转Bt基因棉花根际细菌与古菌群落结构分析

在一年内棉花的四个生长时期（苗期,蕾期,花铃期,吐絮期）分别采集转Bt基因抗虫棉GK12和非转基因亲本棉花泗棉3号根际土壤,以及未种植棉花的背景土壤,利用末端标记限制性片段长度多态性（T-RFLP）分析技术,分析三种土壤中细菌和古菌的16S rRNA基因片段多态性,结合克隆文库建立和测序,研究了土壤中细菌和古菌群落结构的变化.结果表明：在棉花生长的各个时期,背景土壤中细菌群落结构发生了明显的变化,生物多样性指数明显降低,古菌群落结构也有一定的变化,说明季节性变化对土壤中微生物群落产生了明显的影响.与背景土壤相比,棉花种植后根际土壤中细菌和古菌群落发生显著的变化.转基因棉花与非转基因棉花相比,根际土壤细菌和古菌的种类和种群大小的分布也发生了明显的改变.克隆文库和测序结果表明土壤中主体微生物为目前未培养的、功能特性未知的细菌和古菌,转基因棉花种植对这些细菌和古菌影响的原因、环境危害和生态风险目前尚不清楚.与古菌群落相比,棉花种植对细菌群落结构的影响较小.     

一个红壤剖面微生物群落的焦磷酸测序法研究

利用定量PCR和454焦磷酸测序法,研究了湖南湘阴县一典型红壤剖面微生物相关基因的多度及微生物(古菌、细菌、真菌)群落结构.结果显示,随剖面深度增加,土壤黏粒含量增多,有机质和全氮含量、碳氮比则下降.每克干土微生物基因拷贝数也趋于下降,其值为:10 7.09～ 109.30(古菌16S rDNA),108.10～109.70(细菌16S rDNA),106.54～107.95(真菌18S rDNA),10 7.24～108.61(古菌amoA基因),104.76～106.25(细菌amoA基因),105.94～ 107.88(nirK基因),106.81～109.21(nirS基因),107.03～ 109.46(nosZ基因).焦磷酸测序得到了6 459条古菌16S rRNA基因序列,平均长度为496 bp;28 626条细菌16S rRNA基因序列,平均长度为448 bp;4 683条真菌18S rRNA基因序列,平均长度为534 bp.OTU(97％相似度)分析表明,微生物群落d-多样性与所测土壤理化性质均无显著相关.Jaccard差异度分析表明同一剖面各土壤层次间微生物群落结构更为相似,而不同位点的三个表层土之间的差异较大;Mantel检验发现,与微生物群落变化相关的主要土壤因子是黏粒含量.在所有土样中,古菌以泉古菌门中的热变形菌纲(89％)为主,其分布与土壤黏粒含量相关.细菌的主要类群为酸杆菌门(33％)、变形菌门(17％)、绿弯菌门(12％)、厚壁菌门(10％)和放线菌门(7％),分类地位不明确的细菌约占11％.其中,酸杆菌门和变形菌门的相对多度在表层土中高于非表层土;而绿弯菌门和厚壁菌门的相对多度则在非表层土中更高,与土壤深度呈显著正相关.所有真菌序列分属于三个门,即子囊菌门(87％)、担子菌门(9％)和球囊菌门(4％),在纲一级的分类水平上,各样品间群落结构无明显差异.     

缙云山不同森林植被下土壤微生物群落结构特征研究

为了解缙云山国家自然保护区不同森林植被对表层土中微生物群落结构和丰度的影响,以缙云山4种森林植被(针叶林、常绿阔叶林、针-阔混交林和竹林)土壤为研究对象,采用克隆文库、末端限制性片段多态性分析(Terminal restriction fragment length polymorphism analysis,T-RFLP)和荧光定量PCR(qPCR)等分子技术,研究不同森林植被对细菌、真菌和古菌群落结构和丰度的影响。结果表明:1)在4种植被类型中,针叶林土壤中微生物的拷贝数均低于其他植被。细菌16S rDNA拷贝数在3种微生物中最高且受植被影响最为明显(P0.05)。微生物拷贝数与土壤理化性质的皮尔逊相关分析显示:细菌和古菌拷贝数分别与pH(r=0.607,P0.05)和含水量(r=-0.919,P0.01)显著相关。2)根据T-RFLP图谱,群落结构的α-多样性指数显示:真菌的群落结构多样性最高,而古菌最低且受植被变化影响最显著(P0.05)。非度量多维尺度分析(Non-metric multidimensional scaling,NMDS)和热图分析(Heatmapanalysis)均显示:在不同植被间,土壤微生物群落组成表现出显著差异(P0.05),其中针叶林土壤中细菌和真菌群落结构最独特;3)不同植被中土壤微生物均存在不同的优势种群。其中,竹林土壤中微生物优势种群最突出。4)冗余分析(Redundancy analysis,RDA)显示3种微生物的群落结构显著受pH、钾和磷元素的影响(P0.05)。在缙云山地区,植被类型的变化对土壤表层微生物的群落结构和丰度均有显著影响。以上研究有助于了解土壤微生物与森林生产力及其发展演替的关系,为天然林的保护和可持续经营提供科学依据。     

