马缨杜鹃根系微生物群落结构及其变化

【目的】为了解野生马缨杜鹃根系微生物的群落结构特征,比较百里杜鹃内马缨杜鹃根际土壤、根表及根内3个生态位微生物群落组成差异,探究杜鹃根系生态位之间、变化菌属间的相互关系,以期为今后杜鹃根系微生物研究提供具有参考价值的数据。【方法】对百里杜鹃内野生马缨杜鹃根系微生物16S rRNA V4区和ITS1区进行高通量测序,比较分析根际土壤、根表及根内微生物群落多样性及组成差异;并基于共变化网络分析进一步探究差异菌属间的相互关系。【结果】马缨杜鹃根系不同的生态位之间,微生物群落结构存在差异,其中以根际土壤与根表、根内差异更为显著,且细菌群落差异小于真菌群落。且从根际-根表-根内,马缨杜鹃根系细菌α-多样性显著下降。马缨杜鹃根系微生物分布于41细菌门和6个真菌门。优势细菌门为变形菌门(Proteobacteria,39.64%±0.08,69.47%±0.12,77.34%±0.07)、酸杆菌门(Acidobacteria,34.10%±0.11,11.03%±0.04,9.18%±0.04)以及放线菌门(Actinobacteria,10.19%±0.03,8.70%±0.02,7.08%±0.01),它们占整体细菌群落总丰度的80%以上。同时8个细菌菌门的相对丰度在根际土壤、根表和根内间显著变化,且它们的相对丰度占细菌群落总丰度的75%以上。真菌主要分布于接合菌门(Zygomycota)、担子菌门(Basidiomycota)和子囊菌门(Ascomycota),它们占整体菌群的99%以上。马缨杜鹃根系存在589个属的细菌,390个属的真菌,从根际-根表-根内,其中25个细菌属和10个真菌属的相对丰度发生显著变化。马缨杜鹃根系微生物群落共变化网络分析表明:在马缨杜鹃根系不同生态位间,除Waitea外,包括枝孢菌属(Cladosporium)、拟盘多毛孢属(Pestalotiopsis)等在内的8个差异真菌菌属均与细菌菌属显著相关,它们相互作用调控微生物群落结构的变化。Bryobacter、Nocardia、Rhizomicrobium和Telmatobacter等核心菌属对马缨杜鹃根系微生物群落共变化网络的变化具有十分重要的调控作用。【结论】百里杜鹃地区马缨杜鹃根际土壤、根表以及根内3个生态位间,微生物群落组成存在差异;而造成微生物组成存在差异这一结果,可能与马缨杜鹃根系密切相关。同时,共变化网络分析揭示出马缨杜鹃根系生态位之间,细菌和真菌彼此间互作。     

