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1.
Fluorescent microspheres were applied in a novel fashion during subsurface drilling of permafrost and ground ice in the Canadian High Arctic to monitor the exogenous microbiological contamination of core samples obtained during the drilling process. Prior to each drill run, a concentrated fluorescent microsphere (0.5-μm diameter) solution was applied to the interior surfaces of the drill bit, core catcher, and core tube and allowed to dry. Macroscopic examination in the field demonstrated reliable transfer of the microspheres to core samples, while detailed microscopic examination revealed penetration levels of less than 1 cm from the core exterior. To monitor for microbial contamination during downstream processing of the permafrost and ground ice cores, a Pseudomonas strain expressing the green fluorescent protein (GFP) was painted on the core exterior prior to processing. Contamination of the processed core interiors with the GFP-expressing strain was not detected by culturing the samples or by PCR to detect the gfp marker gene. These methodologies were quick, were easy to apply, and should help to monitor the exogenous microbiological contamination of pristine permafrost and ground ice samples for downstream culture-dependent and culture-independent microbial analyses.  相似文献   

2.
The current understanding of microbes inhabiting deeply buried marine sediments is based largely on samples collected from continental shelves in tropical and temperate latitudes. The geographical range of marine subsurface coring was expanded during the Integrated Ocean Drilling Program Arctic Coring Expedition (IODP ACEX). This expedition to the ice-covered central Arctic Ocean successfully cored the entire 428 m sediment stack on the Lomonosov Ridge during August and September 2004. The recovered cores vary from siliciclastic sediment low in organic carbon (< 0.2%) to organic rich (∼3%) black sediments that rapidly accumulated in the early middle Eocene. Three geochemical environments were characterized based on chemical analyses of porewater: an upper ammonium oxidation zone, a carbonate dissolution zone and a deep (> 200 m below sea floor) sulfate reduction zone. The diversity of microbes within each zone was assessed using 16S rRNA phylogenetic markers. Bacterial 16S rRNA genes were successfully amplified from each of the biogeochemical zones, while archaea was only amplified from the deep sulfate reduction zone. The microbial communities at each zone are phylogenetically different and are most closely related to those from other deep subsurface environments.  相似文献   

3.
The validation of microbiological results from non-aseptically drilled deep ice cores is challenging because exogenous microbial cells can be transported into the core interior and compromise the existing microbial populations. The NEEM (North Eemian) ice core in Greenland provided a first-time opportunity to use fluorescent microspheres as tracers for assessing potential microbial contamination of glacial ice. We developed specific procedures to coat the surfaces of selected NEEM core samples representing bubbly (93–100 m), brittle (633–644 m) and clathrated (1,730 and 2,050 m) ice with melamine-based carboxylated fluorescent microspheres and tracked periodically their penetration into the core interior for 2.5 years using flow cytometry. Sufficient ice surface coating was achieved by immersing retrieved cores in plastic bags containing suspensions of pre-counted 1- and 10-μm microspheres or by down-hole microsphere deployment in plastic sleeves attached to the drill barrel and liberated during drilling. We examined the relationship between microspheres penetration and ice core depth, structure and time after coating. One consistent observation for all cores (except the brittle ice) was that removing a few millimeters of the outer layer drastically reduced microsphere counts, independent of timing, indicating that penetration was mostly limited to the surface layers. Any deeper penetration was found to be microsphere size dependent. The brittle ice showed significant microsphere penetration possibly due to microfractures. Overall, the use of fluorescent microspheres as tracers and microbial surrogates proved to be a sensitive approach for testing potential contamination during deep core projects.  相似文献   

4.
Characterization of trace fossils in marine core sediments is, most times, difficult due to the weak differentiation between biogenic structures and the host sediment, especially in pelagic and hemipelagic facies. This problem is accentuated where a high degree of bioturbation is associated with composite ichnofabrics. Simple methods are presented here based on modifications to image features such as contrast, brightness, vibrance, saturation, exposure, lightness, and color balance using the software Adobe Photoshop CS6 (Adobe Systems, San Jose, CA, USA) to enhance visibility and thus allow for a better identification of the trace fossils. Adjustments involving brightness, levels and vibrance generally give better results. This approach was applied to marine cores of pelagic and hemipelagic sediments obtained from the Integrated Ocean Drilling Program Expedition 339, Site U1385. Enhancing the digital images facilitates ichnological analysis through improving the visibility of weakly observed trace fossils, and in some cases revealing traces not detected previously.  相似文献   

