氮掺杂碳纳米颗粒对稻田根际土壤细菌群落的影响

氮掺杂碳纳米颗粒(N-CNPs)具有较高的农田氮肥增效潜力,但其对稻田根际土壤细菌群落结构和功能的影响尚不明确。本研究以连续3年施用低(1.2%,N-CNPs1)、中(6.7%,N-CNPs2)和高(9.3%,N-CNPs3)氮掺杂碳纳米颗粒的稻田根际土壤为研究对象,采用高通量测序技术和PICRUSt 功能预测方法研究其细菌群落组成和代谢功能变化。结果表明: 连续3年配施N-CNPs能提升稻田根际土壤细菌群落多样性,改变细菌群落功能;不同氮掺杂量水平间存在差异,其中以中氮掺杂量(N-CNPs2)碳纳米颗粒处理变化幅度最大。细菌群落分析结果指出,配施N-CNPs提升了根际土壤中变形菌门、酸杆菌门和疣微菌门的相对丰度,降低了浮霉菌门、绿弯菌门、硝化螺旋菌门和芽单胞菌门的相对丰度。PICRUSt 功能预测结果表明,在二级预测功能分类中,配施N-CNPs处理的氨基酸代谢、碳水化合物代谢和脂类代谢功能得到增强,而其他代谢功能则受到减弱。KEGG 直系同源基因簇丰度热图结果显示,N-CNPs2处理能提升根际土壤碳、氮代谢相关的细菌群落的相对丰度。     

间作黄芪对当归根际土壤微生物的影响

目的：探讨根际土壤微生物对中药材种植模式的响应方式。方法：以间作黄芪及单作下当归根际土壤为研究对象,基于高通量测序技术,分析土壤微生物在不同季节及种植模式下群落组成及功能的差异。结果：间作下Chao1指数、ACE指数高于单作,变形菌门、放线菌门、酸杆菌门、绿弯菌门和芽单胞菌门为间作下的优势菌门,芽单胞菌门的相对丰度在间作下高于单作。11月间作下γ变形菌纲、7月间作下全噬菌纲的丰度显著高于单作。KEGG功能预测表明,在不同时间及间作下根际土壤细菌与细胞过程、环境信息处理、遗传信息处理、代谢功能下属的23类二级功能基因的相对丰度存在显著差异;参与氮循环的功能基因K00371(narH/narY/nxrB)、（K00374 narI/narV）等OTU数在间作下显著高于单作;不同门、纲在间作下的共生网络比单作下连接紧密且更复杂。结论：当归间作黄芪影响土壤细菌群落组成,增加其丰富度及功能的丰富性,影响土壤氮循环能力,促进土壤微生物间的交互作用。     

辣椒连作对土壤细菌群落的影响

【目的】土壤微生物对农业生态系统的长期可持续性至关重要。为探讨不同连作年限对辣椒土壤细菌群落结构和潜在功能的影响。【方法】采用16S rRNA基因高通量测序PICRUSt功能预测相结合的研究方法,对不同连作年限下(1Y、3Y、5Y和10Y)的辣椒土壤细菌微生物群落结构和功能进行分析。【结果】微生物多样性指数和共生网络复杂度随连作年限的延长而降低,同时,连作年限变化对细菌群落组成有显著影响。不同的土壤细菌种群对连作措施的响应程度不一,长期连作增加了变形菌门和拟杆菌门的相对丰度,但降低了绿弯菌门、酸杆菌门、厚壁菌门和髌骨细菌门的相对丰度。PICRUSt功能预测结果表明,延长连作年限改变了土壤细菌整体的氮、磷代谢能力,导致细菌群预测功能基因发生了变化,能量代谢、氨基酸代谢和碳水化合物代谢等重要代谢功能基因减少,而折叠、分类和降解、复制和修复、膜转运、细胞生长与死亡等功能基因丰度明显增加。冗余分析表明,土壤有机质和有效磷是影响细菌群落迁移和功能变化的关键土壤理化因子。【结论】延长辣椒连作年限后,细菌群落结构改变和多样性下降导致土壤微生物群落功能失调可能是造成辣椒连作障碍的原因之一。     