烟株生长过程中土壤微生物的变化特征

为有效防治烟草青枯病等土传病害,探究了烟株生长过程中土壤微生物的变化特征。分别在烟株不同生长期采集根部土壤进行可培养微生物数量测定和16S/18S rDNA基因测序,以分析烟株生长过程中微生物数量、多样性以及群落结构的变化。结果表明,可培养细菌、放线菌数量随烟株生长先增多后减少,其中旺长期数量最多;真菌数量先减少后增多,以旺长期数量最少。细菌群落多样性无明显变化,真菌群落多样性在旺长期最低。微生物群落结构在旺长期变化较大,细菌优势菌群Acidobacteria(酸杆菌门)丰度较团棵期减少30%±12%,Actinobacteria(放线菌门)丰度增加116%±19%,真菌优势菌群Ascomycota(子囊菌门)丰度增加57%±36%,norankk-Fungi丰度减少83%±17%。烟株生长发育改变了土壤微生物的数量和群落结构,旺长期微生物群落结构的改变与青枯病发生存在一定联系,特别是真菌优势菌的变化可能会影响青枯病的发生。     

间隙灌溉和控释肥施用对稻田土壤产甲烷微生物的影响

间隙灌溉和控释肥施用影响稻田CH_4的产生和排放,然而其微生物机理尚不清楚。本研究通过采集稻季田间原位试验新鲜土样,采用核酸定量技术(qPCR)和末端限制性片段长度多态性(T-RFLP)技术,研究间隙灌溉和控释肥施用对稻田土壤产甲烷微生物群落丰度和结构的影响。结果表明,稻季CH_4排放量与古菌、产甲烷菌(mcr A基因)和甲烷氧化菌(pmo A基因)数量均呈极显著正相关关系(P0.01),而与细菌数量无显著相关性。间隙灌溉显著影响产甲烷菌和甲烷氧化菌数量的季节变化,其中烤田抑制产甲烷菌生长,而对甲烷氧化菌数量没有显著影响。与尿素相比,施用控释肥增加了稻田土壤细菌、古菌和产甲烷菌数量,降低了甲烷氧化菌数量。土壤古菌群落的优势T-RFs片段为184bp和391bp,其中184bp片段的相对丰度随着间隙灌溉的进行由45%~55%降低到23%~30%;而391bp片段则相反,其相对丰度由12%~18%增加到23%~26%。典型相关性分析(CCA)表明间隙灌溉显著影响土壤古菌群落结构(P0.001),而控释肥施用对土壤古菌群落结构没有明显影响。     

红壤稻田不同生育期土壤氨氧化微生物群落结构

以福建省红壤稻田土壤为对象,通过提取土壤总DNA,利用特异引物进行PCR(聚合酶链反应)扩增和DGGE(变性梯度凝胶电泳)并结合DNA克隆测序,研究了水稻生长过程中稻田土壤氨氧化细菌和氨氧化古菌群落结构的变化。结果显示:稻田土壤具有丰富的氨氧化细菌和氨氧化古菌资源。水稻生长过程中土壤氨氧化细菌群落组成较为稳定,只表现出水稻生长前期(苗期、分蘖期)和中后期(孕穗期、成熟期)间存在一定差异。而土壤氨氧化古菌群落组成变化较大,在水稻生长的苗期、分蘖期、孕穗期和成熟期4个时期间均存在一定差异。在水稻生长过程中,土壤氨氧化细菌群落多样性指数无显著性变化,但氨氧化古菌群落多样性指数随水稻生长明显提高,孕穗期后才达到平稳。水稻生长前期土壤硝化势也具有显著上升趋势,孕穗期时达到最高,而后有所下降。土壤硝化势与氨氧化古菌群落多样性指数具有显著正相关性,与氨氧化细菌没有相关性。研究表明,氨氧化古菌对红壤稻田土壤硝化作用的影响程度较大,证实了氨氧化微生物尤其是氨氧化古菌在稻田土壤微生物组成及其生态系统功能中的重要性。     

