淹水培养过程中水稻土地杆菌科微生物群落结构变化特征

采用淹水非种植水稻土微环境模式系统,对水稻土进行1 h和1、5、10、20、30 d淹水培养,利用PCR-DGGE技术检测、多元统计分析淹水培养过程中地杆菌科微生物的群落结构和多样性变化规律及其影响因子。结果表明,淹水培养过程中地杆菌科微生物群落结构发生了明显的演替性变化：由r-对策优势种群演替至k-对策优势种群,且群落结构由不稳定向稳定演变（培养1 h和1 d处理间相似性最低,群落结构变化最大,20 d和30 d处理间相似性最高,群落结构变化最小）;该过程中,地杆菌科微生物物种丰富度指数和Shannon-Weiner指数在1 h处理中均为最小,5 d处理的最大;CCA相关性分析表明,淹水培养过程中Fe（Ⅱ）浓度与群落结构多样性指数呈正相关,证实该类微生物对于异化铁还原能力具有重要作用;测序结果表明,19个优势DGGE条带与来自水稻土中的未培养地杆菌科微生物亲缘关系相近。     

不同施肥处理对农田土壤微生物区系和功能的影响

本研究采用DGGE和Biolog两种方法, 研究了五种不同施肥处理对土壤微生物区系组成和功能的影响。采用UPGMA对DGGE试验结果进行聚类分析得出,小麦季中不施肥对照（T1）和常规氮磷钾肥（T2）聚为一类,相似性为41%,常规氮磷钾肥+秸秆还田（T4）和常规氮磷钾肥+秸秆还田+秸秆腐熟剂（T5）聚为一类,相似性为52%,而70%常规氮磷钾肥+有机肥（T3）单独聚为一类;玉米季也得到类似的结果,只是T1和T2的相似性为68%,T4和T5相似性达78%,而T3依然归为一类,这说明不同施肥处理间土壤微生物区系存在相似性。经过切胶测序及BLAST比对,发现大多为不可培养细菌,可培养细菌中多为芽孢杆菌属和类芽孢杆菌属。Biolog试验采用主成份分析得出,T1和T2土壤微生物功能类似,T4和T5土壤微生物也具有相似的功能,而T3则单独分为一类。其中,T5和T4的土壤细菌群落对底物碳源的代谢活性最强,T3处理次之,T2和T1最低。通过这两种不同试验方法的分析可以看出,不同施肥处理对土壤微生物区系和功能的影响存在关联性。     

石油污染土壤鞘氨醇单胞菌遗传多样性16S rDNA-PCR-DGGE分析

鞘氨醇单胞菌是降解多环芳烃(PAHs)的重要功能微生物。然而,采用属特异引物直接从PAHs污染土壤中检测鞘氨醇单胞菌进而研究鞘氨醇单胞菌在污染土壤中的多样性、种群结构及其与PAHs污染的关系鲜有报道。本研究自行设计鞘氨醇单胞菌属特异性引物,通过16S rDNA-PCR-DGGE技术对沈抚灌区石油污染土壤鞘氨醇单胞菌遗传多样性进行了研究。结果表明,自行设计的鞘氨醇单胞菌属引物732f-982r能够特异、灵敏的从环境样品中检出鞘氨醇单胞菌。当沈抚灌区原位污染土壤的PAHs浓度小于5 mg kg-1时,鞘氨醇单胞菌多样性随着PAHs浓度的增加而增加;而初始PAHs浓度高的实验室模拟实验土壤,其鞘氨醇单胞菌多样性较低。鞘氨醇单胞菌种群结构受污染土壤总石油烃(TPH)含量的影响,TPH含量接近的土壤,鞘氨醇单胞菌的群落结构较为相似。     

Analysis of bacterial communities on alkaline phosphatase genes in soil supplied with organic matter