黄土高原苜蓿-粮食作物轮作下土壤细菌群落特征和生态功能预测

为揭示多年种植苜蓿后轮作不同作物对黄绵土细菌群落的影响,本研究通过布设在黄土高原雨养农业区的长期定位试验,采用16S rRNA基因高通量测序技术和PICRUSt方法探究苜蓿(LC)、苜蓿-休闲-小麦(L_FW)、苜蓿-休闲-玉米(L_FC)、苜蓿-马铃薯(LP)与苜蓿-谷子(LM)对土壤细菌群落结构和多样性的影响,并利用PICRUSt法预测了其生态功能。结果表明: 半干旱区黄绵土细菌优势门为放线菌门(20.3%～32.0%)、变形菌门(19.2%～23.0%)、酸杆菌门(12.4%～14.2%)和绿弯菌门(11.0%～12.7%),其中苜蓿翻耕轮作玉米土壤优势细菌属为芽孢杆菌属(1.9%),其余处理土壤细菌优势属均为假节杆菌属(2.5%)。多年生苜蓿翻耕轮作不同粮食作物后显著降低了放线菌门相对丰度,但显著提高了绿弯菌门和厚壁菌门的相对丰度。冗余分析表明,影响苜蓿及轮作作物土壤细菌群落结构的主要环境因子是硝态氮、铵态氮和全氮。PICRUSt功能预测结果表明,新陈代谢(78.6%～79.1%)为黄绵土细菌群落的主要功能,苜蓿翻耕轮作作物显著降低了土壤细菌碳水化合物代谢功能基因丰度,但明显提高了土壤细菌辅助因子和维生素代谢、神经退行性疾病、免疫系统等功能基因丰度。综上,多年生苜蓿翻耕轮作一年生作物改变了土壤细菌群落结构和生态功能,该结果可为黄绵土细菌群落演替特征的探索和苜蓿适宜后茬作物的确定提供理论参考。     

轮作和连作对胡萝卜根际和非根际细菌多样性的影响

细菌是土壤最重要的组成部分,土壤细菌的群落结构对土壤的健康至关重要,可以直接影响植物的生长。胡萝卜的长年连作导致其产量低、质量差等一系列问题的发生,连作问题已成为不可忽视的问题。本研究通过HiSeq PE250高通量测序和生物信息学方法获得了玉米胡萝卜轮作种植和胡萝卜连作种植中胡萝卜根际和非根际土壤细菌的组成结构。研究结果表明,相较于胡萝卜连作,玉米胡萝卜轮作种植改变了胡萝卜根际土壤细菌的组成和群落多样性。RM.M (玉米胡萝卜轮作根际土壤样品)样品中的优势菌门为放线菌门和厚壁菌门,RM.R (胡萝卜连作根际土壤样品)的优势菌门是变形菌门;有益菌如芽孢杆菌属和根瘤菌属在玉米胡萝卜轮作种植中的胡萝卜根际富集。RM.M与RM.R的细菌类群差异显著,群落多样性较低;NRM.M(玉米胡萝卜轮作非根际土壤样品)和NRM.R (胡萝卜连作非根际土壤样)的细菌类群差异不明显,群落多样性较高。与连作根际土壤相比,轮作根际土壤中有益菌的相对丰度较大,细菌相对丰度明显增加。本研究结果对通过调节根际土壤细菌组成来保证胡萝卜产量和质量的稳定,解决连作问题具有重要的意义。     

连作对地黄根际土壤细菌群落多样性的影响

采用末端限制性片段长度多态性(T-RFLP)技术研究地黄连作下根际土壤细菌群落的动态变化.结果表明:地黄根际土壤细菌群落的香农多样性指数、丰富度指数和相似性指数均为对照(CK)1年2年,地黄连作下细菌优势种群的比例显著下降,种植1年土壤中厚壁菌门的芽孢杆菌纲在整个细菌群落中处于主导地位,而种植2年土壤中变形菌门ε-变形菌纲处于主导地位.地黄连作使其根际土壤细菌种类大量减少,群落结构趋于简单.连作后细菌群落多样性水平的变化导致根际土壤微生物群落功能的失调,可能是引发连作障碍的原因之一.     

不同种植年限香榧根际土壤微生物多样性

为探明不同种植年限对香榧根际土壤微生物群落特征的影响,采用高通量测序技术,分析种植5 a、10 a和15 a香榧根际土壤细菌、真菌的群落结构和多样性特征.结果表明: 在种植15 a的香榧土壤中细菌Chao1指数、ACE指数和Shannon指数显著降低,Simpson指数无显著变化.NMDS分析显示,种植年限对细菌群落结构变化有显著影响,而种植5 a和10 a香榧林地土壤具有相似的细菌群落.细菌相对丰度、多样性以及群落结构(基本上由变形菌、放线菌、酸杆菌和绿弯菌组成)的变化与有机质、C/N、全氮呈极显著相关.香榧根际土壤真菌Chao1指数和ACE指数随种植年限的增加显著降低,Shannon指数和Simpson指数在种植10 a香榧林地中较高.真菌NMDS分析显示,相同种植年限土壤真菌群落聚在一起,不同种植年限之间能明显分开.真菌优势菌群主要包括子囊菌门、担子菌门、接合菌门.有机质是影响真菌丰富度、多样性和群落结构变化的主要因子.综上,香榧根际土壤微生物群落随种植年限不同而发生明显变化,种植年限、C/N、土壤全氮和有机质含量是影响香榧根际土壤微生物群落结构的主要因子.     

