用gfp基因标记法研究大豆根瘤菌在大豆根部定殖结瘤情况

采用三亲本杂交的方法,将绿色荧光蛋白基因(gfp)转入高效、抗逆、广适应性的快生大豆根瘤菌Sinorhizobium frediiCCBAU 01287中,获得含gfp基因的转基因菌株CBAU 01287(G);平板传代和共生检测表明:外源质粒在CCBAU 01287中能够自我复制,稳定遗传。进一步研究表明,gfp标记菌CCBAU 01287(G)可用于实时监测根瘤菌在大豆根部的早期定殖情况和定殖密度的测定;标记菌株对大豆的生长及生物量的积累与出发菌株的效果无显著差异。     

AMF和饭豆根瘤菌对饭豆、玉米套种促生作用的研究

将从饭且根瘤中分离的饭豆根瘤菌(Rhizobium sp.CYY3302,Rhizobium sp.HCY9101,Rhizobium SP.JMC1402)与ANF(Arbuscular Mycorrltizal Fungi)共同接种于饭豆,进行饭豆、玉米田间小区各种试验。结果表明,接种饭豆根瘤菌和AMF的处理与未接种的处理相比,饭豆的结瘸率比对照提高52％-134％;饭豆及玉米的菌根感染率比对照分别增加43．1％-80％和46．8％-97．6％;饭豆的产量提高了54％-67％,而玉米的产量提高了2．4％-19．5％。研究结果还表明：豆科作物接种根瘸菌,即使在种过豆科作物的老区,也是有效的。     

植物内生细菌的侵染定殖规律研究进展

详细综述了植物内生细菌的侵染定殖过程,即吸附、侵入、定殖三个阶段。着重阐述了对植物内生细菌的定殖检测方法,包括抗生素标记法、免疫学方法、基因标记法及特异性寡核苷酸片段标记法等。另外,对植物内生细菌的来源及定殖影响因子也进行了系统讨论,并对未来植物内生细菌定殖研究前景作了展望。     

植物内生菌定殖检测技术及其应用

自然环境中内生菌定殖于植物体内,对宿主植物产生多种有益效应,但是内生菌定殖情况难以检测,相关研究不够深入系统。目前在该领域使用较为广泛的检测技术包括：荧光标记、抗生素标记、荧光定量PCR和高通量测序等。内生菌通过孔隙伤口和降解细胞壁等方式侵染植物,通过种子垂直传递核心内生菌。对植物内生菌定殖的侵染方式、定殖方法和检测技术进行了归纳和整理,介绍了内生菌多种侵染和迁移途径,总结了目前内生菌定殖在生物防治、促进植物生长和污染修复等方面的功能,综述了多种检测方式在应用中的特点,以期为内生菌定殖植物的相关研究及其应用提供参考依据。     

外源基因标记的紫云英根瘤菌在水稻根部的定殖研究

前期研究中已证实紫云英根瘤菌(Rhizobium astragalus)JS5A16菌株对水稻生长有一定的促生作用,利用gusA基因标记的JS5A16菌株(编号为JS5A16G)接种水稻种子并检测其在水稻(汕优63)生长初期的根固定殖动态及分布。结果表明菌株JS5A16G在水稻出苗后2d根固定殖密度大量增加,第4天达到最大值16d后趋于稳定。将水稻根表面灭菌后,检测菌株JS5A16G在根内的定殖情况,发现在“汕优63”出苗后2d检测不出菌株JS5A16G,第4天可检测出。根部直接染色显示,菌株JS5A16G在根部的分布并不均匀,主要是在根系的某些部位形成微菌落。同时利用luxAB发光酶基因标记紫云英根瘤菌JS5A16菌株(编号为JS5A16L)研究其在不同品种水稻根部的定殖动态。结果表明,菌株JS5A6L在不同水稻品种“汕优63”、“汕优64”和“马协l18—2”根部的定殖密度不同且可以进入不同水稻品种的根内。在整个水稻生长期内菌株JS5A16L在“汕优64”根部的定殖密度明显高于其在“汕优63”根部的定殖密度,在“马协ll8—2”的定殖密度与其在“汕优63”、“汕优64”根部相比没有显著差异。但菌株JS5A16L在不同水稻根部的定殖动态相似,数量均在水稻生长到60-75d时(即水稻的孕穗期)达到最高值。     

