技术,对连作4年(C4)、连作5年(C5)和连作7年(C7)设施百合红壤中细菌和真菌群落组成和多样性的变化进行了研究。结果显示,所有样品测序后获得细菌和真菌有效序列分别是249003和451044个,细菌和真菌OTUs总数分别是906和298个。Alpha多样性分析显示,随连作年限延长设施百合红壤中细菌香农指数和辛普森指数显著升高,真菌香农指数和辛普森指数显著下降。在物种组成分析中,属于细菌优势菌种的有变形菌门(Proteobacteria)、放线菌门(Actinomycetes)、酸杆菌门(Acidobacteria)、绿弯菌门(Chloroflexi),且C4、C5和C7处理土壤中优势菌种占细菌总数比例分别是85.17%、81.04%和81.64%;而真菌菌门中,只有子囊菌门(Ascomycota)一个优势菌种,并且C4、C5和C7处理土壤中优势菌种占真菌总数比例分别93.69%、92.20%、84.31%。不同连作年限土壤中,子囊菌门镰刀菌属(Fusarium)丰度比例达44.02%～58.83%。相关性分析显示,p H值、有机碳、总氮与变形菌门、放线菌门、酸杆菌门丰度显著相关;p H与青霉属(Penicillium)显著正相关,与镰刀菌属显著负相关。由此可以认为,连作后土壤细菌微生物群落多样性指数显著上升,真菌微生物多样性显著下降,同时土壤中细菌的优势菌种有变形菌门、放线菌门、酸杆菌门、绿弯菌门,在真菌群落组成中子囊菌门占主导,连作后子囊菌门中占主导地位的镰刀菌属数量的增长可能是引起设施百合红壤连作障碍的主要原因之一。     

PCR-RFLP技术分析沼气池厌氧活性污泥细菌的多样性

应用PCR-RFLP和rRNA分析法研究了户用沼气池厌氧活性污泥细菌的多样性。采用直接提取法提取了户用沼气池微生物宏基因组DNA,构建了细菌的16S rDNA克隆文库。随机挑取了144个准确含有16S rDNA的阳性克隆进行PCR-RFLP分析,聚类得到46个OTUs（operational taxonomic units）,其中3个OTUs是优势类群,分别占14％,10％和9％,21个OTUs只含有单个克隆。随机挑取了26个克隆进行测序,并构建了系统发育进化树。结果表明：农村户用沼气池中细菌种类较为丰富,占优势的类群分别为Firmicutes（28％）、Delta-proteobacteria（18％）和Bacteroidetes（17％）,大多数16S rDNA序列与GenBank数据库中未培养细菌相似性最高（91％～99％）,为进一步研究、利用沼气池能源提供了基础资料。     

后续施肥措施改变对水稻土团聚体有机碳分布及其周转的影响

利用一个长达30 a且已进行适当变更的长期定位施肥试验,改施C4玉米秸秆以替代C3水稻秸秆,运用δ~(13)C自然丰度方法,研究长期施用高量有机肥、常量有机肥、化肥及当其施肥措施改变(化肥改为常量有机肥、常量有机肥改为高量有机肥、高量有机肥改为化肥、常量有机肥改为化肥)3 a后对红壤性水稻土团聚体有机碳分布及其周转的影响。结果表明:在所有施肥处理条件下红壤性水稻土团聚体分布以大团聚体(0.25 mm)为主,占72.48%~86.33%。与施用化肥30 a相比,长期施用常量有机肥、高量有机肥有利于促进红壤性水稻土粗大团聚体(2 mm)的形成,并提高团聚体平均重量直径(MWD)。团聚体中有机碳含量随着团聚体粒径的增大而增大,大团聚体更有利于有机碳富集。长期常量有机肥、高量有机肥处理下红壤性水稻土中有机碳主要贮存在粗大团聚体(2 mm)中,而长期化肥处理下以细大团聚体(2~0.25 mm)对土壤有机碳贡献率最高。外源新碳施入量越多,全土和各粒径团聚体新碳含量越高,且外源新碳主要分布在大团聚中。在后续施肥措施改变3年后,增加有机肥施入量(化改常、常改高)2 mm粗大团聚体、MWD、全土及各粒径团聚体中有机碳含量将分别显著提高7.08%~73.13%、5.38%~44.22%、14.53%~38.50%、0.70%~35.86%;而减少有机肥施入量(高改化、常改化)则与之相反,分别降低28.17%~43.20%、21.17%~31.54%、17.54%~27.30%、11.49%~29.77%。因此,在我国南方红壤性稻作区的农业生产过程中应继续或加大施用有机肥,从而进一步维持或改善土壤结构,提高土壤有机碳含量。     

稻虾共作对稻田土壤nirK反硝化微生物群落结构和多样性的影响

稻虾共作是水稻种植与克氏螯虾共作形成的互利共生的稻田种养复合生态模式。目前对稻虾共作模式稻田反硝化微生物多样性和群落结构的影响尚不清楚。本研究以江汉平原常规中稻模式(MR)为对照,设置连续3年(2014—2016年)稻虾共作模式(CR)为处理,通过特异引物提取中稻抽穗期稻田土壤nirK基因,采用Illumina Miseq高通量测序技术,探讨稻虾共作模式对稻田土壤nirK反硝化微生物多样性和群落结构的影响。结果表明:稻虾共作模式显著提升水稻抽穗期稻田土壤中硝态氮、全氮及全碳的含量,对土壤碳氮比、碱解氮和铵态氮含量没有显著影响。稻虾共作模式显著增加稻田土壤nirK基因微生物的丰富度指数,但对nirK基因微生物的多样性指数影响不显著。稻虾共作模式改变了nirK基因微生物在目、科、属、种水平的群落组成,较常规中稻模式,稻虾共作模式在各分类水平组成类群均减少;稻虾共作模式较常规中稻模式改变了目的种类,对共有目相对丰度没有显著性改变。RDA分析表明稻虾共作模式对土壤nirK基因菌群的群落结构有一定的改变,但稻虾共作模式与常规中稻模式在群落结构上仍保留着一定的相似性。硝态氮含量是影响nirK反硝化细菌群落结构的主效因子。可见,稻虾共作模式对微生物多样性指数没有显著影响,但显著增加了微生物丰富度指数,改变了稻田土壤nirK反硝化微生物在目、科、属、种的群落结构。     