健康与感染青枯病烟株根际土壤与茎秆细菌群落结构与多样性

【目的】了解健康烟株与感染青枯病烟株在根际土壤、茎杆发病部位、茎杆病健交界部位以及未发病茎杆的细菌群落结构与多样性。【方法】分别对土壤与茎杆样品中细菌的16S rRNA基因V3-V4区进行扩增,采用Illumina MiSeq测序技术对扩增片段进行高通量测序,然后对健康烟株与感染青枯病烟株不同部位细菌群落结构与多样性进行分析。【结果】感染青枯病烟株发病茎杆及根际土壤的细菌群落多样性高于健康烟株茎杆及其根际土壤样品,病健交界茎杆样品细菌群落多样性低于健康烟株。变形菌门(Proteobacteria)在所有样品中均为优势菌门;所有烟株根际土壤的优势菌门为拟杆菌门(Bacteroidetes)、酸杆菌门(Acidobacteria)、放线菌门(Actinobacteria)和绿弯菌门(Chloroflexi);健康烟株茎杆部位的优势菌门为蓝细菌门(Cyanobacteria);感染青枯病烟株发病茎杆和病健交界茎杆部位的优势菌门为蓝细菌门(Cyanobacteria)和厚壁菌门(Firmicutes)。所有根际土壤样品的优势菌属为劳尔氏菌属(Ralstonia)、假单胞菌属(Pseudomonas)、鞘脂单胞菌属(Sphingomonas)、黄杆菌属(Flavobacterium)和代尔夫特菌属(Delftia),而感染青枯病烟株根际土壤的劳尔氏菌属(Ralstonia)和假单胞菌属(Pseudomonas)相对丰度显著高于健康烟株根际土壤,鞘脂单胞菌属相对丰度显著低于健康烟株根际土壤。烟株茎杆的优势菌属为劳尔氏菌属和假单胞菌属等。感染青枯病烟株病健交界茎杆中劳尔氏菌属、肠杆菌属(Enterobacter)和泛菌属(Pantoea)相对丰度显著低于健康烟株样品。【结论】健康与感染青枯病烟株茎杆样品细菌群落的丰富度和多样性明显低于相应的根际土壤样品。较健康烟株而言,感染青枯病烟株根际土壤和茎杆样品细菌群落丰富度和多样性均表现出不同程度地增加,且根际土壤细菌群落结构变化较茎杆样品明显,而病健交界茎杆样品细菌群落丰富度和多样性降低。烟草青枯病为典型土传病害,其病原茄科劳尔氏菌尽管能在烟株维管束中蔓延扩增,但主要还是分布于土壤中;它的存在似乎对土壤细菌群落的影响大于茎杆样品的。该研究结果提示对于青枯病的防治不能局限于烟株本身,田间土壤也应加大防治力度。     

大豆不同生育期根际土壤细菌群落结构的变化

为了解大豆根际细菌群落结构多样性及根际细菌群落结构的变化,该研究以大豆苗期和成熟期的根际土壤为材料,采用Illumina高通量测序技术测定细菌16S rRNA V3+V4区序列,探究大豆不同生育期根际土壤细菌群落结构的变化。对原始数据进行拼接、过滤、去除嵌合体序列和聚类分析等数据处理,并对OTU进行分类学注释。在此基础上运用ANOVA分析物种组成变化,Alpha多样性指数研究细菌多样性变化。结果表明:细菌丰富度和多样性在不同生育期有显著变化,其中成熟期土壤中的细菌丰富度和多样性指数均明显高于苗期; 变形菌、放线菌、酸杆菌是大豆根际的优势菌门,其含量在不同生育期也有显著变化; 假诺卡氏菌属、糖丝菌属、鞘氨醇单胞菌属是大豆根际的优势菌属,这些菌属中的部分菌群属于根际促生菌,具有潜在的促生效应。这些结果证实大豆的生育期对根际土壤细菌群落结构有重要影响。     

黑老虎内生真菌及根际土壤真菌的群落结构与生态功能分析

为探讨黑老虎(Kadsura coccinea)根际土壤和组织内生真菌菌群的组成及其生态功能，该研究采用ITS高通量测序技术对成熟黑老虎(根、茎、叶)内生真菌及根际土壤真菌群落结构、多样性和生态功能进行了分析。结果表明：(1)从12个样品中共获得2 241个可操作分类单元(OTU),涉及10门、41纲、95目、212科、367属，内生真菌(根、茎、叶)和根际土壤真菌OTU数分别为386、536、258、1 435个，其中共有的OTU为18个。在门水平上，黑老虎内生真菌及根际土壤真菌优势群落均为子囊菌门和担子菌门，其中子囊菌门在叶和茎中占比分别高达96.99%和95.37%;在属水平上，黑老虎根际土壤真菌中腐生真菌被孢霉属占比较高(为13.5%),叶和茎等生长旺盛的组织中子囊菌门未分类属和痂囊腔菌属占比较高。(2)α多样性分析结果显示，黑老虎根际土壤真菌群落的丰度和多样性明显高于内生真菌，茎中内生真菌丰度显著高于根和叶，而根、茎和叶组织间内生真菌多样性差异不显著；PCoA分析结果显示，叶和茎的真菌群落结构相似性更高。(3)利用FUNGuild数据库进行的功能预测分析结果显示，黑老虎根际土...     

