Effects of Cinnamic Acid on Bacterial Community Diversity in Rhizosphere Soil of Cucumber Seedlings Under Salt Stress

To investigate the effects of a plant autotoxin, cinnamic acid, on bacterial communities in the rhizosphere soil of cucumber seedlings under salt stress, we used cucumber as the experimental material, cinnamic acid as the autotoxin, and NaCl to apply salt stress. Bacterial communities in the rhizosphere soil were analyzed using polymerase chain reaction （PCR）, denaturing gradient gel electrophoresis （DGGE）, and clone sequencing. Salt stress decreased the diversity of bacterial species in rhizosphere soil of cucumber seedlings at several growth stages. Cinnamic acid exacerbated the effects of salt stress at high concentrations, but alleviated its effects at low concentrations. Cloning and sequencing results indicated that DGGE bands amplified from soil samples showed high homology to uncultured bacterial species. Cinnamic acid at 50 mg kg^-1 soil improved cucumber growth and was the most effective treatment to alleviate the effects of salt stress on bacterial communities.     

Soil fumigation and compost amendment alter soil microbial community composition but do not improve tree growth or yield in an apple replant site

Apple replant disease (ARD) is a disease complex that reduces survival, growth and yield of replanted trees, and is often encountered in establishing new orchards on old sites. Methyl bromide (MB) has been the fumigant used most widely to control ARD, but alternatives to MB and cultural methods of control are needed. In this experiment, we evaluated the response of soil microbial communities and tree growth and yield to three pre-plant soil treatments (compost amendment, soil treatment with a broad-spectrum fumigant, and untreated controls), and use of five clonal rootstock genotypes (M.7, M.26, CG.6210, G.30 and G.16), in an apple replant site in Ithaca, New York. Polymerase chain reaction (PCR)—denaturing gradient gel electrophoresis (DGGE) analysis was used to assess changes in the community composition of bacteria and fungi in the bulk soil 8, 10, 18 and 22 months after trees were replanted. PCR-DGGE was also used to compare the community composition of bacteria, fungi and pseudomonads in untreated rhizosphere soil of the five rootstock genotypes 31 months after planting. Tree caliper and extension growth were measured annually in November from 2002 to 2004. Apple yield data were recorded in 2004, the first fruiting year after planting. Trees on CG.6210 rootstocks had the most growth and highest yield, while trees on M.26 rootstocks had the least growth and lowest yield. Tree growth and yield were not affected by pre-plant soil treatment except for lateral extension growth, which was longer in trees growing in compost-treated soil in 2003 as compared to those in the fumigation treatment. Bulk soil bacterial PCR-DGGE fingerprints differed strongly among the different soil treatments 1 year after their application, with the fingerprints derived from each pre-plant soil treatment clustering separately in a hierarchical cluster analysis. However, the differences in bacterial communities between the soil treatments diminished during the second year after planting. Soil fungal communities converged more rapidly than bacterial communities, with no discernable pattern related to pre-plant soil treatments 10 months after replanting. Changes in bulk soil bacterial and fungal communities in response to soil treatments had no obvious correlation with tree performance. On the other hand, rootstock genotypes modified their rhizosphere environments which differed significantly in their bacterial, pseudomonad, fungal and oomycete communities. Cluster analysis of PCR-DGGE fingerprints of fungal and pseudomonad rhizosphere community DNA revealed two distinct clusters. For both analyses, soil sampled from the rhizosphere of the two higher yielding rootstock genotypes clustered together, while the lower yielding rootstock genotypes also clustered together. These results suggest that the fungal and pseudomonad communities that have developed in the rhizosphere of the different rootstock genotypes may be one factor influencing tree growth and yield at this apple replant site.     