红壤稻田不同生育期土壤氨氧化微生物群落结构和硝化势的变化

以福建省红壤稻田土壤为对象,通过提取土壤总DNA,利用特异引物进行PCR(聚合酶链反应)扩增和DGGE(变性梯度凝胶电泳)并结合DNA克隆测序,研究了水稻生长过程中稻田土壤氨氧化细菌和氨氧化古菌群落结构的变化。结果显示:稻田土壤具有丰富的氨氧化细菌和氨氧化古菌资源。水稻生长过程中土壤氨氧化细菌群落组成较为稳定,只表现出水稻生长前期(苗期、分蘖期)和中后期(孕穗期、成熟期)间存在一定差异。而土壤氨氧化古菌群落组成变化较大,在水稻生长的苗期、分蘖期、孕穗期和成熟期4个时期间均存在一定差异。在水稻生长过程中,土壤氨氧化细菌群落多样性指数无显著性变化,但氨氧化古菌群落多样性指数随水稻生长明显提高,孕穗期后才达到平稳。水稻生长前期土壤硝化势也具有显著上升趋势,孕穗期时达到最高,而后有所下降。土壤硝化势与氨氧化古菌群落多样性指数具有显著正相关性,与氨氧化细菌没有相关性。研究表明,氨氧化古菌对红壤稻田土壤硝化作用的影响程度较大,证实了氨氧化微生物尤其是氨氧化古菌在稻田土壤微生物组成及其生态系统功能中的重要性。     

西藏高原土壤中可培养细菌群落结构分析

以4个西藏高海拔(4 056～5 015 m)高原土壤为材料,经室内恒温短期碳源富集培养后,建立4个土壤可培养细菌库.采用细菌16S rDNA的序列分析技术测定供试土壤可培养细菌库的群落结构特征.结果表明,从XZ02、XZ06、XZ08和XZ12共4个土样的细菌库中,分别获得21,37,31,32个细菌的16S rDNA序列,共产生45个OTU类型.不同样品产生的OTU类型个数和种类有差异,不同样品之间存在共有的优势OTU,但比例不同.多样性指数分析表明,XZ08的Shannon-Wiener指数(H’)和物种丰富度指数(dMa)均为最大,XZ02的辛普森指数(Simpson index,Ds)和物种均匀度指数(E)均为最大,表明不同土壤可培养细菌的多样性指数大小不同;PCA分析表明,XZ06和XZ12群落结构相近,XZ02和XZ08与其群落结构差异大.典型OTU进化定位分析表明,4个土样的细菌主要分布在厚壁菌门和变形菌门中,XZ02和XZ12以芽孢杆菌为主,而XZ02和XZ12以芽孢杆菌和假单胞菌为主.不同采样点土壤的可培养细菌群落结构多样性和分布上均有差异.     