消除共生质粒的费氏中华根瘤菌HND29SR在大豆根圈的定殖动态

比较研究了费氏中华根瘤菌（Sinorhizobium fredii)HN01(出发菌）、发光酶基因标记菌HNO1L（参照菌）、消除HN01共生质粒的菌株HND29SR在无菌砂培条件下的大豆根圈定殖动态。供试菌单独接种时：HN01、HN01L和HND29SR的定殖动态基本一致,其早期定殖密度下降较快,播种后第16天时HN01和HN01L分别达到较高的定殖水平6.49logcfu/g鲜根和6.78logcfu/g鲜根,然后维持相对稳定的定殖水平。但HND29SR的定殖密度持续下降到播种后第16天时才开始上升,至第35天时仍维持相对稳定的定殖密度6.94logcfu/g鲜根。等量混合接种时供试菌在根圈定殖群体中各自定殖密度在测定过程中基本相等。结果表明消除HN01的共生质粒对其在大豆根圈中定殖能力无显著影响。     

硅酸盐细菌NBT菌株在小麦根际定殖的初步研究

对硅酸盐细菌NBT菌株进行了耐药性标记,得到稳定的链霉素抗性标记菌NBT菌株,采用选择性培养基分离计数,通过琼脂平板和盆栽试验,研究了标记菌NBT在小麦根际的定殖动态及影响因素。结果表明,在灭菌土盆栽中,播种后9d左右NBT菌株在小麦根际的定殖水平达最高(1．4×10^8cfu·g^-1根土),播种后54d左右趋向稳定,NBT菌株细胞数量为2．4×10^3cfu·g^-1根土;未灭菌土盆栽中,播种后9d左右NBT菌株的定殖水平达最高(3．8×10^8cfu·g^-1根土),60d左右趋向稳定,菌数为3．1×10^3cfu·g^-1根土,牛物和非牛物因素对NBT菌株定殖小麦根系有影响。     

费氏中华根瘤菌HN01DL在大豆根圈的定殖动态与结瘤研究

以发光酶基因luxAB为标记,在根盒缩影条件下研究了费氏中华根瘤菌HN01DL在大豆根圈的定殖动态、分布范围及其结瘤情况.结果表明,HN01DL在根盒灭菌土壤和非灭菌土壤缩影中的大豆全根系定殖动态与水平明显不同,前者在第12d时达到最高定殖密度(8.65logcfu·g^-1),而后者的早期定殖数量下降较快,且于第15d时达到最高定殖密度(6.88logcfu·g^-1).HN01DL在大豆播种5d后在大豆根部的A(0～4cm)区根段上达到最高定殖密度(7.05logcfu·g^-1),然后开始缓慢下降,至第19d时仍维持相对稳定,在第33d时又开始回升.至播种后第46d时HN01DL可散布至种子下方16cm处的根段部位.HN01DL在A区根段的定殖密度持续较高,所形成的发光根瘤总数(16.3个)及发光比例(68.8%)最高,且发光根瘤主要集中于该区段主根上.发光根瘤比例沿A-E区段逐渐下降,在E区段未检测到发光根瘤.     

基因标记枯草芽孢杆菌BS-68A在黄瓜上定殖

目的:野生型枯草芽孢杆菌Bacillus subtilisBS-68能有效地防治由Pythium spp.和Fusarium oxporum引起的黄瓜立枯病和枯萎病。为了探究该菌株的生防机制,利用该菌株的黄绿荧光蛋白基因和氯霉素抗性基因标记菌株BS-68A研究其在黄瓜植株各个部位的定殖能力、种群动态和在根围的分布。方法和结果:用基因标记菌株发酵液分别对黄瓜种子进行浸种和浇穴处理,播种后30d,该菌能在黄瓜根部和茎基部定殖,不能在茎部和叶部定殖。浸种处理,该菌在茎基部的种群数量为3.1×104cfu/株,大于根部的种群数量4.1×102cfu/株;浇穴处理,该菌在茎基部的种群数量8.0×103cfu/株,低于根部的种群数量2.5×104cfu/株。     

gfp基因标记的重组杆状病毒对棉铃虫幼虫的侵染历程

 用携带杆状病毒极晚期多角体蛋白基因启动子驱动gfp表达的重组病毒rHa FGP感染棉铃虫三龄幼虫 .在感染后不同时间取样 ,分离不同组织 ,制片 ,置于倒置荧光显微镜下观察基因的表达 .结果发现 ,随着感染时间的推移 ,荧光产生的部位出现更替 ,随后荧光强度也发生相应的变化 .从荧光出现的先后初步推断出杆状病毒对昆虫幼虫的侵染路线 :中肠上皮→血淋巴→气管系统→脂肪体 真皮 .在幼虫感染后 12h荧光即出现于中肠细胞中 ,表明此时已有极晚期蛋白表达 .说明利用杆状病毒极晚期基因启动子驱动苏云金芽孢杆菌杀虫晶体蛋白基因 (cry)表达 ,从而提高杆状病毒的杀虫毒力是可行的     

Identification of pneumococcal colonization determinants in the stringent response pathway facilitated by genomic diversity

Background

Understanding genetic determinants of a microbial phenotype generally involves creating and comparing isogenic strains differing at the locus of interest, but the naturally existing genomic and phenotypic diversity of microbial populations has rarely been exploited. Here we report use of a diverse collection of 616 carriage isolates of Streptococcus pneumoniae and their genome sequences to help identify a novel determinant of pneumococcal colonization.