芽胞杆菌浸种对水稻内生细菌群落结构的影响

水稻内生细菌群落是反映植株内环境是否健康稳定的重要生物学指标,芽胞杆菌是防治水稻病害的重要生防微生物。为揭示芽胞杆菌浸种处理对水稻内生细菌群落结构的影响,采用Illumina MiSeq测序的方法对水稻内生细菌的16S rRNA基因进行测序,剖析了芽胞杆菌浸种处理对不同水稻组织内生细菌的微生态调控作用。结果表明,3种芽胞杆菌浸种处理可以提高水稻根和茎部内生细菌群落的丰富度和均匀度,降低叶部内生细菌群落的丰富度和均匀度,显著增加根部内生细菌群落多样性。变形菌门(Proteobacteria)、厚壁菌门(Firmicutes)和拟杆菌门(Bacteroidetes)是水稻根部和茎部共有优势菌门,厚壁菌门和芽胞杆菌属(Bacillus)是叶部共有优势菌门和属。芽胞杆菌浸种处理显著提高了叶部内生厚壁菌门和芽胞杆菌属的相对丰度,增加了根系和茎部组织内生细菌的分类单元OTU(Operational Taxonomic Units)数量,对叶部组织影响不明显;降低了茎部和叶部中参与各种代谢通路的内生细菌丰度,显著增加了根部参与代谢通路的内生细菌丰度。因此,3种芽胞杆菌浸种处理可以显著改变水稻根部、茎部和叶部内生细菌群落结构,改善水稻生长的微生态环境。     

基于加权共变化网络分析水稻根系微生物群落间的差异

为了解水稻根系微生物群落间的差异,比较水稻根内、根表以及根际3个生态位微生物群落组成差异;探究水稻根系生态位之间、变化种群间的相互关系;以期为今后水稻根系微生物研究提供具有参考价值的依据.本研究利用WGCNA算法对水稻根系3个生态位的微生物群落数据分别构建共表达网络,找出根内、根表以及根际微生物群落间的差异网络,以网络为单位比较分析不同生态位间微生物群落的差异,并基于共变化网络分析进一步探究差异种群间的相互关系.通过WGCNA算法对水稻根系3个生态位的微生物群落进行共表达网络分析,结果发现:在水稻根内-根表-根际3个生态位间,微生物群落构成的共表达互作网络存在差异.进一步分析3个生态位间差异网络,发现根际-根表差异网络中的OTUs分布于6个门18个属中,优势菌门为变形菌门(Proteobacteria,72.97％);在根际-根内差异网络中的OTUs分布于9个门35个属,优势菌门为变形菌门(Proteobacteria,66.36％)、放线菌门(Actinobacteria,9.09％)、拟杆菌门(Bacteroidetes,10.9％);根表-根内差异网络中的OTUs分布于12个门36个属中,其中优势菌门为变形菌门(Proteobacteria,41.41％)、拟杆菌门(Bacteroidetes,10.10％)、厚壁菌门(Firmicutes,12.12％)、疣微菌门(Verrucomicrobia,10.10％).Rhodobacter、No-vosphingobium等3个核心菌属、Blvii28、Dechloromonas等6个核心菌属和Cellvibrio、Geobacter等5个核心菌属,分别在根际-根表差异种群微生物共变化网络、根际-根内差异种群微生物共变化网络和根表-根内差异种群微生物共变化网络中起重要的调控作用.     