原料差异对厌氧消化微生物群落的影响

以餐厨垃圾、果蔬垃圾、麦秸3种不同原料分别进行厌氧消化,研究了各反应器在最佳运行条件下的消化特性和微生物群落组成。结果表明:VS产气率由高到低依次为餐厨垃圾(756.4mL·g-1VS-1)、麦秸(696.5mL·g-1VS-1)和果蔬垃圾(433.5mL·g-1VS-1),甲烷含量在51.5%～55.1%之间,利用PCR-DGGE技术系统地分析了不同原料消化系统内细菌和古菌的群落结构构成及差异。结果表明,虽然3组样品中细菌和古菌的群落存在相同的优势微生物,但其数量和群落结构差异也较为明显,细菌中以拟杆菌(Bacteroidetes)以及古菌中甲烷鬃菌属(Methanosaeta)和甲烷螺菌属(Methanospirillum)均为样品共有的优势微生物。     

PCR-DGGE的原理及在动物肠道菌群分析中的应用

肠道菌群是机体常在菌群的重要组成部分,机体的健康和疾病的发生和发展与其多样性及种群的变化有着密切关系。因此,对肠道菌群进行研究具有重要意义。变性梯度凝胶电泳(DGGE)主要是基于突变型和野生型核酸序列的不同而导致其变性浓度的差异,利用变性梯度胶进行分离。它是一种分析微生物群落的有效工具,可以用于研究肠道菌群结构多样性和种群结构的变化。作者对PCR-DGGE的原理、优缺点及在动物肠道菌群分析中的应用和前景作一简要综述。     

应用PCR-DGGE分析南美白对虾肠道微生物多样性

从南美白对虾肠道中提取微生物基因组总DNA,以细菌16SrRNA基因通用引物341F/534R进行V3高变异区域PCR扩增,长约200bp的PCR产物纯化后经变性梯度凝胶电泳(DGGE)分离,获得微生物群落的特征DNA指纹图谱。通过DGGE图谱的半定量分析,发现样品的优势群落明显。结果表明,PCR-DGGE是研究水产动物肠道微生物多样性的可行方法。     

抗生素对桉树内生细菌群落及青枯病抗性的影响

 为了探明桉树内生细菌群落变化与桉树对青枯病抗性间的关系,试验用加入抗生素的培养基继代培养尾叶桉组培苗,采用PCR-DGGE技术检测了经抗生素处理后桉苗内生细菌的变化,并测定其对青枯病的抗性。结果显示,浓度为60 mg·L^-1的氯霉素和150 mg·L^-1的氨苄青霉素显著降低了桉树组培苗根部内生细菌的数量,但对茎、叶中内生细菌的数量没有影响。DGGE图谱显示,氨苄青霉素处理的桉苗与对照苗的条带基本一致,氯霉素处理后与对照条带有明显的区别,表明氨苄青霉素只影响了桉苗内生细菌的数量,氯霉素使桉苗内生细菌的优势菌发生了变化。对DGGE条带克隆测序和Blast比对发现,A、B、C条带的序列(KU363009、KU363010和KU363011)与GenBank中不可培养细菌的序列(KJ655389.1、KF006350.1和FJ832152.1)相似性分别为100%、99%和99%;D条带序列(KU363012)与不可培养的色球藻属(Chroococcidiopsis sp.)序列(LN878320.1)相似性达到98%。氨苄青霉素和氯霉素处理后,桉苗青枯病的初发病时间与对照相比延后1~2 d,氨苄青霉素处理的桉苗发病率显著低于对照。氯霉素处理的前6 d发病率显著低于对照,之后发病率急剧上升与对照无显著差异。上述结果表明,氨苄青霉素和氯霉素可以减少桉苗根中内生细菌的数量,并推迟桉树青枯病的发病时间。     