Abstract

We studied the effects of the application of organic matter (OM) and chemical fertilizer (CF) on soil alkaline phosphatase (ALP) activity and ALP-harboring bacterial communities in the rhizosphere and bulk soil in an experimental lettuce field in Hokkaido, Japan. The ALP activity was higher in soils with OM than in soils with CF, and activity was higher in the rhizosphere for OM than in the bulk soil. Biomass P and available P in the soil were positively related to the ALP activity of the soil. As a result, the P concentration of lettuce was higher in OM soil than in CF soil. We analyzed the ALP-harboring bacterial communities using polymerase chain reaction based denaturing gradient gel electrophoresis (DGGE) on the ALP genes. Numerous ALP genes were detected in the DGGE profile, regardless of sampling time, fertilizer treatment or sampled soil area, which indicated a large diversity in ALP-harboring bacteria in the soil. Several ALP gene fragments were closely related to the ALP genes of Mesorhizobium loti and Pseudomonas fluorescens. The community structures of the ALP-harboring bacteria were assessed using principal component analysis of the DGGE profiles. Fertilizer treatment and sampled soil area significantly affected the community structures of ALP-harboring bacteria. As the DGGE bands contributing to the principal component were different from sampling time, it is suggested that the major bacteria harboring the ALP gene shifted. Furthermore, there was, in part, a significant correlation between ALP activity and the community structure of the ALP-harboring bacteria. These results raise the possibility that different ALP-harboring bacteria release different amounts and/or activity of ALP, and that the structure of ALP-harboring bacterial communities may play a major role in determining overall soil ALP activity.     

不同细菌饲喂细菌线虫对土壤细菌数量、活性以及群落结构的影响

The effects of bacterial-feeding nematodes on bacterial number, activity, and community composition were studied through a microcosm experiment using sterilized soil inoculated with soil bacteria （soil suspension） and with bacteria and three species of bacterial-feeding nematodes （ Cephalobus persegnis, Protorhabditis filiformis, and Caenorhabditis elegans）. Catalyzed reporter deposition-fluorescence in situ hybridization, CO2 evolution, and denaturing gradient gel electrophoresis （DGGE） of PCR ampli- fied 16S rRNA gene fragments were used to investigate bacterial numbers, antivity, and community composition, respectively. Our results showed that bacterial numbers and activity significantly increased in the presence of bacterial-feeding nematodes, which indicated that bacterial-feeding nematodes had a significant positive effect on soil bacteria. The different nematode species had different effects on bacterial numbers and activity. C. persegnis and P. filiformis, isolated from native soil, increased the bacterial number and activity more than C. elegans. The DGGE analysis results showed that dominant bacterial species significantly differed among the treatments, which suggested that bacterial-feeding nematode species modified the bacterial community composition in soil. Further gene sequence analysis results showed that the dominant bacterial species in this study were gram-negative bacteria. Given the completely same conditions except nematode species, the varied selective feeding behavior of different nematode species was the most likely reason for the altered bacterial community composition. Overall, the alteration of bacterial numbers, activity and community composition resulting from the bacterial-feeding nematodes may ult!mately affect soil ecological functioning and processes.     

分子生物学技术在产甲烷古菌研究中的应用

鉴于产甲烷古菌在环境和能源两大方面的特殊作用,对它的研究一直是微生物学研究的焦点之一。现代分子生物学技术的发展与应用,进一步推动了对产甲烷古菌的研究。本文将综述产甲烷古菌基因克隆研究进展以及几项有代表性的分子生物学技术在产甲烷古菌研究中的应用。     

暗纹东方鲀几种组织中可培养细菌的组成分析

采用16S rDNA特征序列PCR-DGGE法,分析了不同饵料饲养的暗纹东方鲀的表皮、肠道和河鲀毒素累积组织(肝和卵巢)中可培养细菌的群落组成.根据分子系统发育分析,共鉴定出45种可培养细菌,在这些细菌中,以变形细菌的gamma亚群占多数,其它分别隶属于低GC含量革兰氏阳性菌和高GC含量革兰氏阳性菌.摄食不同饵料的暗纹东方鲀,其肠道、表皮或河鲀毒素累积组织中的细菌菌落组成是不同的,但不管是摄食人工配合饲料或天然饵料,在暗纹东方鲀的肠道、表皮或河鲀毒素累积组织中,均发现已有报道的可产河鲀毒素的细菌类群,表明饵料来源对暗纹东方鲀的河鲀毒素产生不是必需的.     