“使它隆”对玉米根部不同微生环境细菌群落多样性的影响

【目的】研究除草剂"使它隆"施用后对玉米根部不同微生环境细菌群落结构和多样性的影响。【方法】利用Illumina Miseq高通量测序技术,对玉米根系内生菌、根际和非根际土壤细菌16S rRNA的V4–V5可变区序列进行测定,分析不同生长期喷施除草剂使它隆对玉米土壤细菌及根系内生菌群落结构和多样性的影响。【结果】本研究15个样品共得到544393条有效序列,333565条优质序列。多样本共有OTU分析表明,非根际和根际土壤的群落结构更为相似,在一定程度上说明玉米根部相关细菌的定殖具有选择性并且是从根际到根系逐步专一化。丰度等级曲线和Alpha多样性结果显示非根际和根际土壤群落的丰富度和均匀度较高,而玉米根系内生菌群落的丰富度和均匀度都比较低,且成熟期玉米根系内生菌群落的丰富度在施用除草剂使它隆后下降比较剧烈。群落组成分析发现,使它隆除草后,玉米根部相关细菌各时期在门及属水平上的分布都发生了较大变化。菌群代谢功能预测结果表明玉米生长从苗期到成熟期,微生物的生长压力逐渐加大,需要消耗更多的能量用于新陈代谢和环境适应。【结论】施用除草剂使它隆后会降低玉米根部土壤细菌群落的多样性,使它隆对成熟期玉米根系内生菌群落影响最为显著。     

不同生境黑果枸杞根际与非根际土壤微生物群落多样性

研究典型生境黑果枸杞根际与非根际土壤微生物群落多样性及其与土壤理化性质间的关系,为进一步研究黑果枸杞抗逆性提供理论数据。采集新疆精河县艾比湖地区(EB)盐碱地、乌苏市(WS)路旁荒地、五家渠市(WQ)人工林带的黑果枸杞根际与非根际土壤,利用Illumina-MiSeq高通量测序技术分析细菌和真菌群落组成和多样性。结果表明:根际土壤细菌多样性高于非根际土壤(WQ除外),而根际真菌多样性低于非根际土壤。WQ非根际土壤细菌和真菌多样性均高于EB和WS;根际细菌多样性排序为EBWSWQ,根际真菌多样性排序为WSEBWQ。根际土壤优势细菌门依次是变形菌门、拟杆菌门、放线菌门、酸杆菌门,真菌优势门为子囊菌门、担子菌门。根际土壤细菌变形菌门、拟杆菌门、酸杆菌门的相对丰度高于非根际土壤,而厚壁菌在根际土壤中的丰度显著降低,真菌优势门丰度在根际土和非根际土中的变化趋势因地区而异; Haliea、Gp10、Pelagibius、Microbulbifer、假单胞菌属、Thioprofundum、Deferrisoma是根际土壤细菌优势属;多孢子菌属、支顶孢属、Corollospora、Cochlonema是根际真菌优势属。细菌、真菌优势类群(门、属)的组成以及丰富度存在地区间差异,厚壁菌门在EB地区的丰富度显著高于含盐量较低的WS、WQ;盐碱生境EB中根际土壤嗜盐细菌的丰度高于非盐碱生境(WQ、WS),如盐单胞菌属、动性球菌属、Geminicoccu、Pelagibius、Gracilimonas、Salinimicrobium等。小囊菌属是EB根际真菌的最优势属,Melanoleuca是WQ和WS的最优势属,地孔菌属、Xenobotrytis、Brachyconidiellopsis、多孢子菌属等在EB根际土壤中的丰度显著高于WQ和WS。非盐碱生境(WS和WQ)的微生物群落之间的相似性较高,并且高于与盐碱环境(EB)之间的相似性,表明土壤含盐量对微生物群落组成丰度具有重要的影响。     