5.
Decontamination of ice cores is a critical issue in phylogenetic studies of glacial ice and subglacial lakes. At the Vostok drill site, a total of 3650 m of ice core have now been obtained from the East Antarctic ice sheet. The ice core surface is coated with a hard-to-remove film of impure drilling fluid comprising a mixture of aliphatic and aromatic hydrocarbons and foranes. In the present study we used 16S rRNA gene sequencing to analyze the bacterial content of the Vostok drilling fluid sampled from four depths in the borehole. Six phylotypes were identified in three of four samples studied. The two dominant phylotypes recovered from the deepest (3400 and 3600 m) and comparatively warm (-10 degrees C and -6 degrees C, respectively) borehole horizons were from within the genus Sphingomonas, a well-known degrader of polyaromatic hydrocarbons. The remaining phylotypes encountered in all samples proved to be human- or soil-associated bacteria and were presumed to be drilling fluid contaminants of rare occurrence. The results obtained indicate the persistence of bacteria in extremely cold, hydrocarbon-rich environments. They show the potential for contamination of ice and subglacial water samples during lake exploration, and the need to develop a microbiological database of drilling fluid findings.  相似文献   

6.
Calcareous Nannofossils are widely utilized in biostratigraphic studies of Cenozoic sediments. In recent years large datasets have been acquired, and several bioevents showed to be unreliable when correlated over distant areas. New biostratigraphic investigations of middle Eocene-upper Oligocene deep-sea cores have highlighted problematic areas in the currently used calcareous nannofossil zonal schemes for the Southern Ocean. Quantitative analysis on sediments from seven ODP (Ocean Drilling Program) sites from this area, characterized by abundant, diverse, and moderately to well-preserved nannofloral assemblages, have enabled a revision of the existing zonation for the Southern Ocean, and the development of a high-resolution zonal scheme. Eleven zones and six subzones are introduced or emended to replace the ten zones and two subzones of the Wei and Wise (1990a) and Wei and Thierstein (1991), with the identification of several new biohorizons. New age calibrations are provided improving regional correlations and evaluating the reliability of the identified events for supraregional correlations. Comparisons are made between the proposed zonation and the existing schemes, both on nannofossils from different geographic areas, and on foraminifers from southern high latitudes.  相似文献   

7.
Methane hydrates represent an enormous carbon and energy source in many low temperature deep marine sediments. However, little information is available concerning the nature of the microbial communities associated with these structures. Here, we describe a phylogenetic analysis based on ribosomal DNA (rDNA) sequences obtained from sediment and fluid samples present in a region of gas hydrate formation in shallow sediments within the Cascadia margin in and around Ocean Drilling Program (ODP) Site 892B. Our studies detected diverse sulfur-utilizing microbes, methanogens, methanotrophs, and non-thermophilic members of the kingdom Crenarchaeota. This is the first culture-independent phylogenetic analysis of a gas hydrate habitat.  相似文献   

8.
Previous data have shown that reducing agents disrupt the structure of vaccinia virus (vv). Here, we have analyzed the disulfide bonding of vv proteins in detail. In vv-infected cells cytoplasmically synthesized vv core proteins became disulfide bonded in the newly assembled intracellular mature viruses (IMVs). vv membrane proteins also assembled disulfide bonds, but independent of IMV formation and to a large extent on their cytoplasmic domains. If disulfide bonding was prevented, virus assembly was only partially impaired as shown by electron microscopy as well as a biochemical assay of IMV formation. Under these conditions, however, the membranes around the isolated particles appeared less stable and detached from the underlying core. During the viral infection process the membrane proteins remained disulfide bonded, whereas the core proteins were reduced, concomitant with delivery of the cores into the cytoplasm. Our data show that vv has evolved an unique system for the assembly of cytoplasmic disulfide bonds that are localized both on the exterior and interior parts of the IMV.  相似文献   

