乌鲁木齐地震断裂带泉水古菌群落对水文地球化学元素的响应

[目的]揭示乌鲁木齐地震断裂带泉水中古菌群落对水文地球化学元素变化的响应.[方法]采用微孔滤膜法收集泉水中菌体,直接提取环境总DNA,嵌套式PCR扩增古菌16S rDNA基因V3区,变性梯度凝胶电泳(DGCE)检测古菌群落结构的变化,所得信息与监测的地球化学指标进行典型相关分析.[结果]DGGE分析及切胶测序共得到古菌14个主要类群,分属于广域古菌和泉古菌两个门,全部为不可培养类群,其中前者占绝对优势.典型相关性分析发现类群B-11和B-12与He以及CH<,4>含量呈正相关,与硫化物呈负相关;类群B-2、B-3和B-9与F<'->离子含量成正相关而类群B-13与它呈负相关;而仅有的泉古菌B-7与CH呈负相关.另外,所得绝大部分古菌类群与其它冷泉或者低温环境中发现的古菌类群具有95;左右的相似性.[结论]乌鲁木齐断裂带泉水古菌群落能够对泉水中的某些地球化学元素变化产生一定的响应,并且可能存在大量嗜冷新类群.     

The Introduction of Woody Plants for Freshwater Wetland Restoration Alters the Archaeal Community Structure in Soil

Due to the severe degradation of wetland ecosystems in China, great efforts, such as the reconstruction of forested wetlands, have been devoted to restore the damaged and degraded wetlands to support species diversity and ecosystem services. However, less attention has been given to the diversity and ecological significance of prokaryotes of the domain Archaea compared with prokaryotes of the domain Bacteria during the reconstruction of forested wetlands. Here, the effects of introduced woody plants (Taxodium distichum and Alnus trabeculosa ) on the archaeal community in a freshwater wetland in the Yangtze estuary were investigated. The results showed that Thaumarchaeota obviously predominated at three studied sites in the freshwater wetland, the relative abundance of which decreased with increasing depth, ranging from 93.9% (0–10 cm) to 1.9% (30–40 cm) in mudflats, from 100% (0–10 cm) to 64.8% (30–40 cm) in T. distichum sediment and from 100% (0–10 cm) to 66.7% (40–50 cm) in A. trabeculosa sediment. The abundances of the archaeal amoA gene in woody plant sediments, ranging from 3.27 × 10⁷ to 2.45 × 10⁸ copies g⁻¹ dry soil, were significantly higher than those in bare mudflat, ranging from 9.23 × 10⁶ to 1.35 × 10⁷ copies g⁻¹ dry soil. The archaeal community, which was significantly affected by pH, microbial carbon and SO₄²⁻ contents according to a canonical correspondence analysis, was significantly altered by plants and soil depth (p < 0.05). These results indicated that the introduction of woody plants stimulates the proliferation of Thaumarchaeota, especially ammonia‐oxidizing archaea, which could be important contributors to the N cycle in forested wetland ecosystems. Copyright © 2017 John Wiley & Sons, Ltd.     

Variation of Potential Nitrification and Ammonia-Oxidizing Bacterial Community with Plant-Growing Period in Apple Orchard Soil

In this study, we investigated the potential nitrification and community structure of soil-based ammonia-oxidizing bacteria （AOB） in apple orchard soil during different growth periods and explored the effects of environmental factors on nitrification activity and AOB community composition in the soil of a Hanfu apple orchard, using a culture-dependent technique and denaturing gradient gel electrophoresis （DGGE）. We observed that nitrification activity and AOB abundance were the highest in November, lower in May, and the lowest in July. The results of statistical analysis indicated that total nitrogen （N） content, NH4＋-N content, NO3-N content, and pH showed significant correlations with AOB abundance and nitrification activity in soil. The Shannon-Winner diversity, as well as species richness and evenness indices （determined by PCR-DGGE banding patterns） in soil samples were the highest in September, but the lowest in July, when compared to additional sampled dates. The DGGE fingerprints of soil-based 16S rRNA genes in November were apparently distinct from those observed in May, July, and September, possessing the lowest species richness indices and the highest dominance indices among all four growth periods. Fourteen DGGE bands were excised for sequencing. The resulting analysis indicated that all AOB communities belonged to the 13-Proteobacteria phylum, with the dominant AOB showing high similarity to the Nitrosospira genus. Therefore, soil-based environmental factors, such as pH variation and content of NHa＋-N and NO3--N, can substantially influence the abundance of AOB communities in soil, and play a critical role in soil-based nitrification kinetics.     

综述：土壤甲烷生成及其营养的研究进展

Global warming,as a result of an increase in the mean temperature of the planet,might lead to catastrophic events for humanity.This temperature increase is mainly the result of an increase in the atmospheric greenhouse gases(GHG)concentration.Water vapor,carbon dioxide(CO2),methane(CH4)and nitrous oxide(N2O)are the most important GHG,and human activities,such as industry,livestock and agriculture,contribute to the production of these gases.Methane,at an atmospheric concentration of 1.7μmol mol-1currently,is responsible for 16%of the global warming due to its relatively high global warming potential.Soils play an important role in the CH4cycle as methanotrophy(oxidation of CH4)and methanogenesis(production of CH4)take place in them.Understanding methanogenesis and methanotrophy is essential to establish new agriculture techniques and industrial processes that contribute to a better balance of GHG.The current knowledge of methanogenesis and methanotrophy in soils,anaerobic CH4 oxidation and methanotrophy in extreme environments is also discussed.     

