Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by geographic features

Here, we examine soil-borne microbial biogeography as a function of the features that define an American Viticultural Area (AVA), a geographically delimited American wine grape-growing region, defined for its distinguishing features of climate, geology, soils, physical features (topography and water), and elevation. In doing so, we lay a foundation upon which to link the terroir of wine back to the soil-borne microbial communities. The objective of this study is to elucidate the hierarchy of drivers of soil bacterial community structure in wine grape vineyards in Napa Valley, California. We measured differences in the soil bacterial and archaeal community composition and diversity by sequencing the fourth variable region of the small subunit ribosomal RNA gene (16S V4 rDNA). Soil bacterial communities were structured with respect to soil properties and AVA, demonstrating the complexity of soil microbial biogeography at the landscape scale and within the single land-use type. Location and edaphic variables that distinguish AVAs were the strongest explanatory factors for soil microbial community structure. Notably, the relationship with TC and TN of the <53 μm and 53–250 μm soil fractions offers support for the role of bacterial community structure rather than individual taxa on fine soil organic matter content. We reason that AVA, climate, and topography each affect soil microbial communities through their suite of impacts on soil properties. The identification of distinctive soil microbial communities associated with a given AVA lends support to the idea that soil microbial communities form a key in linking wine terroir back to the biotic components of the soil environment, suggesting that the relationship between soil microbial communities and wine terroir should be examined further.     

Wood ash fertilization alters the forest humus Archaea community

The combined and separate effects of Cd and wood ash on Archaea from coniferous forest humus were studied in a microcosm experiment. Nonmetric multidimensional scaling of the denaturing gradient gel analysis of polymerase chain reaction amplified 0.9 kb 16S ribosomal DNA fragments revealed changes in archaeal communities due to the ash treatments. Cd with or without ash did not further influence the result. Representatives of the ash and control communities were cloned, grouped by restriction fragment length polymorphism analysis and finally sequenced. All sequences belonged to non-thermophilic Crenarchaea.     

The origin of the A genome donor of wheats (Triticum: Poaceae) – a perspective based on the sequence variation of the 5S DNA gene units

In a prior study on the haplomes of wheat using the 5S rRNA gene we assigned the long A1 and short A1 unit classes to the A haplome in the diploid T. monococcum. The short A1 unit class is absent in the tetraploids T. turgidum and T. timopheevii and in the hexaploid T. aestivum, although present in the hexaploid T. zhukovskyi. Both T. turgidum and T. aestivum contained a different 5S DNA unit class labeled the short A2.The purpose of this paper was to study the short A2 units in the two diploid species to shed light on the theory that the A haplome donor of T. turgidum and T. aestivum was T. urartu. Fifty eight clones were obtained from 12 accessions, sequenced and analyzed. As expected T. baeoticum, which is often classified as a subspecies of T. monococcum, contained the long A1 and the short A1 5S DNA units. Unexpectedly, T. urartu had the long A1 and the short G1 unit classes instead and other units not found so far in Triticum. These findings support the hypothesis that the donor of the A genome in T. zhukovskyi was T. monococcum, as identified by the short A1 units. However, the short A1 units are absent in T. timopheevii, also a carrier of the A genome. The short G1 units found in T. urartu also identify it as a possible donor of the G genome to T. timopheevii. The short G1 units were also found in T. aestivum in our prior study. The long G1 unit class was not found in T. urartu but reported from T. timopheevii and T. zhukovskyi. The implications of these and related findings on the evolution of wheats are discussed.     

一株分离自葛藤根际高效溶磷细菌特性研究及菌株鉴定

对分离自葛藤(Pueraria lobata L.)根际的一株高效溶磷细菌GTR15进行促生特性、主要生理生化指标测定和16S rDNA序列分析。结果表明,菌株GTR15的HD/CD值(溶磷圈直径HD,菌落直径CD)为2.22,28℃液体振荡培养7 d后对磷酸钙的溶解量为138.72 mg.L-1,分泌IAA(3-吲哚乙酸)及有机酸量分别为14.44 mg.L-1、46.00 mmol.L-1。菌株革兰氏染色为阴性,细胞短杆状;淀粉水解、吲哚、V-P(二乙酰试验)、苯丙氨酸脱氨酶、明胶液化及M-R(甲基红)试验呈阴性;柠檬酸盐、过氧化氢酶、硫化氢及硝酸盐还原等试验呈阳性,结合菌株16S rDNA序列分析结果,初步鉴定为肠杆菌(Enterobacter sp.)。该菌株在研制高效微生物磷肥接种剂方面可能具有较大潜力。     

沙田柚黄龙病病原16S rDNA片段的克隆与序列分析

采集田间表现斑驳症状的沙田柚叶脉,用CTAB法提取总DNA。根据柑橘黄龙病病原16S rDNA的核苷酸序列设计引物P1/P2,进行PCR扩增,获得1条大小为1 167 bp的片段。酶切分析显示,该片段可被切成大小分别约为640 bp和520 bp的2个片段。扩增产物经纯化,与pM D 18-T V ector连接,转化大肠杆菌(E scherich ia coli)DH 5α,筛选克隆重组子。对PCR产物进行测序及序列分析,结果表明,与柑橘黄龙病病原亚洲种16S rDNA的同源性为99%,与非洲种的同源性为97%,与美洲种的同源性为96%。认为,沙田柚的斑驳症状是由黄龙病病原引致的,称之为沙田柚黄龙病。该沙田柚黄龙病病原属于柑橘黄龙病病原亚洲种(L iberobacter as iaticus)中的一个成员。系统进化树分析显示,沙田柚黄龙病病原与中国柑橘黄龙病病原亲缘关系最近,推测是直接来自中国柑橘黄龙病病原。     