暗纹东方鲀几种组织中可培养细菌的组成分析

采用16S rDNA特征序列PCR-DGGE法,分析了不同饵料饲养的暗纹东方鲀的表皮、肠道和河鲀毒素累积组织(肝和卵巢)中可培养细菌的群落组成.根据分子系统发育分析,共鉴定出45种可培养细菌,在这些细菌中,以变形细菌的gamma亚群占多数,其它分别隶属于低GC含量革兰氏阳性菌和高GC含量革兰氏阳性菌.摄食不同饵料的暗纹东方鲀,其肠道、表皮或河鲀毒素累积组织中的细菌菌落组成是不同的,但不管是摄食人工配合饲料或天然饵料,在暗纹东方鲀的肠道、表皮或河鲀毒素累积组织中,均发现已有报道的可产河鲀毒素的细菌类群,表明饵料来源对暗纹东方鲀的河鲀毒素产生不是必需的.     

甘草内生真菌多样性及群落结构

以新疆塔里木盆地的光果甘草(Glycyrrhiza glabra)和胀果甘草(G.inflate)为研究对象,采用变性梯度凝胶电泳(PCR-DGGE)技术研究甘草内生真菌的多样性及群落结构。结果显示,光果甘草和胀果甘草间及同一种类不同组织间的内生真菌多样性和群落结构均存在明显差异。其中,胀果甘草根(B1)的内生真菌多样性最丰富,光果甘草果(L4)的内生真菌多样性最差。对DGGE条带进行回收测序,共获得25条序列,归于枝顶孢属(Acremonium)、绿僵菌属(Metarhizium)、绿僵虫草属(Metacordyceps)、镰刀菌属(Fusarium)、链格孢属(Alternaria)、枝孢属(Cladosporium)、锤舌菌属(Leotiomycetes)、链格孢属(Alternaria)、帚枝霉属(Sarocladium)、假裸囊菌属(Pseudogymnoascus)、曲霉属(Aspergillus)11个真菌属,其中链格孢属为优势菌属,占总数的32%。甘草根、茎、叶、果、皮组织的内生真菌存在丰富的多样性,其中根与茎组织多样性最丰富。研究结果表明,新疆塔里木盆地药用植物甘草蕴藏着丰富的内生真菌资源,可作为一种较理想的分离内生真菌的植物来源。     

Parent material and vegetation influence bacterial community structure and nitrogen functional genes along deep tropical soil profiles at the Luquillo Critical Zone Observatory

Microbial communities mediate every step of the soil nitrogen cycle, yet the structure and associated nitrogen cycle functions of soil microbial communities remain poorly studied in tropical forests. Moreover, tropical forest soils are often many meters deep, but most studies of microbial nitrogen cycling have focused exclusively on surface soils. The objective of our study was to evaluate changes in bacterial community structure and nitrogen functional genes with depth in soils developed on two contrasting geological parent materials and two forest types that occur at different elevations at the Luquillo Critical Zone Observatory in northeast Puerto Rico. We excavated three soil pits to 140 cm at four different sites representing the four soil × forest combinations (n = 12), and collected samples at ten-centimeter increments from the surface to 140 cm. We used bacterial 16S rRNA gene-DGGE (denaturant gradient gel electrophoresis) to fingerprint microbial community structures, and quantitative PCR to measure the abundance of five functional genes involved in various soil nitrogen transformations: nifH (nitrogen fixation), chiA (organic nitrogen decomposition), amoA (ammonia oxidation), nirS (nitrite reduction) and nosZ (nitrous oxide reduction). Multivariate analyses of DGGE fingerprinting patterns revealed differences in bacterial community structure across the four soil × forest types that were strongly correlated with soil pH (r = 0.69, P < 0.01) and nutrient stoichiometry (r² ≥ 0.36, P < 0.05). Across all soil and forest types, nitrogen functional genes declined significantly with soil depth (P < 0.001). Denitrification genes (nirS and nosZ) accounted for the largest proportion of measured nitrogen functional genes. Measured nitrogen functional genes were positively correlated with soil carbon, nitrogen and phosphorus concentrations (P < 0.001) and all genes except amoA were significantly more abundant in the Inceptisol soil type compared with the Oxisol soil type (P < 0.03). Greater abundances and a stronger vertical zonation of nitrogen functional genes in Inceptisols suggest more dynamic nitrogen transformation processes in this soil type. As the first study to examine bacterial nitrogen functional gene abundances below the surface 20 cm in tropical forest soils, our work provides insight into how pedogenically-driven vertical gradients control the nitrogen-cycling capacity of soil microbial communities. While previous studies have shown evidence for redox-driven hotspots in tropical nitrogen cycling on a watershed scale, our study corroborates this finding on a molecular scale.