9.
International drilling projects for the study of microbial communities in the deep-subsurface hot biosphere have been expanded. Core samples obtained by deep drilling are commonly contaminated with mesophilic microorganisms in the drilling fluid, making it difficult to examine the microbial community by 16S rRNA gene clone library analysis. To eliminate mesophilic organism contamination, we previously developed a new method (selective phylogenetic analysis [SePA]) based on the strong correlation between the guanine-plus-cytosine (G+C) contents of the 16S rRNA genes and the optimal growth temperatures of prokaryotes, and we verified the method's effectiveness (H. Kimura, M. Sugihara, K. Kato, and S. Hanada, Appl. Environ. Microbiol. 72:21-27, 2006). In the present study we ascertained SePA's ability to eliminate contamination by archaeal rRNA genes, using deep-sea hydrothermal fluid (117 degrees C) and surface seawater (29.9 degrees C) as substitutes for deep-subsurface geothermal samples and drilling fluid, respectively. Archaeal 16S rRNA gene fragments, PCR amplified from the surface seawater, were denatured at 82 degrees C and completely digested with exonuclease I (Exo I), while gene fragments from the deep-sea hydrothermal fluid remained intact after denaturation at 84 degrees C because of their high G+C contents. An examination using mixtures of DNAs from the two environmental samples showed that denaturation at 84 degrees C and digestion with Exo I completely eliminated archaeal 16S rRNA genes from the surface seawater. Our method was quite useful for culture-independent community analysis of hyperthermophilic archaea in core samples recovered from deep-subsurface geothermal environments.  相似文献   

10.
The Brazos-Trinity Basin on the slope of the Gulf of Mexico passive margin was drilled during Integrated Ocean Drilling Progam Expedition 308. The buried anaerobic sediments of this basin are largely organic-poor and have few microbial inhabitants compared with the organic-rich sediments with high cell counts from the Peru Margin that were drilled during Ocean Drilling Program Leg 201. Nucleic acids were extracted from Brazos-Trinity Basin sediments and were subjected to whole-genome amplification and pyrosequencing. A comparison of the Brazos-Trinity Basin metagenome, consisting of 105 Mbp, and the existing Peru Margin metagenome revealed trends linking gene content, phylogenetic content, geological location and geochemical regime. The major microbial groups (Proteobacteria, Firmicutes, Euryarchaeota and Chloroflexi) occur consistently throughout all samples, yet their shifting abundances allow for discrimination between samples. The cluster of orthologous groups category abundances for some classes of genes are correlated with geochemical factors, such as the level of ammonia. Here we describe the sediment metagenome from the oligotrophic Brazos-Trinity Basin (Site 1320) and show similarities and differences with the dataset from the Pacific Peru Margin (Site 1229) and other pyrosequenced datasets. The microbial community found at Integrated Ocean Drilling Program Site 1320 likely represents the subsurface microbial inhabitants of turbiditic slopes that lack substantial upwelling.  相似文献   

11.
Surface microbiological investigations are critically dependent on the procedures used to collect samples for study. It can be difficult to distinguish between indigenous organisms and those encountered as contaminants during the drilling process. We found that coliform bacteria contaminated drilling mud slurries. These bacteria proved useful as tracer organisms in evaluating the degree of microbial contamination accidentally encountered while drilling for subterranean samples. While these organisms were found in high numbers in both the circulating muds and in the mud reservoir, few subsurface samples harbored conforms. Subsurface slurries did not inhibit the growth of a known coliform inoculum. These results indicate that the methods used to collect and field‐process cores from Atlantic coastal plain sediments were sufficient to prevent a large degree of bacterial contamination in most samples. The microflora in drilling fluids did not quantitatively or qualitatively account for the number and diversity of bacteria in subsurface samples. We conclude that a large and viable bacterial community is present in deep regions of the terrestrial subsurface.  相似文献   