不同药用植物根际土壤原核微生物多样性研究

为研究不同药用植物根际土壤中的原核微生物多样性,分别采集白术(Atractylodes macrocephala)、白芍(Paeonia sterniana)、牡丹(Paeonia suffruticosa)、玄参(Scrophularia ningpoensis)四种药用植物的根际土壤以及非种植区的土壤,针对16S rRNA基因的V3～V4区进行测序,分析土壤细菌群落的组成。结果表明,药用植物根际土壤中的细菌群落多样性指数显著高于非种植区土壤。五组样本的优势类群差异不大,总体相对丰度较高的有变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)、放线菌门(Actinobacteria)、芽单胞菌门(Gemmatimonadetes)、绿弯菌门(Chloroflexi)等,药用植物根际中的放线菌相对丰度高于非种植区。属水平上四种药用植物根际细菌和非种植区的群落结构有较大差异,四种中药材的根际土壤中各自富集了特异性的有益细菌属。药用植物根际土壤中的NMD1、Dongia、Gaiella、Streptomyces等相对丰度高于非种植区,而非种植区土壤中Lysoba...     

同质园环境和遗传分化影响锦鸡儿属植物根际土壤固氮菌多样性和群落结构

环境和遗传分化共同影响植物的功能性状,进而能够通过根系分泌物影响根际微生物。本研究利用同质园试验,通过高通量测序技术,基于固氮酶基因nifH的同源性,分析同质园栽培的不同种源小叶锦鸡儿(Caraganamicrophylla)、中间锦鸡儿(C. liouana)和荒漠锦鸡儿(C.roborovskyi)根际土壤固氮菌多样性,并探究其与种源地气候及同质园土壤属性的关系。结果表明, 3种锦鸡儿植物根际土壤固氮菌隶属6门9纲18目21科33属72种,其中变形菌门、疣微菌门和蓝细菌门为优势门,优势属为中慢生根瘤菌属(Mesorhizobium)、固氮氢自养单胞菌属(Azohydromonas)和慢生根瘤菌属(Bradyrhizobium)。3种锦鸡儿根际土壤固氮菌α多样性种间差异不显著,但中间锦鸡儿和荒漠锦鸡儿根际土壤固氮菌的α多样性存在显著的种内差异(P<0.05),小叶锦鸡儿和荒漠锦鸡儿根际土壤固氮菌群落结构存在显著的种内差异(P<0.05)。冗余分析表明同质园土壤p H和种源地年均温分别是影响3种锦鸡儿根际土壤固氮菌多样性和群落结构变化的主要因子,说明3种锦鸡儿属植物根际土壤...     

DGGE Fragments Oscillate with or Counter to Fluctuations in Cultivable Bacteria Along Wheat Roots

Previously, we showed that bacterial populations oscillate in response to a moving substrate source such as a root tip, resulting in moving wavelike distributions along roots. For this article, we investigated if bacterial communities fluctuate as a whole or if there is a succession in bacterial composition from peak to peak or within peaks. Rhizosphere microbial communities along roots of wheat Triticum aestivum L. were studied in detail (20–25 rhizosphere and bulk soil samples along the total root length) in two related soils by colony enumeration and culture-independent DNA analysis. Similar to our previous findings, the numbers of copiotrophic and oligotrophic bacteria oscillated with significant harmonics along each root, independent of soil moisture or lateral roots. Shifts in amplified eubacterial 16S rDNA fragments from denaturing gradient gel electrophoresis (DGGE) analysis were detected along the roots. The most abundant and intensively amplified fragments fluctuated in phase with colony-forming unit (CFU) oscillations; fewer amplified fragments with less intensive bands fluctuated out of phase or were restricted to certain root zones. The bacterial species richness along the root was negatively correlated with the numbers of oligotrophic bacterial CFUs. Discriminant analyses on DGGE patterns distinguished between soil types, rhizosphere and bulk soil, and waxing and waning phases in the oscillations along roots. Bacterial compositions shifted within oscillations but were repeated from oscillation to oscillation, supporting the idea that the most abundant bacterial taxa were growing and dying over time and consequently in space, whereas other taxa counterfluctuated or hardly responded to the substrate supplied by the passing root tip.     

Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments

The microbiomes of rhizocompartments (nodule endophytes, root endophytes, rhizosphere and root zone) in soya bean and alfalfa were analysed using high‐throughput sequencing to investigate the interactions among legume species, microorganisms and soil types. A clear hierarchical filtration of microbiota by plants was observed in the four rhizocompartments – the nodule endosphere, root endosphere, rhizosphere and root zone – as demonstrated by significant variations in the composition of the microbial community in the different compartments. The rhizosphere and root zone microbial communities were largely influenced by soil type, and the nodule and root endophytes were primarily determined by plant species. Diverse microbes inhabited the root nodule endosphere, and the corresponding dominant symbiotic rhizobia belonged to Ensifer for alfalfa and Ensifer–Bradyrhizobium for soya bean. The nonsymbiotic nodule endophytes were mainly Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. The variation in root microbial communities was also affected by the plant growth stage. In summary, this study demonstrated that the enrichment process of nodule endophytes follows a hierarchical filtration and that the bacterial communities in nodule endophytes vary according to the plant species.     

Secretion activity of white lupin’s cluster roots influences bacterial abundance,function and community structure

White lupin (Lupinus albus L. cv. Amiga) reacts to phosphate deficiency by producing cluster roots which exude large amounts of organic acids. The detailed knowledge of the excretion physiology of the different root parts makes it a good model plant to study plant-bacteria interaction. Since the effect of the organic acid exudation by cluster roots on the rhizosphere microflora is still poorly understood, we investigated the abundance, diversity and functions of bacteria associated with the cluster roots of white lupin, with special emphasis on the influence of root proximity (comparing root, rhizosphere soil and bulk soil fractions) and cluster root growth stages, which are characterized by different excretion activities. Plants were grown for five weeks in microcosms, in the presence of low phosphate concentrations, on acidic sand inoculated with a soil suspension from a lupin field. Plate counts showed that bacterial abundance decreased at the stage where the cluster root excretes high amounts of citrate and protons. In vitro tests on isolates showed that the frequencies of auxin producers were highest in juvenile and mature cluster roots and significantly decreased in senescent cluster roots. However, no significant difference in the frequency of auxin producers was found between cluster and non cluster roots. The diversity and structure of bacterial communities were investigated by DGGE of 16S rDNA and 16S rRNA. The diversity and community structure were mostly influenced by root proximity and, to a lesser extent, by cluster root stage. The richness of bacterial communities decreased with root proximity, whereas the proportion of active populations increased. The high citrate and proton excretion occurring at the mature stage of cluster roots had a strong impact on the structure and richness of the bacterial communities, both in the root and in the rhizosphere soil.     

Changes in microbial activity and composition in a pasture ecosystem exposed to elevated atmospheric carbon dioxide

Elevated atmospheric CO₂ increases aboveground plant growth and productivity. However, carbon dioxide-induced alterations in plant growth are also likely to affect belowground processes, including the composition of soil biota. We investigated the influence of increased atmospheric CO₂on bacterial numbers and activity, and on soil microbial community composition in a pasture ecosystem under Free-Air Carbon Dioxide Enrichment (FACE). Composition of the soil microbial communities, in rhizosphere and bulk soil, under two atmospheric CO₂ levels was evaluated by using phospholipid fatty acid analysis (PLFA), and total and respiring bacteria counts were determined by epifluorescence microscopy. While populations increased with elevated atmospheric CO₂ in bulk soil of white clover (Trifolium repens L.), a higher atmospheric CO₂ concentration did not affect total or metabolically active bacteria in bulk soil of perennial ryegrass (Lolium perenne L.). There was no effect of atmospheric CO₂ on total bacteria populations per gram of rhizosphere soil. The combined effect of elevated CO₂ on total root length of each species and the bacterial population in these rhizospheres, however, resulted in an 85% increase in total rhizosphere bacteria and a 170% increase in respiring rhizosphere bacteria for the two plant species, when assessed on a per unit land area basis. Differences in microbial community composition between rhizosphere and bulk soil were evident in samples from white clover, and these communities changed in response to CO₂ enrichment. Results of this study indicate that changes in soil microbial activity, numbers, and community composition are likely to occur under elevated atmospheric CO₂, but the extent of those changes depend on plant species and the distance that microbes are from the immediate vicinity of the plant root surface.     