Influence of repeated prescribed burning on the soil fungal community in an eastern Australian wet sclerophyll forest

A long-term prescribed burning experiment, incorporating replicated plots that receive burning biennially (2 yr burn) or quadrennially (4 yr burn) and unburned controls, has been maintained in a wet sclerophyll forest at Peachester, Queensland, Australia since 1972. In 2003 we extracted DNA from soil collected from the experimental plots and investigated the influence of the burning on the soil fungal community by comparing denaturing gradient gel electrophoresis (DGGE) profiles of PCR-amplified partial rDNA internal transcribed spacer regions (ITS1). Canonical analysis of principal coordinates (CAP) of the DGGE profiles of the upper 10 cm of the soil profile grouped the data strongly according to treatment, indicating that both burning regimes significantly altered fungal community structure compared to the unburned controls. In contrast, no obvious trend was observed for soil from a depth of 10-20 cm of the profile. Sequencing of selected DGGE bands found no obvious patterns of presence/absence of taxonomic groups between the treatments. Analysis of soil nitrogen and carbon by mass spectrometry indicated that total soil C and N, along with both gross and net N mineralisation, were significantly lower in 2 yr plots compared to control and 4 yr plots.     

高产水稻土细菌多样性的培养法与非培养法比较研究

利用细菌的通用引物扩增江西余江县高产水稻土红壤细菌总DNA和平板培养细菌混合总DNA的16S rDNA基因片段,在此基础上分别建立两种16S rDNA文库(文库a和文库b)。从两个文库中各随机挑选100个克隆,扩增出阳性克隆中的插入片段后选用HhaⅠ和RsaⅠ两种四碱基酶进行ARDRA(amplified rDNA restriction analysis)分析。统计比较分析发现,文库a的Shannon-Wienner指数、Simpson指数、丰富度、均一度分别为4.432、0.987、18.885和0.973,均高于文库b中相应的多样性参数(分别为2.271、0.758、5.736和0.501),即平板培养方法所展现的细菌群落结构多样性低于土壤中原始的多样性。结果表明,传统培养方法存在着很大的局限性,必须结合新的分子生物学技术手段才能更全面完善地认识土壤微生物群落结构多样性,以期充分利用其中丰富的微生物资源。     

植物内生菌研究进展及其存在的问题

\t\t\t\t\t目的\t\t\t\t\t植物内生菌(Endophyte)是近年来深受重视的一种新型的微生物能源,具有固氮、促进植物生长、增强宿主植物抗逆性等作用,目前研究表明：内生菌可增强宿主植物合成活性物质的能力,甚至它们本身也能产生与宿主植物相同或相近的生物活性物质。\t\t\t\t\t\t\t\t\t\t\t\t\t方法\t\t\t\t\t以传统药用植物滇重楼(Pairs polyphylla var.yunnanensis)为研究对象,从滇重楼地下块茎中分离得到23株内生菌,对其进行分子鉴定,之后与滇重楼组培苗进行共生培养,一段时间后利用高效液相色谱法检测组培苗的皂苷含量。\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t结果\t\t\t\t\t最终筛选出2株对滇重楼组培苗皂苷含量有促进作用的菌株。\t\t\t\t\t\t\t\t\t\t\t\t\t结论\t\t\t\t\t人参生柱隔孢和木霉菌能促进滇重楼皂苷类活性成分的积累。\t\t\t\t     

覆土细菌群落在双孢菇栽培过程中的动态变化

微生物尤其是细菌,是双孢菇Agaricus bisporus栽培覆土的重要组成部分,对双孢菇菌丝体和子实体的生长发育有深远影响。利用16S rDNA测序技术,快速、准确检测不同生长阶段的双孢菇覆土中细菌生态群落动态变化,探究其中变化规律。在所有阶段覆土样品中,变形菌门Proteobacteria占据绝对主导地位,占菌群组成的38.67%～47.93%;其次是拟杆菌门Bacteroidetes,占总丰度的18.13%～37.80%。主要细菌组成较为稳定,有金黄杆菌属Chryseobacterium、鞘氨醇单胞菌属Sphingomonas、黄杆菌属Flavobacterium、丛毛单胞菌属Comamonas、节杆菌属Arthrobacter等。总丰度占比最高的金黄杆菌属Chryseobacterium,在0 d覆土中丰度较低,覆土4 d时其丰度显著上升,8 d后呈下降趋势,并在培养结束前保持稳定。整个过程中,细菌属丰度变化分为3个阶段：0 d、4～17 d和17 d以后,4～17 d的苯基杆菌属Phenylobacterium丰度较高,而0 d 的unclassified_Rhizobiales丰度较高。所有细菌属中,苯基杆菌属Phenylobacterium对土壤微生物菌群关联影响最大。     

基于ITS和形态学系统分析新疆桦木属种间系统发育关系

以新疆桦木属的6个种和其他10种桦木属植物为材料,利用Clustal Omega和MEGA 7.0软件对ITS基因序列进行遗传分析,同时利用SPSS 25.0软件对7个形态性状进行主成分和聚类分析,探讨新疆桦木属植物的系统发育关系。结果表明：在ITS遗传演化分析中,新疆桦木属中的桦木亚组和柴桦亚组遗传距离较近,为0.0047,桦木亚组内部绝对遗传距离为0.0060;在形态性状主成分分析中,特征值大于1的累计贡献率为84.5%,桦木属植物分类性状主要取决于生活型、叶片形状、果苞背部被毛、树皮剥裂及纹路;新疆桦木属植物ITS序列和形态学聚类结果基本一致,盐桦与甸生桦聚为一组,与《中国植物志》中盐桦归属于桦木亚组,而甸生桦属于柴桦亚组的分类存在一定差异,但与《新疆植物志》中两者被划分在柴桦亚组的结论有相似之处。