Results

A spontaneously arising laboratory variant (SpnYL101) of a capsule-switched TIGR4 strain (TIGR4:19F) showed reduced ability to establish mouse nasal colonization and lower resistance to non-opsonic neutrophil-mediated killing in vitro, a phenotype correlated with in vivo success. Whole genome sequencing revealed 5 single nucleotide polymorphisms (SNPs) affecting 4 genes in SpnYL101 relative to its ancestor. To evaluate the effect of variation in each gene, we performed an in silico screen of 616 previously published genome sequences to identify pairs of closely-related, serotype-matched isolates that differ at the gene of interest, and compared their resistance to neutrophil-killing. This method allowed rapid examination of multiple candidate genes and found phenotypic differences apparently associated with variation in SP_1645, a RelA/ SpoT homolog (RSH) involved in the stringent response. To establish causality, the alleles corresponding to SP_1645 were switched between the TIGR4:19F and SpnYL101. The wild-type SP_1645 conferred higher resistance to neutrophil-killing and competitiveness in mouse colonization. Using a similar strategy, variation in another RSH gene (TIGR4 locus tag SP_1097) was found to alter resistance to neutrophil-killing.

Conclusions

These results indicate that analysis of naturally existing genomic diversity complements traditional genetics approaches to accelerate genotype-phenotype analysis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1573-6) contains supplementary material, which is available to authorized users.     

The purB gene controls rhizosphere colonization by Pantoea agglomerans

Aims: To isolate the rhizosphere competence‐defective transposon Tn5 mutant of Pantoea agglomerans NBRISRM (SRM) and to identify the gene causing defect in its root colonization ability. Methods and Results: From over 5000 clones containing Tn5, one mutant P. agglomerans NBRISRMT (SRMT) showing 6 log units less colonization when compared with SRM, after 30 days in sand‐nonsterilized soil assay system was selected for further work to determine the effects of the mutation on rhizosphere competence. Southern hybridization analysis of restricted genomic DNA of SRMT demonstrated that the mutant had a single Tn5 insert. SRM increased in titre to about 2 × 10⁸ CFU g^?1 root, compared with the indigenous bacterial population of heterotrophs of about 5 × 10⁷ CFU g^?1 root. In contrast, 30 days later, the titre value of SRMT was almost undetectable at 1 × 10² CFU g^?1 root, demonstrating its inability to survive and colonize the rhizosphere. Sequencing of the flanking region of the Tn5 mutant revealed that Tn5 disrupted the purB gene. Conclusions: A defect in the colonization phenotype of the SRMT was attributed to the disruption in adenylosuccinate lyase (EC 4.3.2.2) which is encoded by the pur B gene and is required for rhizosphere colonization in P. agglomerans. Significantly less exopolysaccharide and biofilm was formed by SRMT when compared to SRM, because of the disruption of the purB gene. Significance and Impact of the Study: This work provides the first evidence for a functional role of purB gene in rhizosphere competence and root colonization by any rhizobacteria.     

Monitoring the colonization of sugarcane and rice plants by the endophytic diazotrophic bacterium Gluconacetobacter diazotrophicus marked with gfp and gusA reporter genes

Aims: To evaluate the colonization process of sugarcane plantlets and hydroponically grown rice seedlings by Gluconacetobacter diazotrophicus strain PAL5 marked with the gusA and gfp reporter genes. Methods and Results: Sugarcane plantlets inoculated in vitro with PAL5 carrying the gfp::gusA plasmid pHRGFPGUS did not present green fluorescence, but β‐glucuronidase (GUS)‐stained bacteria could be observed inside sugarcane roots. To complement this existing inoculation methodology for micropropagated sugarcane with a more rapid colonization assay, we employed hydroponically grown gnotobiotic rice seedlings to study PAL5–plant interaction. PAL5 could be isolated from the root surface (10⁸ CFU g^?1) and from surface‐disinfected root and stem tissues (10⁴ CFU g^?1) of inoculated plants, suggesting that PAL5 colonized the internal plant tissues. Light microscopy confirmed the presence of bacteria inside the root tissue. After inoculation of rice plantlets with PAL5 marked with the gfp plasmid pHRGFPTC, bright green fluorescent bacteria could be seen colonizing the rice root surface, mainly at the sites of lateral root emergence, at root caps and on root hairs. Conclusion: The plasmids pHRGFPGUS and pHRGFPTC are valid tools to mark PAL5 and monitor the colonization of micropropagated sugarcane and hydroponic rice seedlings. Significance and Impact of the Study: These tools are of use to: (i) study PAL5 mutants affected in bacteria–plant interactions, (ii) monitor plant colonization in real time and (iii) distinguish PAL5 from other bacteria during the study of mixed inoculants.     