硫化叶菌超表达载体构建及Mre11的表达

利用araS启动子并在穿梭载体pZC1及pEXA的基础上构建硫化叶菌超表达载体pZC2,成功超表达了带有C端6×His标签序列的DNA双链断裂修复蛋白Mre11,进一步采用共纯化法鉴定到Mre11蛋白的作用配体Rad50,确定上述蛋白在高浓度盐(500mmol/L NaCl)中仍能形成MR复合体,表明该复合物在逆性条件下可能仍保持DNA断链修复的功能。进一步共纯化分析表明,基因组DNA片段是MR复合体形成的必需条件,在缺乏基因组DNA片段的情况下古菌分子伴侣蛋白结合并可能保护Mre11,该表达系统能够有效地应用于鉴定蛋白质的体内作用网络。     

Effects of inorganic fertilizer and manure on soil archaeal abundance at two experimental farms during three consecutive rotation-cropping seasons

Soil archaeal population dynamics at two experimental sites of the same clay-loam type in Ottawa and Woodslee, Ontario, were investigated to determine fertilizer and manure effects following their different long-term crop rotation and fertilization schemes. Phylogenetic analysis of cloned soil archaeal 16S rRNA gene libraries of both sites identified them with group 1.1b of Thaumarchaeota. The gene population dynamics subtly varied in the order of 10⁷ copies g⁻¹ soil when monitored by quantitative real-time PCR during three growing seasons (2007–2009). In Ottawa, where plots were amended with dairy-farm manure, soil thaumarchaeal gene abundance was double of the unamended plots. At the Woodslee N-P-K-fertilized plots, it remained at least 30% fewer than that of the unfertilized ones. These cultivated plots showed soil carbon limitation while the fertilized ones were low in soil pH (ca. 5.5). Surface soils from an unfertilized sod plot and an adjacent deciduous forest had higher total carbon content (C:N ratio of 9 and 11, respectively). Their thaumarchaeal gene abundance varied up to 4.8 × 10⁷ and 7.0 × 10⁷ copies g⁻¹ soil, respectively. The former value was also attained at the manure-amended plots in Ottawa, where the C:N ratio was just below 10. Where soil pH was above 6.0, there was a weak and positive correlation between soil total C and the estimated gene abundance. Such gene population dynamics consistently demonstrated the stimulating and suppressive effects of dairy-farm manure (Ottawa site) and inorganic fertilizers (Woodslee site), respectively, on soil thaumarchaea. At both sites archaeal amoA and 16S rRNA gene abundance were similarly affected. Archaeal amoA gene abundance also outnumbered bacterial amoA abundance, suggesting that ammonia-oxidizing archaea might be dominant in these soils. Only minor crop effects on gene population dynamics were detected.     

两株耐碱性亚硝化细菌的初步鉴定和特性研究

从长期碱性条件下驯化的好氧活性污泥中分离出两株亚硝化细菌A1081和A1210，对其形态和生理生化性状进行了分析，并研究了其特性。结果表明，两株菌均属于亚硝化球菌属（Nitrosococcus），它们对碱性环境条件有较好的适应性；在pH值大于9后亚硝酸盐积累量不断增加，A1081在pH10～12积累量最大，而A1210在pH值为11时积累量最大；当培养基中NaCl为20g·L^-1时，两株菌对氨氮有相对较高的处理效率；当培养基氨氮浓度低于500mg·L^-1时，两株菌的氨氧化效率随氨氮浓度的增加而增加。     

Effect of winter-flooding on methanogenic archaeal community structure in paddy field under organic farming

Paddy field is a major emission source of methane. Methane is the terminal product of anaerobic decomposition of organic matter and generated by methanogenic archaea under flooded conditions in paddy fields. This study aimed to reveal the effect of winter flooding on methanogenic archaeal community structure in paddy fields of Andosols under organic farming. Soil samples were collected from experimental paddy fields in the Field Science Center, Tohoku University, for two years. They were under flooding conditions during winter with organic farming, under non-flooding conditions during winter with organic farming and under non-flooding conditions during winter with conventional farming (non-organic farming). Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis of methanogenic archaeal 16S rRNA gene revealed that the DGGE patterns were nearly the same irrespective of the treatment and sampling times. Twenty-three bands were observed from each treatment and 4, 13 and 6 sequences were closely related to Methanomicrobiales, Methanosarcinales and Methanocellales, respectively. Real-time quantitative PCR analysis indicated that the abundance of methanogenic archaeal 16S rRNA gene and mcrA gene, encoding α subunit of methyl-coenzyme M reductase, was not significantly different among the paddy fields. This study first revealed a methanogenic archaeal community in an Andosol paddy field and showed that the community was not affected by winter flooding under organic farming.