Isolation of bacteria and 16S rDNAs from Lake Vostok accretion ice

Lake Vostok, the largest subglacial lake in Antarctica, is separated from the surface by ≈ 4 km of glacial ice. It has been isolated from direct surface input for at least 420 000 years, and the possibility of a novel environment and ecosystem therefore exists. Lake Vostok water has not been sampled, but an ice core has been recovered that extends into the ice accreted below glacial ice by freezing of Lake Vostok water. Here, we report the recovery of bacterial isolates belonging to the Brachybacteria , Methylobacterium , Paenibacillus and Sphingomonas lineages from a sample of melt water from this accretion ice that originated 3593 m below the surface. We have also amplified small-subunit ribosomal RNA-encoding DNA molecules (16S rDNAs) directly from this melt water that originated from α- and β-proteobacteria, low- and high-G+C Gram-positive bacteria and a member of the Cytophaga / Flavobacterium / Bacteroides lineage.     

Bacterial diversity in malan ice core from the Tibetan Plateau

Three ice core samples were collected from the Malan ice core drilled from the Tibetan Plateau, and three 16S rDNA clone libraries by direct amplification from the ice-melted water were established. Ninety-four clones containing bacterial 16S rDNA inserts were selected. According to restriction fragment-length polymorphism analysis, 11 clones were unique in the library from which they were obtained and used for partial sequence and phylogenetic analysis, and compared with 8 reported sequences from the same ice core at depth 70 m. Differences among the samples were apparent in clone libraries. The phylotypes were dominated by the Proteobacteria group, Acinetobacter sp. and Cytophaga-Flavobacterium-Bacteroides (CFB) group. They accounted for 92.5% (Proteobacteria), 100% (Acinetobacter sp.), 34.4% (CFB) and 100% (beta-Proteobacteria) in the clone libraries from the samples at ice depths 35, 64, 70, and 82 m, respectively. The Acinetobacter sp. was only found in the deposition at ice depth 82 m and closely clustered with gamma-Proteobateria. Two members (Malan A-21 and 101) of alpha-Proteobacteria from the sample of 35 m and two (Malan B-26 and 48) of beta-Proteobacteria of 64 m were loosely clustered (< 95% similarity) with known bacteria, represented new genera in ice bacteria.     

Diversity and association of psychrophilic bacteria in Antarctic sea ice.

The bacterial populations associated with sea ice sampled from Antarctic coastal areas were investigated by use of a phenotypic approach and a phylogenetic approach based on genes encoding 16S rRNA (16S rDNA). The diversity of bacteria associated with sea ice was also compared with the bacterial diversity of seawater underlying sea ice. Psychrophilic (optimal growth temperature, < or = 15 degrees C; no growth occurring at 20 degrees C) bacterial diversity was found to be significantly enriched in sea ice samples possessing platelet and bottom ice diatom assemblages, with 2 to 9 distinct (average, 5.6 +/- 1.8) psychrophilic taxa isolated per sample. Substantially fewer psychrophilic isolates were recovered from ice cores with a low or negligible population of ice diatoms or from under-ice seawater samples (less than one distinct taxon isolated per sample). In addition, psychrophilic taxa that were isolated from under-ice seawater samples were in general phylogenetically distinct from psychrophilic taxa isolated from sea ice cores. The taxonomic distributions of psychrotrophic bacterial isolates (optimal growth temperature, > 20 degrees C; growth can occur at approximately 4 degrees C) isolated from sea ice cores and under-ice seawater were quite similar. Overall, bacterial isolates from Antarctic sea ice were found to belong to four phylogenetic groups, the alpha and gamma subdivisions of the Proteobacteria, the gram-positive branch, and the Flexibacter-Bacteroides-Cytophaga phylum. Most of the sea ice strains examined appeared to be novel taxa based on phylogenetic comparisons, with 45% of the strains being psychrophilic. 16S rDNA sequence analysis revealed that psychrophilic strains belonged to the genera Colwellia, Shewanella, Marinobacter, Planococcus, and novel phylogenetic lineages adjacent to Colwellia and Alteromonas and within the Flexibacter-Bacteroides-Cytophaga phylum. Psychrotrophic strains were found to be members of the genera Pseudoalteromonas, Psychrobacter, Halomonas, Pseudomonas, Hyphomonas, Sphingomonas, Arthrobacter, Planococcus, and Halobacillus. From this survey, it is proposed that ice diatom assemblages provide niches conducive to the proliferation of a diverse array of psychrophilic bacterial species.     