Effects of Rhizosphere and Long-Term Fertilization Practices on the Activity and Community Structure of Denitrifiers Under Double-Cropping Rice Field

The soil physicochemical properties, soil denitrification rates (PDR), denitrifiers via nitrite reductases (nirK and nirS) and nitrous oxide reductase (nosZ), abundance and community composition of denitrifiers in both the rhizosphere and bulk soil from a long-term (32 year) fertilizer field experiment conducted during late rice season were investigated by using the MiSeq sequencing, quantitative PCR, terminal restriction fragment polymorphism (T-RFLP). The experiment including four treatments: without fertilizer input (CK), chemical fertilizer alone (MF), rice straw residue and chemical fertilizer (RF), and organic manure and chemical fertilizer (OM). The results showed that the application of rice straw residue and organic manure increased soil organic carbon (C), total nitrogen (N), and NH₄⁺-N contents. The nirK, nirS, and nosZ copy numbers with OM and RF treatments were significant higher than that of the MF and CK treatments in the rhizosphere and bulk soil (p < 0.05). The principal coordinate analysis (PCoA) analysis showed that the different parts of root zone are the most important factors for the variation of denitrifying bacteria community, and the different fertilization treatments is the second important factors for the variation of denitrifying bacteria community. The MiSeq sequencing result showed that nirK, nirS and nosZ-type denitrifiers communities within bulk soil had lower species diversity compared with rhizosphere soil, and were dominated by Rhizobiales, Rhodobacterales, Burkholderiales, and Pseudomonadales. As a result, the application of fertilization practices had significant effects on soil N and PDR levels, and affected the abundance and community composition of N-functional microbes.     

Manure contaminated with the antibiotic sulfadiazine impairs the abundance of nirK- and nirS-type denitrifiers in the gut of the earthworm Eisenia fetida

The antibiotic sulfadiazine (SDZ) can affect denitrifying bacteria in soil. However, effects on denitrifiers in the gut of earthworms have not been described so far. Therefore, the influence of SDZ-contaminated manure applied to soil on denitrifiers in the gut of the earthworm Eisenia fetida was assessed by quantitative polymerase chain reaction targeting genes coding for nirK- and nirS-type nitrite reductases of denitrifiers. Gut contents of Eisenia fetida contained 2.5 × 10⁶ and 5.1 × 10⁵ gene copies of nirK and nirS, respectively, after 2 weeks in soils amended with manure only. Copy numbers of nirK and nirS in gut contents from manure treatments with SDZ were up to ten times less. Overall, the data indicate a negative impact of SDZ on denitrifiers in the gut of earthworms.     

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.     

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。     

Organic manure input and straw cover improved the community structure of nitrogen cycle function microorganism driven by water erosion

Water erosion process induces differences to the nitrogen (N) functional microbial community structure, which is the driving force to key N processes at soil-water interface. However, how the soil N transformations associated with water erosion is affected by microorganisms, and how the microbial respond, are still unclear. The objective of this study is to investigate the changes of microbial diversity and community structure of the N-cycle function microorganisms as affected by water erosion under application of organic manure and straw cover. On the basis of iso-nitrogen substitution, four treatments were set up: 1) only chemical fertilizer with N 150 kg ha^?1, P₂O₅ 60 kg ha^?1 and K₂O 90 kg ha^?1 (CK); the N was substituted 20% by 2) organic manure (OM); 3) straw (SW); and 4) organic manure + straw (1:1) (OMSW). The results showed that applying organic manure and straw to sloping farmland can increase soil N contents, but reduce runoff depth, K_w, sediment yield and N loss, especially in the OMSW. Straw cover and straw + organic manure increased the diversity (Chao1) of nitrifier (AOB), and both diversity and uniformity (Shannon) of denitrifier (nirK/S) were increased in the OMSW. All erosion control measures reduced N-fixing bacteria diversity and increased their uniformity, and the combined application of organic manure and straw cover was a better erosion control measure than the single application of them. Improved soil chemistry and erodibility were the main drives for the changes of N-functional microbial community structure and the appearance of dominant bacteria with different organic materials.     

Development of PCR primers targeting fungal nirK to study fungal denitrification in the environment

Fungal denitrification in soils is receiving considerable attention as one of the dominant N₂O production processes. However, because of the lack of a methodology to detect fungal denitrification-related genes, the diversity and ecological behavior of denitrifying fungi in soil remains unknown. Thus, we designed a primer set to detect the fungal nitrite reductase gene (nirK) and validated its sensitivity and specificity. Through clone library analyses, we identified congruence between phylogenies of the 18S rRNA gene and nirK of denitrifying fungal isolates obtained from the surface-fertilized cropland soil and showed that fungi belonging to Eurotiales, Hypocreales, and Sordariales were primarily responsible for N₂O emissions in the soil.     

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.