长期不同施肥黑土细菌和古菌群落结构及主效影响因子分析

【目的】依据黑龙江省农科院34年的长期定位试验,探讨影响东北黑土细菌和古菌区系的主效环境因子。【方法】试验采集不施肥(CK)、施氮磷肥(NP)、施氮钾肥(NK)、施磷钾肥(PK)、施氮磷钾肥(NPK)5个施肥处理的耕层土样借助传统化学分析方法和Illumina Miseq高通量测序技术解析土壤化学性状和细菌与古菌的群落结构特征,并对细菌和古菌群落结构与环境因子进行相关性分析。【结果】1)不同施肥处理土壤细菌和古菌群落结构存在显著差异与CK相比,4种施肥处理均降低了古菌丰富度,NPK处理增加了土壤细菌的丰富度、多样性以及古菌的多样性;变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)是所有土样中的优势菌群,占细菌与古菌总量的38.2%~42.9%。施肥条件下,放线菌门(Actinobacteria)、浮霉菌门(Planctomycetes)、绿弯菌门(Chloroflexi)、蓝藻门(Cyanobacteria)的相对丰度降低芽单胞菌门(Gemmatimonadetes)、厚壁菌门(Firmicutes)的相对丰度升高而其他菌门的相对丰度对不同施肥处理的响应不同。2)施用氮肥显著改变了土壤化学性状,长期施氮(尿素)处理的土壤全氮、速效氮和有机质含量显著高于不施氮处理而pH则显著降低。3)RDA分析结果显示,pH对土壤细菌和古菌群落结构的影响最大解释了66.5%的变化;其他环境因子则共解释了细菌与古菌群落33.5%的变化各因子的贡献率依次为pH速效钾有效磷有机质。Pearson相关性分析结果也表明,细菌和古菌群落与土壤化学指标间存在密切的相关关系。【结论】解析了长期不同施肥条件下土壤细菌和古菌的群落结构特征,确定了pH是影响土壤细菌和古菌区系的主效环境因子,氮磷钾均衡施肥不仅显著提高了作物产量和丰富了土壤养分含量,同时也增加了土壤细菌的丰富度、多样性以及古菌的多样性,有利于维持良好的土壤生态环境。研究结果对揭示东北黑土肥力演变机制、建立合理的施肥制度具有重要的理论价值。     

不同品种水稻土壤氨氧化细菌和氨氧化古菌群落结构组成

本研究通过提取土壤总DNA,利用特异引物进行PCR扩增和变性梯度凝胶电泳(DGGE),研究了不同品种水稻对稻田土壤氨氧化细菌和氨氧化古菌群落结构组成的影响.结果显示:稻田土壤具有丰富的氨氧化细菌和氨氧化古菌,且氨氧化古菌种类更多;不同品种水稻氨氧化细菌群落结构组成差异较大,其中以"天A/Km71"、"闽优1027"和"Km62/1027"3个品种相似性较高,且明显不同于其余3个品种:而氨氧化古菌群落结构组成在不同土层间表现出较大差异,其中以"天A/Km71"和"Km62/1027"的表土与根际土氨氧化古菌群落组成差异最大.研究表明不同水稻品种及土壤层次对氨氧化微生物群落结构组成具有一定影响,证明氨氧化微生物尤其是氨氧化古菌在稻田土壤生态系统中占有重要地位.     

Microbial activity and community structure in two drained fen soils in the Ljubljana Marsh

Fen peatlands are specific wetland ecosystems containing high soil organic carbon (SOC). There is a general lack of knowledge about the microbial communities that abound in these systems. We examined the microbial activity and community structure in two fen soils differing in SOC content sampled from the Ljubljana Marsh under different seasonal conditions. Substrate-induced respiration and dehydrogenase activity were used as indicators of total microbial activity. Both methods indicated higher microbial activities in the fen soil with the higher SOC content on all dates of sampling. To determine whether the differences in microbial activity were associated with differences in the microbial community structures, terminal restriction fragment length polymorphism (T-RFLP) of bacterial 16S rRNA genes was performed. Comparison of the T-RFLP profiles revealed very similar community structures in both fens and in the two seasonal extremes investigated. This suggested a stable community structure in the two fens, which is not affected by the SOC content or seasonal variation. In addition, a bacterial 16S ribosomal RNA gene based clone library was prepared from the fen soil with the higher SOC content. Out of 114 clones analysed, approximately 53% belonged to the Proteobacteria, 23% to the Acidobacteria, 21% to a variety of other taxa, and less than 3% were affiliated with the Firmicutes.     

Effect of Colletia hystrix (Clos), a pioneer actinorhizal plant from the Chilean matorral, on the genetic and potential metabolic diversity of the soil bacterial community

Colletia hystrix are dominant shrubs in the sclerophyllous matorral, a natural ecosystem in the central valley of Chile affected by erosion, soil with low fertility and limiting nitrogen. The soil microbial communities associated to these pioneer plants have received little attention even though they may have an important role in the ability of these to colonize the nutrient-poor soils from these semi-arid ecosystems. T-RFLP profiles using 16S rDNA were used to compare the bacterial community structure from soil samples (enriched and unenriched) associated to C. hystrix and neighboring soil without plant cover (bulk soil). Additionally, the microbial communities from both habitats were compared at the metabolic profile level using the Biolog EcoPlate™ system. Our results showed that the bacterial community from samples of soil associated to these plants formed a separate cluster from samples derived from the neighboring soil. These data suggest that soil associated to C. hystrix is a different microhabitat to bulk soil. When an enrichment step was performed on the samples, the T-RFLP profiles obtained showed few T-RFs suggesting that only some species were recovered. The enriched samples exhibited a low similarity between them and are clearly separated from the unenriched samples. On the other hand, the comparison of the unenriched samples from both habitats based on sole-carbon-source utilization profiles was unable to differentiate the samples according to their habitat.     