玉米和花生间作根际细菌群落结构与PICRUSt的功能预测

禾本科/豆科作物间作能够促进作物生长与产量形成，而根际微生物组被认为与间作产量优势形成关系密切。将玉米和花生进行盆栽间作并设置以下三种根系分隔方式：塑料膜分隔(即全隔玉米与全隔花生)、尼龙网分隔(即网隔玉米与网隔花生)、无分隔处理(即无隔玉米与无隔花生),采用基于16S rRNA基因的高通量测序技术及PICRUSt功能预测分析不同模式下二者根际细菌群落结构与功能类群的变化，以期从土壤微生物组角度阐明玉米/花生间作产量优势形成的内在机制。结果显示：玉米/花生间作明显改变了二者根际细菌群落结构，无隔、网隔玉米的根际细菌群落结构更为相似并区别于全隔玉米，而网隔花生根际细菌群落结构明显区别于无隔、全隔花生。而且，无隔、网隔玉米根际放线菌门的相对丰度显著高于全隔玉米，网隔花生根际放线菌门、厚壁菌门的相对丰度显著高于全隔、无隔花生，而芽单胞菌门呈现相反的变化趋势。在玉米和花生根际，无隔、网隔处理高于全隔处理的OTU也均主要注释为放线菌门。共存网络分析发现，作为玉米根际细菌网络重要节点的Streptomyces、Actinomadura、Arthrobacter、Bacillus等菌属其丰度变化表现...     

连作对白肋烟根际土壤细菌群落多样性的影响

以种植白肋烟1年、2年和4年的土壤为研究对象,采用末端限制性片段长度多态性(T-RFLP)技术分析根际土壤细菌群落的动态变化.结果表明:白肋烟根际土壤细菌群落香农指数和丰富度指数随着种植年限的增加呈现出先增后减的趋势,连作4年后细菌群落的多样性水平显著降低,细菌群落结构较单一.随着种植年限的增加,根际土壤细菌群落与对照的相似性指数逐渐降低.种植年限为1年、2年的土壤和对照土壤中放线菌门放线菌纲是优势类群,种植年限为4年的土壤中放线菌纲所占的比例下降,而厚壁菌门的芽孢杆菌纲成为优势类群.白肋烟连作使根际鞘氨醇单胞菌属和链霉菌属等益生菌数量减少、蜡状芽孢杆菌等潜在致病菌增加,破坏了烟草根际土壤微生物群落的平衡,使其微生态环境恶化.     

濒危植物大别山五针松根际细菌群落特征与功能分析

植物根际微生物群落对植物健康生长有重要影响, 每种植物根际都有其特定的微生物群落。大别山五针松(Pinus dabeshanensis)被国际自然保护联盟列为濒危物种, 具有重要研究价值。该研究采用16S rRNA高通量测序技术与生物信息学方法, 对濒危植物大别山五针松根际细菌群落特征与功能进行分析。结果表明, 大别山五针松根际微生物的主要种类为变形菌门、放线菌门、酸杆菌门和疣微菌门。网络分析表明, 大别山五针松根际细菌类群存在显著相关性, 其中Bryobacter属、Bradyrhizobium属和未定义的TK10属是互作网络中的重要节点。PICRUSt1功能预测表明其微生物组功能主要为氨基酸运输和代谢、细胞壁/膜/膜生物发生以及能量产生和转换。FAPROTAX功能预测表明, 大别山五针松根际富含的优势菌群具有丰富的化学异养、纤维素水解、需氧化学异养和固氮功能, 其对植物生长发育具有重要作用。研究结果可为培育健康的大别山五针松根际微生物菌群及微生物资源的开发利用提供重要依据。     

Bacterial Communities in the Rhizosphere of Biofuel Crops Grown on Marginal Lands as Evaluated by 16S rRNA Gene Pyrosequences

