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1.
Characterization of bacterial community structure in vestimentiferan tubeworm Ridgeia piscesae trophosomes 总被引：1，自引：0，他引：1
Terminal‐restriction fragment length polymorphisms (T‐RFLPs) were used to address the question whether there are multiple phylotypes of bacteria within the trophosome of the vestimentiferan tubeworm Ridgeia piscesae in addition to the known endosymbiont. Clone libraries were constructed to aid in the identification of the additional bacterial phylotypes. Individual R. piscesae specimens were collected from Juan de Fuca Ridge, Axial Caldera and Explorer Ridge, Magic Mountain. Clone library analyses revealed only one bacterial phylotype (expected R. piscesae endosymbiont) within the Explorer Ridge trophosomes. However, the Axial Caldera clone library revealed five operational taxonomic units (OTUs). Three of the resulting phylotypes detected (designated RAE) were putative thioautotrophic symbionts within the γ‐Proteobacteria which belonged to the anticipated endosymbiont group (RAE OTU 1), the Maorithyas hadalis symbiont II group (RAE OTU 3), and the Halothiobacillus group (RAE OTU 4). The remaining two phylotypes were most likely opportunistically derived. RAE OTU 5 was an α‐Proteobacterium within the Roseobacter group and RAE OTU 2 was within the Cytophaga–Flavobacterium–Bacteroidetes. T‐RFLP analyses revealed that all 15 trophosomes evaluated contained at least RAE OTUs 1 and 4. Five of the 15 trophosomes contained at least RAE OTUs 1, 3, and 4 and two of the trophosomes contained at least five RAE OTUs. Cluster analysis of the T‐RFLP data revealed three distinct clusters. The number of taxa within the trophosome may be an indication of the general health of the tubeworm. This study strongly suggests that we have discovered and identified more than one bacterial phylotype within the trophosome of vestimentiferan R. piscesae. 相似文献
2.
Groundwater plays an important role in New Zealand water supplies and hence monitoring activities are conducted regularly. Most monitoring programmes aim to evaluate groundwater chemistry and almost completely overlook the microbial component in this ecosystem. In our present study, the bacterial community structure of groundwater in the Wairarapa Valley was examined using the terminal restriction fragment length polymorphism (T-RFLP), and relationships between bacterial community structure and groundwater chemistry, aquifer confinement and groundwater usage were explored. In addition, the results from this study were compared with a previous T-RFLP survey of the same area in an attempt to detect changes in bacterial community structure over time. The data obtained suggested that bacterial community structure was related to groundwater chemistry, especially to redox conditions. Species composition showed minimal variation over time if groundwater chemistry remained unchanged. These findings reflect the potential of using bacterial communities as biological indicators to evaluate the health of groundwater ecosystems. We suggest that it is important to include this type of broad bacterial diversity assessment criteria into regular groundwater monitoring activities. 相似文献
3.
Biochemical and microbial features of shallow marine sediments along the Terra Nova Bay (Ross Sea,Antarctica) 总被引：1，自引：0，他引：1
Franco Baldi Davide Marchetto Francesco Pini Renato Fani Luigi Michaud Angelina Lo Giudice Daniela Berto Michele Giani 《Continental Shelf Research》2010
Shallow marine sediments were collected from seven stations (three of which located at Gerlache Inlet, two at Tethys Bay, one at Adelie Cove and one just beneath the Italian Research Base) along the Terra Nova Bay coast (Ross Sea, Antarctica). Their chemical, biochemical and microbiological properties were studied in order to provide further insights in the knowledge of this Antarctic benthic ecosystem. Overall, the organic carbon (OC) represented the major fraction of total carbon (TC) and displayed concentrations similar to or slightly lower than those previously measured in Antarctic bottom sediments. The biopolymeric carbon within OC ranged from 4.1% to 19.9% and showed a wide trophic range (65–834 μg g−1 d.w.). Proteins (PRT) represented on average the main biochemical class contributing to labile organic carbon, followed by lipids (LIP) and carbohydrates (CHO). The activity of aminopeptidase, β-d-glucosidase, alkaline phosphatase and esterase was checked, giving the highest values at Tethys Bay and at the deepest water sediments. The principal component analysis, which was computed considering physical, chemical (elemental and biochemical sedimentary composition) and microbiological parameters (including bacterial abundance, ectoenzymatic activities, T-RFs richness and diversity indices), allowed to obtain two main clusters (“Tethys Bay” and “other stations”). Based on data obtained, two representative 16S rRNA clone libraries using samples from Tethys Bay and Gerlache Inlet were constructed. The sequences of 171 clones were compared to those available in public databases to determine their approximate phylogenetic affiliations. Both aerobic and anaerobic bacteria were disclosed, with the majority of them affiliated with the Gamma- and Deltaproteobacteria, Bacteroidetes and Acidobacteria. The occurrence of strictly anaerobic bacteria suggests that sediments might also undergo anoxic conditions that, in turn, could favor the accumulation of PRT in respect to CHO, assuming that fermentation of amino acids is slower than that of sugars from decomposing polysaccharides. 相似文献
4.