A cross-seasonal comparison of active and total bacterial community composition in Arctic tundra soil using bromodeoxyuridine labeling

Arctic soil microorganisms remain active at ecologically relevant rates in frozen soils. We used bromodeoxyuridine (BrdU) labeling and terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA gene amplicons to examine active bacterial communities in two Alaskan tundra soils collected in summer and winter of 2005. Active community T-RFLP profiles were compared to total community profiles to determine if active bacteria were a subset of the total community. In shrub soils, active bacteria communities differed in composition between summer and winter, and winter-active bacterial taxa were not detected in the total community, suggesting that they are likely rare within the overall community. In contrast, tussock tundra soil contained more bacterial taxa that were active in both summer and winter and also represented a large portion of the total community. Using in silico digest of a sequence library from this site, we attempted to identify the dominant organisms in our samples. Our previous research suggested that the total microbial community was stable throughout the year, but this new study suggests that the active community is more dynamic seasonally. In general, only a subset of the total community was growing at a given time. This temporal niche partitioning may contribute to the high diversity of microbial communities in soils. Understanding which taxa contribute to microbial function under different conditions is the next frontier in microbial ecology and linking composition to biogeochemical cycling.     

Differences in the activity and bacterial community structure of drained grassland and forest peat soils

The microbial activity and bacterial community structure were investigated in two types of peat soil in a temperate marsh. The first, a drained grassland fen soil, has a neutral pH with partially degraded peat in the upper oxic soil horizons (16% soil organic carbon). The second, a bog soil, was sampled in a swampy forest and has a very high soil organic carbon content (45%), a low pH (4.5), and has occasional anoxic conditions in the upper soil horizons due to the high water table level. The microbial activity in the two soils was measured as the basal and substrate-induced respiration (SIR). Unexpectedly, the SIR (μl CO₂ g⁻¹ dry soil) was higher in the bog than in the fen soil, but lower when CO₂ production was expressed per volume of soil. This may be explained by the notable difference in the bulk densities of the two soils. The bacterial communities were assessed by terminal restriction fragment length polymorphism (T-RFLP) profiling of 16S rRNA genes and indicated differences between the two soils. The differences were determined by the soil characteristics rather than the season in which the soil was sampled. The 16S rRNA gene libraries, constructed from the two soils, revealed high proportions of sequences assigned to the Acidobacteria phylum. Each library contained a distinct set of phylogenetic subgroups of this important group of bacteria.     

Linking plant identity and interspecific competition to soil nitrogen cycling through ammonia oxidizer communities

Both plants and microbes influence soil nutrient cycling. However, the links between plants, microbes and nutrient cycling are poorly understood. In this study, we investigated how plant identity and interspecific competition influence soil nitrogen cycling and attempted to link plant identity and interspecific competition to community structures of bacterial and archaeal ammonia oxidizers based on terminal restriction fragment length polymorphism analysis (T-RFLP) of bacterial and archaeal ammonia monooxygenase (amoA) genes. Faba bean and maize monocultures and a faba bean/maize mixture were planted with two nitrogen levels (0 and 100 mg N kg⁻¹ soil as urea). Soil mineral nitrogen, ammonia oxidizer function (potential nitrification activity, PNA) and community structures were measured 28 and 54 days after plant emergence. Faba bean and maize substantially differed in their influences on mineral nitrogen concentrations and PNA in rhizosphere soils. Soil mineral nitrogen and PNA in the rhizosphere soils of the faba bean/maize mixture were closer to those of the maize monoculture than to those of the faba bean monoculture. T-RFLP with restriction enzymes BsaJI and Hpy8I distinguished variations in bacterial and archaeal ammonia oxidizers community structure, respectively, and detected both between-cluster and within-cluster variations in bacterial ammonia oxidizers. T-RFLP data showed that nitrogen addition favored part of a Nitrosospira cluster 3b sequence type and suppressed part of a cluster Nitrosospira 3a sequence type of bacterial ammonia oxidizers, while it had no influence on the archaeal ammonia oxidizer community structure. Although multivariate analysis showed that the function and community structure of bacterial ammonia oxidizers were significantly correlated, plant species and interspecific competition did not significantly change the community structure of bacterial and archaeal ammonia oxidizers. These results indicate that plant species and interspecific competition regulate soil nitrogen cycling via a mechanism of other than alteration in the community structure of ammonia oxidizers as investigated by DNA based methods.     