12.
土壤砷污染对蔬菜砷含量及食用安全性的影响   总被引:64,自引:4,他引:64  
对湖南郴州砷污染区的土壤和蔬菜砷含量进行了研究 ,结果表明该地区土壤含砷量为 19.5~ 2 37.2 mg/ kg、平均为 6 3.9mg/ kg、中值为 4 7.8mg/ kg,比全国平均土壤含砷量 (9.2 m g/ kg)高 2~ 2 5倍 ;蔬菜可食部分砷含量范围为 0 .0 4~ 2 .6 4 m g/ kg、平均为 0 .74 mg/ kg、中值为 0 .5 4 mg/ kg,5 4 %的蔬菜可食部分含砷量超过了《蔬菜卫生标准》规定的最大允许量 (MPC≥ 0 .5mg/ kg) ;菠菜 ,茼蒿和生菜可食部分超标比较严重 ,最大砷含量超出 MPC 5倍左右。  相似文献   

13.
The properties of a nonuniformly distributed biocatalyst, where the active enzymes are immobilized on the exterior or the interior portions o a solid support, are compared with those of a conventional biocatalyst which is uniformly distributed in a spherical geometry. To investigate the performance of nonuniformly distributed biocatalysts their effectiveness factors are computed and compared for six different enzyme distribution configurations: one-half core, one-half shell, one-third center space, one-third middle annulus, one-third outer shell, and the uniformly distributed. According to the results of numerical analysis, the biocatalyst performance of the exterior "shell" configuration is always far more effective for the immobilized enzymes with positive order reaction kinetics such as Michaelis-Menten and competitive product inhibition. However, in the case of negative order enzymatic reaction kinetics such as substrate inhibition, the interior "core" configuration of the biocatalyst can render far greater enzyme utilization efficiency.  相似文献   

14.
International drilling projects for the study of microbial communities in the deep-subsurface hot biosphere have been expanded. Core samples obtained by deep drilling are commonly contaminated with mesophilic microorganisms in the drilling fluid, making it difficult to examine the microbial community by 16S rRNA gene clone library analysis. To eliminate mesophilic organism contamination, we previously developed a new method (selective phylogenetic analysis [SePA]) based on the strong correlation between the guanine-plus-cytosine (G+C) contents of the 16S rRNA genes and the optimal growth temperatures of prokaryotes, and we verified the method's effectiveness (H. Kimura, M. Sugihara, K. Kato, and S. Hanada, Appl. Environ. Microbiol. 72:21-27, 2006). In the present study we ascertained SePA's ability to eliminate contamination by archaeal rRNA genes, using deep-sea hydrothermal fluid (117°C) and surface seawater (29.9°C) as substitutes for deep-subsurface geothermal samples and drilling fluid, respectively. Archaeal 16S rRNA gene fragments, PCR amplified from the surface seawater, were denatured at 82°C and completely digested with exonuclease I (Exo I), while gene fragments from the deep-sea hydrothermal fluid remained intact after denaturation at 84°C because of their high G+C contents. An examination using mixtures of DNAs from the two environmental samples showed that denaturation at 84°C and digestion with Exo I completely eliminated archaeal 16S rRNA genes from the surface seawater. Our method was quite useful for culture-independent community analysis of hyperthermophilic archaea in core samples recovered from deep-subsurface geothermal environments.  相似文献   

15.
There has been an increasing interest in seafloor exploitation such as mineral mining in deep-sea hydrothermal fields, but the environmental impact of anthropogenic disturbance to the seafloor is poorly known. In this study, the effect of such anthropogenic disturbance by scientific drilling operations (IODP Expedition 331) on seabed landscape and megafaunal habitation was surveyed for over 3 years using remotely operated vehicle video observation in a deep-sea hydrothermal field, the Iheya North field, in the Okinawa Trough. We focused on observations from a particular drilling site (Site C0014) where the most dynamic change of landscape and megafaunal habitation was observed among the drilling sites of IODP Exp. 331. No visible hydrothermal fluid discharge had been observed at the sedimentary seafloor at Site C0014, where Calyptogena clam colonies were known for more than 10 years, before the drilling event. After drilling commenced, the original Calyptogena colonies were completely buried by the drilling deposits. Several months after the drilling, diffusing high-temperature hydrothermal fluid began to discharge from the sedimentary subseafloor in the area of over 20 m from the drill holes, ‘artificially’ creating a new hydrothermal vent habitat. Widespread microbial mats developed on the seafloor with the diffusing hydrothermal fluids and the galatheid crab Shinkaia crosnieri endemic to vents dominated the new vent community. The previously soft, sedimentary seafloor was hardened probably due to barite/gypsum mineralization or silicification, becoming rough and undulated with many fissures after the drilling operation. Although the effects of the drilling operation on seabed landscape and megafaunal composition are probably confined to an area of maximally 30 m from the drill holes, the newly established hydrothermal vent ecosystem has already lasted 2 years and is like to continue to exist until the fluid discharge ceases and thus the ecosystem in the area has been altered for long-term.  相似文献   

