Unique community structure of viruses in a glacier soil of the Tianshan Mountains,China

Purpose

Glaciers of the Tianshan Mountains have been geographically isolated for a long time with little human interference. This study aimed to understand the viral community structures and their ecological functions in a unique glacier soil.

Materials and methods

The abundances of purified virus particles and bacteria in the glacier soil were examined using epifluorescence microscopy and quantitative PCR of the 16S rRNA gene, respectively. Metagenomic analysis was employed to investigate the taxonomic and functional compositions as well as the phylogenetic relationship of the functional genes of the viruses in the glacier soil.

Results and discussion

A total of eight double-stranded DNA (dsDNA) virus families were identified in the glacier soil, with Siphoviridae, Podoviridae, and Myoviridae being the more abundant families. The diverse dsDNA viruses and few ssDNA and other types of viruses formed the unique community structure of viruses in the Tianshan Mountains glacier soil. The functional genes identified from the virome mainly belonged to phage-related proteins. The phage terminase of Caudovirales presented high diversity, and its amino acid sequences were different from those in other environments.

Conclusions

The results showed a unique viral diversity and taxonomic composition in the glacier soil, which suggests the significant ecological role of Caudovirales in this environment.

     

Distributions and environmental drivers of archaea and bacteria in paddy soils

Purpose

The aim of this study is to investigate the abundance, diversity, and distribution of archaea and bacteria as affected by environment parameters in paddy soils, with focus on putative functional microbial groups related to redox processes. Because there is generally a high iron content in the soil, we also want to test a hypothesis that soil iron concentration significantly affects microbial diversity and distribution.

Materials and methods

Quantitative PCR and barcoded pyrosequencing of 16S ribosomal RNA genes were employed to investigate the abundance and community composition of archaeal and bacterial communities in 27 surface paddy soil samples. Pearson’s correlation, analysis of variance, partial least squares regression, principal coordinates analysis, and structural equation models were performed for the analyses of gene copy numbers, α-diversity, β-diversity, and relative abundances of archaea and bacteria and their relationships with environmental factors.

Results and discussion

Archaeal abundance was correlated greatest with temperature, but bacterial abundance was affected mainly by soil organic matter and total nitrogen content. Soil pH and concentrations of different ions were associated with archaeal and bacterial β-diversity. The relative abundances of Euryarchaeota and Thaumarchaeota were 61.3 and 13.1% of archaea and correlated with soil pH, which may affect the availability of substrates to methanogens and ammonia oxidizers. Dominant bacterial phyla were Proteobacteria (32.4%), Acidobacteria (17.8%), Bacteroidetes (9.3%), and Verrucomicrobia (6.0%). The relative abundances of putative bacterial reducers of nitrate, Fe(III), sulfate, and sulfur, and oxidizers of ammonia, nitrite, reduced sulfur, and C1 compounds had positive, negative, or non-significant correlations with the concentrations of their substrates. Soil iron concentration was correlated only with the distributions of some putative iron-reducing bacteria.

Conclusions

In paddy soils characterized by dynamic redox processes, archaea and bacteria differ in relationships of abundance, diversity, and distribution with environmental factors. Especially, the concentrations of electron donors or acceptors can explain the distributions of some but not all the putative functional microbial groups related to redox processes. Depending on pH range, soil pH has a strong impact on microbial ecology in paddy soils.

     

铝胁迫条件下小麦根系特异表达基因的研究

利用尼龙膜点阵杂交技术,由耐铝胁迫小麦品系OK91G106根系构建的cDNA差减杂交文库中,鉴定出29个铝胁迫特异诱导基因,包括20个已知生物学功能的基因和9个功能未知基因。这20个已知功能基因归属于植物体内细胞信号转导、活性氧清除、维持膜结构稳定、苹果酸分泌和细胞保护等等类别。表明在铝胁迫下,植株体内在短时间内发生了感受铝胁迫逆境信号并进行了信号转导,调控了植株对铝胁迫逆境响应的复杂分子生物学过程。Northern印迹对5个铝诱导基因转录本的检测结果与尼龙膜点阵技术获得的结果相一致。本研究鉴定出的铝诱导基因中含有1个苹果酸转运蛋白基因,表明苹果酸分泌量的增加可能是供试小麦响应和抵御铝胁迫逆境的重要机制之一。     

小麦应答低磷的钙依赖蛋白激酶基因TaCPK1A和TaCPK10的克隆和表达

采用构建富集磷胁迫特异表达基因cDNA差减文库、序列分析和cDNA-AFLP技术,鉴定了2个应答低磷胁迫的钙依赖蛋白激酶(CDPK)基因的表达序列标签。克隆、测序和比对结果表明,上述基因分别为TaCPK1A和TaCPK10。其cDNA长度分别为2 129 bp和1 696 bp,开放阅读框分别为1 599 bp和1 281 bp,分别编码532和426个氨基酸;具有CDPK的典型结构特征。系统进化分析表明,上述基因的核苷酸序列同源性低,分别来自不同的祖先。在对低磷胁迫的响应上,TaCPK1A在磷胁迫1~24 h范围内根系内的表达水平不断增强,叶内表达水平在1 h内明显被诱导,以后保持稳定;TaCPK10在相应磷胁迫时间范围根叶内的表达水平均呈低—高—低变化,在磷胁迫1 h的表达被诱导,以后又逐渐降至胁迫前水平。TaCPK1A和TaCPK10对氮、钾胁迫没有应答响应。结果表明,CDPK在介导小麦低磷胁迫的信号转导中具有重要作用,小麦中存在两种或多种CDPK介导的磷酸化过程参与低磷信号的转导。     

BMPR-IB和BMP15基因作为湖羊多胎性候选基因的研究

以绵羊BMPR-IB和BMP15基因作为候选基因,以湖羊为研究对象,采用PCR-RFLP方法分析两个基因在湖羊中的多态性。结果发现,湖羊均是BMPR-IB基因突变纯合体(BB),而不带有BMP15突变基因,说明BMPR-IB和BMP15基因并非湖羊多胎性能的主基因。但是,选育后的湖羊总产羔率和第一、第二胎平均产羔数显著高于未经选育的群体,湖羊多胎性状客观存在,其分子机制还需进一步研究。