Bacterial community structure associated with the rhizosphere soils and roots of <Emphasis Type="Italic">Stellera chamaejasme</Emphasis> L. along a Tibetan elevation gradient

The effect of altitude on the composition and diversity of microbial communities have attracted highly attention recently but is still poorly understood. We used 16S rRNA gene clone library analyses to characterize the bacterial communities from the rhizosphere and roots of Stellera chamaejasme in the Tibetan Plateau. Our results revealed that Actinobacteria and Proteobacteria were dominant bacteria in this medicinal plant in the rhizosphere and root communities. The Shannon diversity index showed that the bacterial diversity of rhizosphere follows a small saddle pattern, while the roots possesses of a hump-backed trend. Significant differences in the composition of bacterial communities between rhizosphere and roots were detected based on multiple comparisons analysis. The community of Actinobacteria was found to be significantly negative correlated with soil available P (p?<?0.01), while the phylum of Proteobacteria showed a positive relationship with available P (p?<?0.05). Moreover, redundancy analysis indicated that soil phosphorus, pH, latitude, elevation and potassium positively correlated with bacterial communities associated with rhizosphere soils. Taken together, we provide evidence that bacterial communities associated with S. chamaejasme exhibited some certain elevational pattern, and bacterial communities of rhizosphere soil were regulated by environmental characteristics along elevational gradients in this alpine ecosystem.     

两种盐生植物根际土壤细菌多样性和群落结构

应用高通量测序技术对西北干旱区两种盐生植物黑果枸杞和里海盐爪爪根际土壤细菌的多样性和群落结构进行研究,旨在揭示两种耐盐植物根际土壤细菌之间以及根际与非根际细菌群落结构间的差异,为深入研究盐生植物根际土壤微生物与耐盐性之间的关系提供理论基础。结果表明:黑果枸杞、里海盐爪爪根际细菌多样性丰度高于非根际土,黑果枸杞根际土壤细菌多样性丰度高于里海盐爪爪。根际和非根际土壤细菌群落的组成和丰度存在差异,从黑果枸杞和里海盐爪爪根际土壤中分别检测出细菌21门289属和22门304属,而从非根际土壤中分别检测出28门285属和24门336属;在两种盐生植物根际土壤中,变形菌门和厚壁菌门均为优势门;拟杆菌门、放线菌门、蓝细菌门及浮霉菌门在根际土壤中的丰度显著高于非根际土壤,而厚壁菌门在根际土壤中的丰度低于非根际土壤。两种植物根际土壤中的细菌优势门和优势属的数量均高于非根际土壤,在黑果枸杞和里海盐爪爪的根际土壤中的细菌优势属分别有10个和9个,而二者非根际土壤中的细菌优势属各有4个,其中假单胞菌属是根际和非根际土壤中的共有优势属。黑果枸杞和里海盐爪爪根系细菌群落组成和丰度存在差异,只有假单胞菌属和盐单胞菌属是两种植物根际土壤中的共有优势属。Unifrac分析和聚类分析表明,两种盐生植物根际土壤细菌之间的相似性大于根际和非根际细菌群落间的相似性。细菌多样性与土壤有机碳、有机质、总氮正相关,与pH、电导率负相关,电导率和pH,有机碳和总氮分别是非根际土,根际土壤细菌群落物种组成的主要影响因素。     

Weeds influence soil bacterial and fungal communities

Background and aims

Vineyards harbour a variety of weeds, which are usually controlled since they compete with grapevines for water and nutrients. However, weed plants may host groups of fungi and bacteria exerting important functions.

Methods

We grew three different common vineyard weeds (Taraxacum officinalis, Trifolium repens and Poa trivialis) in four different soils to investigate the effects of weeds and soil type on bacterial and fungal communities colonising bulk soil, rhizosphere and root compartments. Measurements were made using the cultivation-independent technique Automated Ribosomal Intergenic Spacer Analysis (ARISA).