Molecular analysis of bacterial diversity in kerosene-based drilling fluid from the deep ice borehole at Vostok, East Antarctica

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.     

橡树岭军团菌的分离及用16S rDNA测序法的鉴定

军团菌属（Ｌｅｇｉｏｎｅｌａ）自１９７１年确定以来,现已有３９个成员。军团菌属主要分布于供水系统中,如空调冷却塔水和浴池淋浴水中。我们曾于１９９４年从北京某宾馆冷却塔水中分离出一株可疑军团菌,但因缺乏标准抗血清而未能定种。由于核酸分析技术和细菌鉴定观念上进步,使我们能根据１６ＳｒＤＮＡ序列比较推测细菌间进化关系,并进而对未知细菌进行鉴定和检测。我们用以１６ＳｒＤＮＡ为靶序列的ＰＣＲ和测定鉴定,确定了该分离株为橡树岭军团菌（Ｌ．ｏａｋｒｉｄｇｅｎｓｉｓ）。     

Bacterial 16S rRNA Gene Analysis Revealed That Bacteria Related to Arcobacter spp. Constitute an Abundant and Common Component of the Oyster Microbiota (Tiostrea chilensis)

To explore the bacterial microbiota in Chilean oyster (Tiostrea chilensis), a molecular approach that permits detection of different bacteria, independently of their capacity to grow in culture media, was used. Bacterial diversity was assessed by analysis of both the 16S rDNA and the 16S-23S intergenic region, obtained by PCR amplifications of DNA extracted from depurated oysters. RFLP of the PCR amplified 16S rDNA showed a prevailing pattern in most of the individuals analyzed, indicating that a few bacterial species were relatively abundant and common in oysters. Cloning and sequencing of the 16S rDNA with the prevailing RFLP pattern indicated that this rRNA was most closely related to Arcobacter spp. However, analysis by the size of the amplified 16S-23S rRNA intergenic regions revealed not Arcobacter spp. but Staphylococcus spp. related bacteria as a major and common component in oyster. These different results may be caused by the absence of target for one of the primers employed for amplification of the intergenic region. Neither of the two bacteria species found in large abundance was recovered after culturing under aerobic, anaerobic, or microaerophilic conditions. This result, however, is expected because the number of bacteria recovered after cultivation was less than 0.01% of the total. All together, these observations suggest that Arcobacter-related strains are probably abundant and common in the Chilean oyster bacterial microbiota.     

Marine prosthecate bacteria involved in the ennoblement of stainless steel

Ennoblement, a phenomenon in which open-circuit potential is elevated to a noble value, triggers metal corrosion in the environment and is considered to be biologically catalysed. This study investigated the involvement of marine microorganisms in the ennoblement of stainless steel coupons in sea water pumped from Kamaishi Bay. Scanning electron microscopy (SEM) showed significant attachment of prosthecate bacteria on the surfaces of stainless steel coupons in the course of ennoblement. In denaturing gradient gel electrophoresis (DGGE) analyses of polymerase chain reaction-amplified bacterial 16S rDNA fragments, several major bands were detected from the surface of the ennobled coupons, including those affiliated with the alpha and gamma subclasses of the Proteobacteria. After these observations, bacterial strains were isolated from the surface of the ennobled coupon. The 16S rDNA analysis revealed that a bacterial isolate (designated PWB3) corresponded to a major DGGE band representing an alpha-Proteobacterial population; a database analysis showed that its closest relative was Rhodobium spp., albeit with low homology ( approximately 89%). SEM indicated that this bacterium was a prosthecate bacterium that was morphologically similar to those observed on the ennobled coupons. In pure culture of strain PWB3, stainless steel coupons were ennobled when the culture was supplemented with MnCl2. Manganese was recovered from the surface of the ennobled coupons after treatment with a reducing agent. These results suggest that the attachment of manganese-oxidizing prosthecate bacteria triggered the ennoblement of stainless steel in Kamaishi Bay sea water.     