Nitrogen availability decreases prokaryotic diversity in sandy soils

In this study, the interrelation between nitrogen availability and prokaryotic diversity are studied using a well-characterised system from a long-term field experiment on a loamy sandy soil. The prokaryotic potential functional diversity and community composition were assessed using community-level physiological profiling (CLPP), and their phylogenetic diversity was analysed using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) in combination with sequencing analysis. Highest prokaryotic potential functional diversity was measured in the control soil receiving no N fertilisation, indicating an efficient as well as versatile utilisation of the substrates in this soil. Both substrate utilisation richness and substrate utilisation evenness, the two constituents of the functional diversity, were decreased with increasing N supply. Furthermore, distinct prokaryotic community compositions were generated in N-enriched soils compared to unfertilised control soils. These differences suggest a dominance of populations adapted to utilising readily available substrates. We demonstrated that the shift in prokaryotic functional diversity was connected to a shift in the phylogenetic structure of the bacterial and archaeal communities. Taken together, our data clearly show that, for the sandy soil system, prokaryotic diversity and N availability were interrelated.     

PCR-DGGE技术用于猪场沼气池细菌群落分析的条件优化

本研究采用变性梯度凝胶电泳（PCR-DGGE）技术研究猪场沼气池细菌群落,对基于16S rDNAV3区的PCR-DGGE电泳的最佳变性剂梯度范围、电泳时间、染色时间进行优化。研究结果表明,最佳变性剂梯度范围为35%～60%,电泳时间为12h,SYBR Green Fluorescent Dye染料的染色时间是30min,优化后的PCR-DGGE确保了实验的准确性、灵敏度和可重复性。运用此优化后的PCR-DGGE技术对5个猪场沼液细菌群落进行了研究,获得了较丰富的多样性。该实验为深入研究畜禽养殖粪污治理的菌种筛选奠定了基础。     

土壤与基质栽培系统对生菜(Lactuca sativa)根际细菌群落的影响

以生菜（Lactuca sativa）“申选5号”与“罗莎红”为材料,采用PCR-DGGE 和Real-Time PCR 技术,分析了土壤栽培系统和基质栽培系统根际细菌群落的差异。Real-Time PCR 检测结果表明,基质栽培的两个生菜品种根际细菌数量均显著高于土壤（P<0.05）;PCR-DGGE图谱条带结果表明,根际细菌群落多样性基质高于土壤。栽培系统是造成多样性差异的主要原因,但也与品种有关：“申选5 号”基质的Shannon-Wiener 指数（H）,Simpson 指数（D）和均匀度（E）均显著高于土壤（P<0.05）;“罗莎红”基质的H 显著高于土壤,而D和E 无显著差异。结合土壤和基质理化性质的RDA 分析结果,土壤和基质具有不同的细菌群落,pH 值与硝态氮是塑造根际细菌群落的主要因子,含水量、碳氮比和有效磷与细菌群落的形成呈正相关。     

接种溶磷真菌对玉米和大豆根际细菌群落结构多样性的影响

Application of phosphate-solubilizing microorganisms （PSMs） has been reported to increase P uptake and plant growth. However, no information is available regarding the ecological consequences of the inoculation with PSMs. The effect of inoculation with phosphate-solubilizing fungal （PSF） isolates Aspergillus niger P39 and Penicillium oxalicum P66 on the bacterial communities in the rhizospheres of maize （Zea mays L. ‘Haiyu 6＇） and soybean （Glycine max Merr. ‘Heinong 35＇） was examined using culture-dependent methods as well as a culture-independent method, polymerase chain reaction-denaturing gradient gel electrophoresis （PCR-DGGE）. Compared with the control, the number of culturable microbes for soybean was significantly greater with P39, whereas for maize, the same was significantly greater with P66. In addition, a greater number of microbes were found in the rhizosphere of maize compared with soybean. The fingerprint of DGGE for 16S rDNA indicated that inoculation with PSF also increased bacterial communities, with the P66 treatment having higher numbers of DGGE bands and a higher Shannon-Weaver diversity index compared with P39; the composition of the microbial community was also more complex with the P66 treatment. Overall, complex interactions between plant species and exotic PSMs affected the structure of the bacterial community in the rhizosphere, but plant species were more important in determining the bacterial community structure than the introduction of exotic microorganisms.