16.
It was found that inflating tube is most rarely contaminated with microorganisms during the use of ultrasonic inhalator TUR USI 70. Glass cylinder is contaminated more frequently whereas a diaphragm, aerosol preparation, inhaling mask and a pipe joining it with the device are contaminated most frequently. Sporadic contamination of the inflating tube indicate an efficient work of air filters while frequent contamination of the diaphragm, aerosol preparation and glass cylinder prove that the contamination is caused by a coupling fluid. It was also found that ultrasound exerts a destructive effect on microorganisms in the aerosol preparation. The investigations have shown that the inhaling mask and tubes joining it with the device should be changed before each use while the other parts of an inhalator and aerosol preparation may be changed once per 15 inhalations. It was also noted that disinfection of different parts of the device by a 2% aqueous glutaric aldehyde (30 minutes at room temperature) is efficient in about 95%.  相似文献   

17.
Quality assurance and control (QA/QC) is significant for the scientific drilling in order to accurately characterize physical, geochemical, and biological properties in the cored deep subseafloor materials. To explore the deep subseafloor life and its biosphere, identification and control of microbial contamination in drilling cores is critical for highly sensitive molecular analyses as well as cultivations, especially for the evaluation of low biomass and/or extremely harsh deep environments. Here we report some microbiological characteristics of circulation mud fluids before and after the first riser drilling operation by the newly constructed deep-earth research vessel Chikyu. During the Chikyu shakedown expedition CK06-06 in 2006, we used the riser system for drilling 547 to 647 meter below the seafloor into the sediments offshore the Shimokita Peninsula of Japan. Cultivation experiments showed that no microbial growth was observed in the precirculation mud fluid, while 4 × 105 colonies per 1 ml were observed in the postcirculation mud fluid; all cultured bacterial isolates were found to be Halomonas. Using culture-independent molecular analysis, 16S rRNA gene sequences of Xanthomonas, which is used for industrial production of the mud fluid viscosifier “xanthan gum”, were predominantly detected in the precirculation mud fluid, while Halomonas sequences consistently dominated the clone library constructed from the postcirculation mud fluid. Archaeal 16S rRNA genes were amplified only from the postcirculation mud fluid; these archaeal clone sequences were affiliated to the Marine Crenarchaeota Group I (MGI), Marine Euryarchaeota Group II (MGII), Miscellaneous Crenarchaeotic Group (MCG), South African Gold Mine Euryarchaeotic Group (SAGMEG), Soil Group, and Methanococcus aeolicus. These results suggest that Halomonas contaminated and grew in the tank of circulation mud fluids, and other indigenous deep subseafloor microbial components, especially deep subsurface archaea, were also mixed into the post-circulation mud fluid.  相似文献   

18.
Subseafloor sulfate concentrations typically decrease with depth as this electron acceptor is consumed by respiring microorganisms. However, studies show that seawater can flow through hydraulically conductive basalt to deliver sulfate upwards into deeply buried overlying sediments. Our previous work on IODP Site C0012A (Nankai Trough, Japan) revealed that recirculation of sulfate through the subducting Philippine Sea Plate stimulated microbial activity near the sediment–basement interface (SBI). Here, we describe the microbial ecology, phylogeny, and energetic requirements of population of aero‐tolerant sulfate‐reducing bacteria in the deep subseafloor. We identified dissimilatory sulfite reductase gene (dsr) sequences 93% related to oxygen‐tolerant Desulfovibrionales species across all reaction zones while no SRB were detected in drilling fluid control samples. Pore fluid chemistry revealed low concentrations of methane (<0.25 mM), while hydrogen levels were consistent with active bacterial sulfate reduction (0.51–1.52 nM). Solid phase total organic carbon (TOC) was also considerably low in these subseafloor sediments. Our results reveal the phylogenetic diversity, potential function, and physiological tolerance of a community of sulfate‐reducing bacteria living at ~480 m below subducting seafloor.  相似文献   