Results

Weeds have a substantial effect on roots but less impact on the rhizosphere and bulk soil, while soil type affects all three compartments, in particular the bulk soil community. The fungal, but not the bacterial, bulk soil community structure was affected by the plants at the late experimental stage. Root communities contained a smaller number of Operational Taxonomic Units (OTUs) and different bacterial and fungal structures compared with rhizosphere and bulk soil communities.

Conclusions

Weed effect is localised to the rhizosphere and does not extend to bulk soil in the case of bacteria, although the structure of fungal communities in the bulk soil may be influenced by some weed plants.     

Soil-plant compartments affect fungal microbiome diversity and composition in grapevine

Plant compartments provide unique niches that lead to specific microbial associations. The microbiota colonizing the endophytic compartment (endorhizosphere) and the rhizosphere contribute to productivity, plant growth, phytoremediation and carbon sequestration. The main objective of this study was to investigate how fungal communities are enriched in different habitats outside and inside of grapevine roots. For this purpose, the spatial dynamics of the fungal communities associated with three soil-plant compartments (bulk soil, rhizosphere and endorhizosphere) were characterized by ITS high-throughput amplicon sequencing (HTAS). Fungal communities were largely affected in their diversity and composition by soil-plant compartments, whereas the spatial variation (i.e. across five vineyards) was low. The endorhizosphere compartment differed most from the other two, suggesting that the root tissues entail a barrier for fungal colonization. The results of functional prediction via FUNGuild suggested an increase in the relative abundances of potential plant pathogens, endophytes and arbuscular mycorrhiza, and a decrease in wood, dung and undefined saprotrophs from bulk soil towards the endorhizosphere. Roots of asymptomatic vines were a microbial niche that is inhabited by soilborne fungi associated with grapevine trunk diseases, which opens up new perspectives in the study of the endophytic role of these pathogens on grapevines. Results obtained in this study provide helpful information to better know how the host shapes its microbiome and the implications for vineyard productivity and management.     

The host niches of soybean rather than genetic modification or glyphosate application drive the assembly of root-associated microbial communities

Plant roots significantly influence soil microbial diversity, and soil microorganisms play significant roles in both natural and agricultural ecosystems. Although the genetically modified (GM) crops with enhanced insect and herbicide resistance are thought to have unmatched yield and stress resistance advantages, thorough and in-depth case studies still need to be carried out in a real-world setting due to the potential effects of GM plants on soil microbial communities. In this study, three treatments were used: a recipient soybean variety Jack, a triple transgenic soybean line JD321, and the glyphosate-treated JD321 (JD321G). Three sampling stages (flowering, seed filling and maturing), as well as three host niches of soybean rhizosphere [intact roots (RT), rhizospheric soil (RS) and surrounding soil (SS)] were established. In comparison to Jack, the rhizospheric soil of JD321G had higher urease activity and lower nitrite reductase at the flowering stage. Different treatments and different sampling stages existed no significant effects on the compositions of microbial communities at different taxonomic levels. However, at the genus level, the relative abundance of three plant growth-promoting fungal genera (i.e. Mortierella, Chaetomium and Pseudombrophila) increased while endophytic bacteria Chryseobacterium and pathogenic bacteria Streptomyces decreased from the inside to the outside of the roots (i.e. RT → RS → SS). Moreover, two bacterial genera, Bradyrhizobium and Ensifer were more abundant in RT than in RS and SS, as well as three species, Agrobacterium radiobacter, Ensifer fredii and Ensifer meliloti, which are closely related to nitrogen-fixation. Furthermore, five clusters of orthologous groups (COGs) associated to nitrogen-fixation genes were higher in RT than in RS, whereas only one COG annotated as dinitrogenase iron-molybdenum cofactor biosynthesis protein was lower. Overall, the results imply that the rhizosphere host niches throughout the soil–plant continuum largely control the composition and function of the root-associated microbiome of triple transgenic soybean.