Wen Zhang Lin-sheng Song Jang-Seu Ki Chun-Kwan Lau Xiang-Dong Li Pei-Yuan Qian 《Estuarine, Coastal and Shelf Science》2008
Sulfate-reducing bacteria (SRB) are important regulators of a variety of processes in coastal marine sediments regarding organic matter turnover, biodegradation of pollutants, and sulfur and carbon cycles. Yet their community compositions have not been investigated in polluted harbor sediments. This study described the diversity and spatial variation of SRB communities in surface sediments in Victoria Harbor, Hong Kong. The spatial variation of SRB communities was described by terminal restriction fragment length polymorphism (T-RFLP). The results showed that the most diversified terminal restriction fragments were found at polluted sites. In addition, cluster analysis indicated that although the SRB communities were different at the two polluted sites, they were still more similar to each other than to the two more distant reference sites. Based on a dsrAB clone library constructed at a polluted site, diversified SRB were found, represented by 30 Operational Taxonomic Units (OTUs). Upon comparisons among the SRB sequences detected from this study and those in the GenBank, five clades of SRB were found. Three clades belonged to the known families Desulfobacteraceae, Desulfobulbaceae, and Syntrophobacteriaceae. The majority of sequenced clones, which distantly related to sequences in the GenBank, constituted the remaining two unclassified groups, suggesting unique SRB members related to the polluted harbor environment. Statistical analyses indicated that estimated SRB richness correlated with environment factors such as sulfur content, acid volatile sulfate, and redox potential. 相似文献
5.
洪泽湖3种沉水植物附着细菌群落结构及多样性 总被引：1，自引：0，他引：1
沉水植物茎叶表面附着的藻、菌及其他物质,不仅影响沉水植物自身生长,而且影响水体物质循环过程,附着藻类的研究已经有不少报道,但附着细菌的报道相对较少.采用末端限制性片段长度多态性(T-RFLP)技术,研究洪泽湖典型沉水植物——菹草(Potamogeton crispus)、篦齿眼子菜(Potamogeton pectinatus)、金鱼藻(Ceratophyllum demersum)在生长旺盛期叶表面附着细菌的群落结构及多样性特征,并采用冗余分析法探讨环境因子对附着细菌丰度的影响.结果表明,(1)3种沉水植物附着细菌群落结构有明显的差异性.143 bp T-RF在菹草和篦齿眼子菜中的相对丰度平均达到了20%和11%,而在金鱼藻中的相对丰度小于1%;89 bp T-RF在金鱼藻中的相对丰度平均约为13%,而在菹草和篦齿眼子菜中相对丰度小于5%.94 bp T-RF在菹草样品中相对丰度超过15%,而在其他样品中未被检测出.(2)从多样性角度分析,3种沉水植物附着细菌多样性大小依次为篦齿眼子菜菹草金鱼藻.(3)部分限制性片段的丰度受环境因子的影响较大,如89、94、143和227 bp T-RFs.而如167 bp T-RFs在3种沉水植物中的相对丰度分布较为稳定,受上述环境因子的限制较小.根据细菌比对结果,洪泽湖附着细菌的优势菌群可能属于拟杆菌门(Bacteroides)、厚壁菌门(Firmicutes)、变形菌门(Proteobacteria)3个门类. 相似文献
6.
以无震时期细菌群落及水文化学元素信息为背景,阐明有感地震时的泉水细菌群落映震特征． 2010年12月——2011年4月,乌鲁木齐周边先后发生了MS3.1和MS3.6两次有感地震．本文采用末端限制性片段长度多态性法(T-RFLP)分析了该时间段内乌鲁木齐10号泉中细菌群落结构、多样性、稳定性、优势类群及特殊类群变化特征．结果表明,水文地球化学指标对有感地震不敏感,泉水细菌群落结构稳定,地震对其优势类群及多样性影响均不显著,但无震时期部分类群（以82,170, 176, 462 bp为代表）在前后两次地震中丰度变化趋势相似,即震前有小幅上升,震后1——12天内出现极大值,之后丰度逐渐恢复至较低水平,且表现出与震级、震中距具有一定相关性．这表明部分泉水细菌对有感地震映震灵敏． 相似文献
7.