19.
Aquatic mosses in the genera Bryum and Leptobryum form unique tower-like ??moss pillars?? underwater in some Antarctic lakes, in association with algae and cyanobacteria. These are communities with a two-layer structure comprising an oxidative exterior and reductive interior. Although habitats and photosynthetic properties of moss pillars have been reported, microfloral composition of the two-layer structure has not been described. Here we report fatty acid analysis of one moss pillar and molecular phylogenetic analysis, based on the 16S rRNA gene, of this and one other moss pillar. Cluster analysis of the phospholipid fatty acid composition showed three groups corresponding to the exterior, upper interior, and lower interior of the pillar. This suggested that species composition differed by section, with the exterior dominated by photosynthetic organisms such as mosses, algae, and cyanobacteria, the upper interior primarily containing gram-positive bacteria and anaerobic sulfate-reducing bacteria, and the lower interior dominated by gram-negative bacteria. Molecular phylogenetic analysis revealed that Proteobacteria dominate the moss pillar as a whole; cyanobacteria were found on the exterior and the gram-positive obligate anaerobe Clostridium in the interior, while gram-positive sulfate-reducing bacteria were present in the lowest part of the interior. Nitrogen-fixing bacteria and denitrifying bacteria were found in all sections. Thus, fatty acid analysis and genetic analysis showed similar patterns. These findings suggest that microorganisms of different phylogenetic groups inhabit different sections of a single moss pillar and form a microbial community that performs biogeochemical cycling to establish and maintain a structure in an oxidation?Creduction gradient between exterior and interior.  相似文献   

20.
Challenger Mound, a 150‐m‐high cold‐water coral mound on the eastern flank of the Porcupine Seabight off SW Ireland, was drilled during Expedition 307 of the Integrated Ocean Drilling Program (IODP). Retrieved cores offer unique insight into an archive of Quaternary paleo‐environmental change, long‐term coral mound development, and the diagenetic alteration of these carbonate fabrics over time. To characterize biogeochemical carbon–iron–sulfur transformations in the mound sediments, the contents of dithionite‐ and HCl‐extractable iron phases, iron monosulfide and pyrite, and acid‐extractable calcium, magnesium, manganese, and strontium were determined. Additionally, the stable isotopic compositions of pore‐water sulfate and solid‐phase reduced sulfur compounds were analyzed. Sulfate penetrated through the mound sequence and into the underlying Miocene sediments, where a sulfate–methane transition zone was identified. Small sulfate concentration decreases (<7 mm ) within the top 40 m of the mound suggested slow net rates of present‐day organoclastic sulfate reduction. Increasing δ34S‐sulfate values due to microbial sulfate reduction mirrored the decrease in sulfate concentrations. This process was accompanied by oxygen isotope exchange with water that was indicated by increasing δ18O‐sulfate values, reaching equilibrium with pore‐water at depth. Below 50 mbsf, sediment intervals with strong 34S‐enriched imprints on chromium‐reducible sulfur (pyrite S), high degree‐of‐pyritization values, and semi‐lithified diagenetic carbonate‐rich layers characterized by poor coral preservation, were observed. These layers provided evidence for the occurrence of enhanced microbial sulfate‐reducing activity in the mound in the past during periods of rapid mound aggradation and subsequent intervals of non‐deposition or erosion when geochemical fronts remained stationary. During these periods, especially during the Early Pleistocene, elevated sulfate reduction rates facilitated the consumption of reducible iron oxide phases, coral dissolution, and the subsequent formation of carbonate cements.  相似文献   

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