Microbes are key components of the soil environment and are important contributors to the sustainability of agricultural systems, which is especially significant for biofuel crops growing on marginal lands. We studied bacterial communities in the rhizosphere of five biofuel crops cultivated in four locations in Michigan to determine which factors were correlated to changes in the structure of those communities. Three of these sites were marginal lands in that two were not suitable for conventional agriculture and one was regulated as a brownfield due to prior industrial pollution. Bacterial community composition and structure were assessed by 454 sequencing of the 16S rRNA gene. A total of 387,111 sequences were used for multivariate statistical analysis and to test for correlation between community structure and environmental variables such as plant species, soil attributes, and location. The most abundant bacterial phyla found in the rhizosphere of all crops were Acidobacteria, Proteobacteria, Actinobacteria, and Verrucomicrobia. Bacterial communities grouped by location rather than by crop and their structures were correlated to soil attributes, principally pH, organic matter, and nutrients. The effect of plant species was low but significant, and interactions between locations, plant species, and soil attributes account for most of the explained variation in the structure of bacterial communities, showing a complex relationship between bacterial populations and their environment. Bacterial diversity was higher in the agricultural sites compared to adjacent forest sites, indicating that the cultivation of those biofuel crops increased the rRNA diversity.     

Comparison of Soil Bacterial Communities of Pinus patula of Nilgiris, Western Ghats with Other Biogeographically Distant Pine Forest Clone Libraries

The bacterial community structure of the rhizosphere and non-rhizosphere soil of Pinus patula, found in the Nilgiris region of Western Ghats, was studied by constructing 16S rRNA gene clone libraries. In the rhizosphere and non-rhizosphere soil clone libraries constructed, 13 and 15 bacterial phyla were identified, respectively. The clone libraries showed the predominance of members of culturally underrepresented phyla like Acidobacteria and Verrucomicrobia. The Alphaproteobacteria and Acidobacteria clones were predominant in rhizosphere and non-rhizosphere soil samples, respectively. In rhizosphere, amongst Alphaproteobacteria members, Bradyrhizobium formed the significant proportion, whereas in non-rhizosphere, members of subdivision-6 of phylum Acidobacteria were abundant. The diversity analysis of P. patula soil libraries showed that the phylotypes (16S rRNA gene similarity cutoff, ≥97 %) of Acidobacteria and Bacteroidetes were relatively predominant and diverse followed by Alphaproteobacteria and Verrucomicrobia. The diversity indices estimated higher richness and abundance of bacteria in P. patula soil clone libraries than the pine forest clone libraries retrieved from previous studies. The tools like principal co-ordinate analysis and Jackknife cluster analysis, which were under UniFrac analysis indicated that variations in soil bacterial communities were attributed to their respective geographical locations due to the phylogenetic divergence amongst the clone libraries. Overall, the P. patula rhizosphere and non-rhizosphere clone libraries were found significantly unique in composition, evenly distributed and highly rich in phylotypes, amongst the biogeographically distant clone libraries. It was finally hypothesised that the phylogenetic divergence amongst the bacterial phylotypes and natural selection plays a pivotal role in the variations of bacterial communities across the geographical distance.     

水仙根围细菌群落组成

【目的】探究水仙(Narcissus tazetta var.chinensis roem)土壤根围微生物组成及其与水仙生长特性的相关性。【方法】分别采集崇明水仙及漳州水仙健康植株根围土壤,抽提根围土壤中细菌总DNA并纯化,扩增16S r RNA基因并进行高通量测序分析比较不同产地植株根围细菌的组成与多样性。【结果】崇明水仙和漳州水仙根围微生物组成的主要细菌门类相同,均为12种,其中,优势菌为Proteobacteria、Chloroflexi、Bacteroidetes和Acidobacteria。根围微生物OTUs(Operational taxonomic units)分布及主成分分析(PCA)表明崇明水仙和漳州水仙根围微生物组成有较大差异,且Planctomycetales和Xanthomonadales在崇明水仙根围分布显著多于漳州水仙,而Chloroflexales和Chlorobiales在漳州水仙根围的丰度较高。【结论】根围微生物的组成,如厌氧氨氧化细菌、机会致病菌和光合细菌的多样性与丰度可能与水仙生长特性有密切的关系。     

Effects of field-grown genetically modified Zoysia grass on bacterial community structure