The Seine’s estuary (France) waters are the receptacle of effluents originating from wastewater treatment plants (WWTP). In this estuary, mudflats are deposition zones for sediments and their associated contaminants, and play an essential role in the mercury (Hg) biogeochemical cycle mainly due to indigenous microorganisms. Microcosms were used to assess the impact of WWTP-effluents on mercury methylation by monitoring Hg species (total dissolved Hg in porewater, methylmercury and total mercury) and on microbial communities in sediments. After effluent amendment, methylmercury (MeHg) concentrations increased in relation with the total Hg and organic matter content of the WWTP-effluents. A correlation was observed between MeHg and acid-volatile-sulfides concentrations. Quantification of sulfate-reducing microorganisms involved in Hg methylation showed no increase of their abundance but their activity was probably enhanced by the organic matter supplied with the effluents. WWTP-effluent spiking modified the bacterial community fingerprint, mainly influenced by Hg contamination and the organic matter amendment. 相似文献
8.
F. Farías J. Orlando L. Bravo R. Guevara M. Carú 《Journal of Arid Environments》2009,73(12):1117-1124
The spatial heterogeneity of resources in desert and semi-arid shrubland appears to be important in determining higher soil bacteria abundance around plants than in soil without plant cover. Thus, these bacterial communities could be important contributors to nutrient cycling in arid ecosystems. Bacterial diversity from Chilean sclerophyllous matorral was determined by Terminal Restriction Fragment Length Polymorphism (T-RFLP). Soil samples associated with the actinorhizal plant Colletia hystrix, non-actinorhizal plants and interspace soil without plant cover, were collected in May and October. The non-actinorhizal and interspace soil differed significantly in their potassium content in May and pH in October. The T-RFLP analysis revealed differences in the bacterial community structure from the different habitats. The soil bacterial communities associated with plants were the most similar, whereas the interspace soil community differed in both sampling times. The factors that best explained the groupings were potassium and pH. The greatest diversity was observed in the interspace soil. The Microbial Community Analysis showed a significant proportion of T-RFs identified as Firmicutes and Proteobacteria. Likewise, spatial and temporal differences were observed in the main groups' abundance. The dominance of Firmicutes suggests that the sclerophyllous matorral could be a different ecosystem to other arid and semi-arid soils with respect to the bacterial community structure. 相似文献
9.
微微型真核生物在海洋中广泛存在,是初级生产力的重要贡献者,也是微食物环的重要组成部分.由于微微型真核生物形体微小且不同种类缺乏明显形态学特点,故而难以利用电镜等传统方法精确研究其系统发生关系和种类组成.运用分子生物学技术直接对微微型真核生物种类组成进行研究已成为微微型真核生物多样性研究的重要方法.本文概述了目前世界范围内的微微型真核生物分子多样性研究进展以及我国在该领域中的研究状况.综述了微微型真核生物分子多样性研究中常用的靶标基因,包括18S rDNA和ITS序列等真核生物保守基因及psbA和rbcL等功能基因;常用的分子生物学方法,如克隆文库构建、DGGE/TGGE、PCR-RFLP/T-RFLP、FISH、宏基因组等;以及目前研究方法中存在的一些问题. 相似文献
10.
We studied the microbial communities collected from hydrate-bearing sediments on the North Slope of Alaska to determine how abiotic variables (e.g., grain size, hydrate presence, formation fluid gases) may correspond to the type and distribution of microbes in the sediments. The cores were acquired from sub-permafrost, Eocene (46-55 million year old) sediments in the BPXA-DOE-USGS Mount Elbert Gas Hydrate Stratigraphic Test Well within which hydrates are believed to have formed 1.5 mya. Forty samples, eight of which originally contained hydrates, were acquired from depths of ca. 606-666 m below land surface. Five drilling fluid samples acquired from the same depth range were included in the analysis as a control for possible contamination by drilling fluid microbes during the drilling and handling of cores. DNA was extracted from 15 samples (typically <1 ng DNA/g sediment was recovered) and then amplified using polymerase chain reaction with primers specific for bacterial and archaeal 16S rDNA genes, which indicates the likelihood that microbes were present in all analyzed samples. Only bacterial DNA amplicons were detected. Terminal-restriction fragment length polymorphism (T-RFLP) was used to measure bacterial diversity in the respective samples. Non-metric multidimensional scaling (NMS) was used to determine the abiotic variables that may have influenced bacterial diversity. NMS analysis revealed that the microbial taxa present in the sediment were distinct from the taxa present in the drilling fluids suggesting that the sediments were not contaminated by the drilling fluids. Multi-response permutation procedures (MRPP) found no significant difference between three sample groups identified a priori as being from within a hydrate zone, outside of hydrate zone, or on the edge of a hydrate/non-hydrate zone according to downhole nuclear magnetic resonance spectroscopy logs. However, among the several other abiotic parameters that were evaluated mud gas methane concentration and variables related to hydrate presence (e.g., chloride concentration, salinity, and resistivity) appeared to define the arrangement of microbial community signatures in plots resulting from NMS analysis. Communities from hydrate and non-hydrate layers each contained unique taxa as determined by the T-RFLP assay. 相似文献