Root and hyphal interactions influence N transfer by arbuscular mycorrhizal fungi in soybean/maize intercropping systems

In maize-soybean intercropping systems, the transfer of N from soybean to maize gives the intercropping system the advantage of improved N utilization and higher yields. Mycorrhiza acts as an important pathway for N transfer, providing a constant supply of N to sustain the growth and development of maize in its early stages. However, it is not clear how arbuscular mycorrhizal fungi (AMF) drive the transfer of N from soybean to maize in the intercropping system. Therefore, we quantified the amount of N transferred from soybean to maize under low and high N levels in the intercropping system, and the abundance and diversity of AMF involved in N transfer (¹⁵N-AMF) under different conditions by ¹⁵N leaf marker and DNA-SIP technology. We found that the interaction between roots and reducing the application of N fertilizer increased the amount of N transfer from soybean to maize. Compared with plastic plate separation (PS), no separation (NS) and mesh separation (MS) significantly increased the N fixation rate (from 14.33% to 39.09%), and the amount of N transfer under NS was 1.95–3.48 times that under MS. N transfer from soybean to maize ranged from 9.7 to 43.42 mg per pot in the no N treatment, while the addition of N fertilizer reduced N transfer by 14.12–66.28%. This is due to root interaction and reduced N fertilization increased the abundance and diversity of the ¹⁵N-AMF community, thereby promoting AMF colonization of maize and soybean roots. AMF colonization in soybean and maize roots under NS treatment was 6.47–17.24% higher than under MS treatment in all three levels of N addition. The increase of mycorrhiza in root system increased the N transfer from soybean to maize significantly. These results suggest that reduced N fertilizer in maize-soybean intercropping systems can increase N transfer by the mycorrhizal pathway, meeting maize N requirements and reducing chemical N fertilizer, which is important for sustainable agricultural development.     

A multilocus perspective on colonization accompanied by selection and gene flow

The colonization of novel habitats involves complex interactions between founder events, selection, and ongoing migration, and can lead to diverse evolutionary outcomes from local extinction to adaptation to speciation. Although there have been several studies of the demography of colonization of remote habitats, less is known about the demographic consequences of colonization of novel habitats within a continuous species range. Populations of the Eastern Fence Lizard, Sceloporus undulatus, are continuously distributed across two dramatic transitions in substrate color in southern New Mexico and have undergone rapid adaptation following colonization of these novel environments. Blanched forms inhabit the gypsum sand dunes of White Sands and melanic forms are found on the black basalt rocks of the Carrizozo lava flow. Each of these habitats formed within the last 10,000 years, allowing comparison of genetic signatures of population history for two independent colonizations from the same source population. We present evidence on phenotypic variation in lizard color, environmental variation in substrate color, and sequence variation for mitochondrial DNA and 19 independent nuclear loci. To confirm the influence of natural selection and gene flow in this system, we show that phenotypic variation is best explained by environmental variation and that neutral genetic variation is related to distance between populations, not partitioned by habitat. The historical demography of colonization was inferred using an Approximate Bayesian Computation (ABC) framework that incorporates known geological information and allows for ongoing migration with the source population. The inferences differed somewhat between mtDNA and nuclear markers, but overall provided strong evidence of historical size reductions in both white sand and black lava populations at the time of colonization. Populations in both novel habitats appear to have undergone partial but incomplete recovery from the initial bottleneck. Both ABC analyses and measures of mtDNA sequence diversity also suggested that population reductions were more severe in the black lava compared to the white sands habitat. Differences observed between habitats may be explained by differences in colonization time, habitat geometry, and strength or response to natural selection for substrate matching. Finally, effective population size reductions in this system appear to be more dramatic when colonization is accompanied by a change in selection regime. Our analyses are consistent with a demographic cost of adaptation to novel environments and show that it is possible to infer aspects of the historical demography of local adaptation even in the presence of ongoing gene flow.     