Herbicide-tolerant Zoysia grass has been previously developed through Agrobacterium-mediated transformation. We investigated the effects of genetically modified (GM) Zoysia grass and the associated herbicide application on bacterial community structure by using culture-independent approaches. To assess the possible horizontal gene transfer (HGT) of transgenic DNA to soil microorganisms, total soil DNAs were amplified by PCR with two primer sets for the bar and hpt genes, which were introduced into the GM Zoysia grass by a callus-type transformation. The transgenic genes were not detected from the total genomic DNAs extracted from 1.5 g of each rhizosphere soils of GM and non-GM Zoysia grasses. The structures and diversities of the bacterial communities in rhizosphere soils of GM and non-GM Zoysia grasses were investigated by constructing 16S rDNA clone libraries. Classifier, provided in the RDP II, assigned 100 clones in the 16S rRNA gene sequences library into 11 bacterial phyla. The most abundant phyla in both clone libraries were Acidobacteria and Proteobacteria. The bacterial diversity of the GM clone library was lower than that of the non- GM library. The former contained four phyla, whereas the latter had seven phyla. Phylogenetic trees were constructed to confirm these results. Phylogenetic analyses of the two clone libraries revealed considerable difference from each other. The significance of difference between clone libraries was examined with LIBSHUFF statistics. LIBSHUFF analysis revealed that the two clone libraries differed significantly (P?0.025), suggesting alterations in the composition of the microbial community associated with GM Zoysia grass.     

Characterization of the fecal bacteria communities of forage-fed horses by pyrosequencing of 16S rRNA V4 gene amplicons

The diversity of the equine fecal bacterial community was evaluated using pyrosequencing of 16S rRNA gene amplicons. Fecal samples were obtained from horses fed cool-season grass hay. Fecal bacteria were characterized by amplifying the V4 region of bacterial 16S rRNA gene. Of 5898 mean unique sequences, a mean of 1510 operational taxonomic units were identified in the four fecal samples. Equine fecal bacterial richness was higher than that reported in humans, but lower than that reported in either cattle feces or soil. Bacterial classified sequences were assigned to 16 phyla, of which 10 were present in all samples. The largest number of reads belonged to Firmicutes (43.7% of total bacterial sequences), Verrucomicrobia (4.1%), Proteobacteria (3.8%), and Bacteroidetes (3.7%). The less abundant Actinobacteria, Cyanobacteria, and TM7 phyla presented here have not been previously described in the gut contents or feces of horses. Unclassified sequences represented 38.1% of total bacterial sequences; therefore, the equine fecal microbiome diversity is likely greater than that described. This is the first study to characterize the fecal bacterial community in horses by the use of 16S rRNA gene amplicon pyrosequencing, expanding our knowledge of the fecal microbiota of forage-fed horses.     

Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis

The ability of terminal restriction fragment (T-RFLP or TRF) profiles of 16S rRNA genes to provide useful information about the relative diversity of complex microbial communities was investigated by comparison with other methods. Four soil communities representing two pinyon rhizosphere and two between-tree (interspace) soil environments were compared by analysis of 16S rRNA gene clone libraries and culture collections (Dunbar et al., Appl. Environ. Microbiol. 65:1662-1669, 1998) and by analysis of 16S rDNA TRF profiles of community DNA. The TRF method was able to differentiate the four communities in a manner consistent with previous comparisons of the communities by analysis of 16S rDNA clone libraries. TRF profiles were not useful for calculating and comparing traditional community richness or evenness values among the four soil environments. Statistics calculated from RsaI, HhaI, HaeIII, and MspI profiles of each community were inconsistent, and the combined data were not significantly different between samples. The detection sensitivity of the method was tested. In standard PCRs, a seeded population comprising 0.1 to 1% of the total community could be detected. The combined results demonstrate that TRF analysis is an excellent method for rapidly comparing the relationships between bacterial communities in environmental samples. However, for highly complex communities, the method appears unable to provide classical measures of relative community diversity.     

Belowground microbial communities respond to water deficit and are shaped by decades of maize hybrid breeding

Root-associated microbial communities are important for maintaining agricultural productivity. However, belowground microbial community response to drought in temperate maize agroecosystems, as well as how these responses to water-stress are shaped by host genotype are poorly understood. Ten maize hybrids (six newer and four older) were grown in a replicated field trial. The endosphere, rhizosphere and soil bacterial and archaeal communities were sampled and analyzed using 16S rRNA gene amplicon sequencing. Sampling was done at two developmental stages in a water-limited environment with and without supplemental irrigation. Significant shifts in microbial community composition (β-diversity) were measured between two sampling times during the season, in well-watered and water-stressed conditions and in newer and older generation maize hybrids. The microbial community diversity within samples (α-diversity) was not affected by drought stress or host factors. The phyla Actinobacteria and Firmicutes were more abundant in the rhizosphere of newer hybrids under water stress. These results highlight the importance of temporal variation, environmental stress and plant genetics as influenced by breeding history in shaping the composition of root associated microbial communities. These insights may provide new approaches to the improvement of crop stress tolerance through optimizing microbial communities.