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.     

红壤坡地利用方式对土壤细菌群落结构的影响

利用中国科学院桃源农业生态试验站坡地不同利用方式长期定位观测试验场农田、自然恢复和茶园土壤为研究对象,直接从土壤中抽提总DNA,应用T-RFLP和RT-PCR技术研究红壤坡地利用方式对土壤细菌群落结构的影响。结果表明,红壤坡地三种土地利用方式土壤细菌多样性指数农田>茶园>自然恢复(p<0.05),但土壤细菌数量茶园>自然恢复>农田(p<0.05),茶园土壤细菌数量是农田的8.76倍。基于T-RFLP图谱的样品间相似性指数和主要限制性片段(T-RFs)定性分析均表明,农田与茶园和自然恢复土壤均存在显著的差异(p<0.05),而茶园和自然恢复土壤细菌群落比较相似。不同土地利用方式土壤有机质、有效磷和速效钾均对土壤细菌群落结构产生显著影响(p<0.05)。综合考虑经济效益和保持红壤坡地的可持续利用,茶园将成为中国南方红壤丘陵坡地可持续利用的一种有效方式。     

Community-level responses of metabolically-active soil microorganisms to the quantity and quality of substrate inputs

The community fingerprints of both the prevalent and the metabolically active microbial community were related to a quantitative estimation of microbial biomass in an arable soil, revealed by substrate-induced-respiration (SIR). Two concentrations of glucose or l-asparagine, representing those used in the SIR measurement or equivalent to those released in root exudates, were studied. Respiration rates and changes in community structure fingerprints were followed for 48 h. Bacterial and fungal community fingerprints were obtained using both reverse transcribed 16S and 18S ribosomal RNA (rRNA) regions and the corresponding rDNA as a template in PCR. Samples were then analysed by denaturing gradient gel electrophoresis (DGGE). Low concentrations of substrate amendments resulted in minor changes in rRNA or rDNA-based bacterial and fungal banding patterns during the whole 48 h incubation. High concentrations of substrates, especially l-asparagine, increased respiration rates and induced significant changes in both 16S rRNA and rDNA-community fingerprints. The prominent rRNA and rDNA bacterial community sequence types were common to all treatments, but in general the bacterial rDNA fingerprints had fewer bands than the corresponding rRNA profiles that assess the active fraction of the community. In contrast, there was little difference between fungal 18S rRNA and rDNA patterns. The number of fungal ribosomal sequence types in DGGE fingerprints was lower than the number of bacterial types. This study indicated that there was a rapid respiration response by the whole microbial community during SIR estimates in soil, but that community structure did not change during the conventional incubation period. In an extended (8-48 h) incubation with high amounts of l-asparagine increased respiration was associated with growth of the microbial community.     

Effects of PAH-Contaminated Soil on Rhizosphere Microbial Communities

Bacterial associations with plant roots are thought to contribute to the success of phytoremediation. We tested the effect of addition of a polycyclic aromatic hydrocarbon contaminated soil on the structure of the rhizosphere microbial communities of wheat (Triticum aestivum), lettuce (Lactuca sativa var. Tango), zucchini (Cucurbita pepo spp. pepo var. Black Beauty), and pumpkin (C. pepo spp. pepo var. Howden) 16S rDNA terminal restriction fragment length polymorphism (T-RFLP) profiles of rhizosphere microbial communities from different soil/plant combinations were compared with a pairwise Pearson correlation coefficient. Rhizosphere microbial communities of zucchini and pumpkin grown in the media amended with highest degree of contaminated soil clustered separately, whereas communities of these plants grown in unamended or amended with lower concentrations of contaminated soil, grouped in a second cluster. Lettuce communities grouped similarly to cucurbits communities, whereas wheat communities did not display an obvious clustering. The variability of 16S rDNA T-RFLP profiles among the different plant/soil treatments were mostly due to the difference in relative abundance rather than presence/absence of T-RFLP fragments. Our results suggest that in highly contaminated soils, the rhizosphere microbial community structure is governed more by the degree of contamination rather than the plant host type.