Extraintestinal infection of Helicobacter cinaedi induced by oral administration to Balb/c mice

Although Helicobacter cinaedi was initially considered an opportunistic pathogen in immunocompromised patients, it was later shown to also infect immunocompetent and healthy individuals. Sporadic bacteremia due to H. cinaedi has frequently been reported; however, whether the bacterium can be translocated after passage through the intestinal mucosa remains unclear. In the present study, a preclinical small animal model that faithfully reproduces H. cinaedi infection in humans was developed. Balb/c male mice were orally inoculated with a single dose of 6.8 × 10⁷ CFU of a human clinical H. cinaedi strain. The organism persistently colonized the intestinal tract of the mice, particularly the cecum and colon, for at least 56 days, and the bacteria were excreted in the feces. Although inoculated bacteria were recovered from the spleen, liver, kidney, lung, bladder and mesenteric lymph nodes during the first 2 weeks of bacteremia, the organism was not isolated from these organs after 4 weeks, suggesting that complement‐ and antibody‐mediated serum sensitivity account for the relatively low frequency of systemic infection. However, H. cinaedi was isolated from the biceps femoris, triceps branchii, latissimus dorsi, and trapezius muscles beyond 2 weeks after infection and after production of specific anti‐H. cinaedi IgM and IgG antibodies. The present findings suggest that experimental infection of Balb/c mice with H. cinaedi may be a useful model for further studies of H. cinaedi pathogenesis, prophylaxis or therapeutic interventions in vivo.     

Resistance to bacitracin in Streptococcus pyogenes from oropharyngeal colonization and noninvasive infections in Portugal was caused by two clones of distinct virulence genotypes

During 2000–2007 in Lisbon, we identified 45 bacitracin-resistant Streptococcus pyogenes isolates among 1629 isolates: 24 from oropharyngeal healthy carriers (out of 1026), 21 from patients with noninvasive infections (out of 559) and zero from invasive infections (out of 44). Forty-four of those isolates, mainly of colonization, are low-level bacitracin-resistant members of the cMLS_B-macrolide-resistant and tetracycline-susceptible emm 28/ST52 clone previously detected in Europe, but only among clinical samples. One high-level bacitracin-resistant isolate, associated with a tonsillitis/pharyngitis episode, is cMLS_B-macrolide-resistant and tetracycline-resistant member of the emm 74/ST120 lineage, which was not previously known to include bacitracin-resistant isolates. The bcrABDR operon encoding an ATP-binding cassette transporter in Enterococcus faecalis was not detected among these bacitracin-resistant S. pyogenes strains. Virulence profiling indicated that genes coding for exotoxins and superantigens seem to be clone specific. This study provides an increased knowledge about specific bacitracin-resistant S. pyogenes strains, which may be useful in future investigations aiming to understand the mechanism(s) leading to bacitracin resistance and the cause(s) for differences in colonization and/or dissemination potential.     

AMF colonization and community of a temperate invader and co-occurring natives grown under different CO2 concentrations for 3 years

连续3年不同CO₂浓度下一种温带外来入侵植物和两种共存本地植物丛枝菌根真菌群落及侵染率 大气CO₂浓度升高等全球变化过程不仅能促进外来植物入侵,也能改变土壤丛枝菌根真菌(AMF)的群落结构,但我们并不清楚大气CO₂浓度升高促进外来植物入侵是否与其对外来入侵植物和 本地植物AMF共生的影响有关。为回答这一问题,我们在环境和倍增CO₂浓度下连续3年栽培一年生外来入侵植物瘤突苍耳(Xanthium strumarium)与两种共存的一年生本地近缘植物,比较了AMF侵染率、土 壤养分和土壤AMF群落组成的差异。研究结果表明,大气CO₂浓度升高只在少数情况下提高根系AMF侵染率,并且瘤突苍耳AMF侵染率的提高并不比本地种多。在环境CO₂浓度下,栽培第一年瘤突苍耳的AMF侵染侵染率显著高于两种本地植物;而栽培第二年和第三年与两种本地植物的差异不显著,因为两种本地植物的AMF侵染率随种植时间的增加而增加,而瘤突苍耳AMF侵染率受种植时间的影响较小。物种、CO₂浓度和种植时间对AMF侵染率的影响与它们对土壤养分和AMF群落的影响有关,土壤养分对AMF侵染率的影响可能比AMF群落组成的影响更大,因为后者也受土壤养分的影响。上述结果表明,与本地植物相比,入侵植物能更快地与AMF形成共生关系,有利于其适应和入侵新生境;在探究全球变化如大气CO₂浓度升高等对外来植物入侵的影响时,需要考虑AMF的影响和时间效应。