Discovery and characterization of a new bacterial candidate division by an anaerobic sludge digester metagenomic approach

We have constructed a large fosmid library from a mesophilic anaerobic digester and explored its 16S rDNA diversity using a high-density filter DNA–DNA hybridization procedure. We identified a group of 16S rDNA sequences forming a new bacterial lineage named WWE3 (Waste Water of Evry 3). Only one sequence from the public databases shares a sequence identity above 80% with the WWE3 group which hence cannot be affiliated to any known or candidate prokaryotic division. Despite representing a non-negligible fraction (5% of the 16S rDNA sequences) of the bacterial population of this digester, the WWE3 bacteria could not have been retrieved using the conventional 16S rDNA amplification procedure due to their unusual 16S rDNA gene sequence. WWE3 bacteria were detected by polymerase chain reaction (PCR) in various environments (anaerobic digesters, swine lagoon slurries and freshwater biofilms) using newly designed specific PCR primer sets. Fluorescence in situ hybridization (FISH) analysis of sludge samples showed that WWE3 microorganisms are oval-shaped and located deep inside sludge flocs. Detailed phylogenetic analysis showed that WWE3 bacteria form a distinct monophyletic group deeply branching apart from all known bacterial divisions. A new bacterial candidate division status is proposed for this group.     

Total bacterial and species-specific 16S rDNA micro-array quantification of complex samples

AIMS: We describe a novel DNA-micro-array-based method that targets 16S rDNA to quantify changes in both the total bacterial DNA and the species-specific DNA composition. METHODS AND RESULTS: Quantifications were achieved by combining competitive PCR for quantifying total bacterial DNA with quantification of species-specific DNA composition based on signature 16S rDNA sequences. We constructed 11 different probes, which were evaluated on 21 different strains, in addition to complex samples. The signals obtained with sequence-specific labelling of the probes corresponded well with what should be expected based on 16S rDNA phylogenetic reconstruction. The quantification of species-specific DNA composition showed that the micro-array approach could be used to accurately determine differential growth of bacteria in mixed samples. We analysed samples containing mixtures of Lactococcus lactis and different species of propionibacteria during a 2-week incubation period. Lactococcus lactis grew fast, reaching a maximum after 12 h, Propionibacterium acidipropionici and Propionibacterium freudenreichii reached a maximum after 48 h, whereas Propionibacterium jensenii showed a slow increase during the whole growth period. The 16S rDNA total bacterial DNA quantification was compared with real-time PCR, absorbance measurements (ABS600) and colony forming units (CFU). CONCLUSION: The accuracy of the array approach was in the same range or better than the alternative techniques. The potential of the 16S rDNA micro-array method was further demonstrated using a liquid cheese model. SIGNIFICANCE AND IMPACT OF THE STUDY: This is to our knowledge the first time quantification of the total bacterial DNA and the species-specific DNA compositions of mixed populations have been achieved in the same assay.     

Genetic analysis of sea-ice bacterial communities of the Western Baltic Sea using an improved double gradient method

The bacterial diversity of sea ice from Kiel Bight obtained during the rare event of solid ice cover in spring 1996 was analysed by molecular genetic approaches using an improved double gradient denaturing gradient gel electrophoretic method (DG-DGGE) to separate 16S rDNA fragments of approximately 500 bp. The excellent separation of individual bands within these gradient gels allowed us to obtain sequence information and to allocate the phylogenetic position of representative bacteria from the sea ice. The band pattern of the gradient gels revealed a vertical stratification of the bacterial species distribution within the ice and the presence of characteristic bacteria for each layer. According to their 16S rDNA sequences, major bands of the gradient gels represented bacteria closely related to fermenting species of the genera Propionibacterium and Bacteroides and to anoxygenic phototrophic purple sulfur bacteria (Chromatiaceae). Their abundance in horizons of the inner ice core may indicate the existence of oxygen-deficient and anoxic zones or niches and possible primary production by anoxygenic photosynthesis within the investigated Baltic Sea sea ice. This is the first phylogenetic evidence of the presence, and most probably the development, of phototrophic purple sulfur bacteria in sea ice.     

Microbiota within the perennial ice cover of Lake Vida, Antarctica

Lake Vida, located in the McMurdo Dry Valleys, Antarctica, is an 'ice-sealed' lake with approximately 19 m of ice covering a highly saline water column (approximately 245 ppt). The lower portions of the ice cover and the lake beneath have been isolated from the atmosphere and land for circa 2800 years. Analysis of microbial assemblages within the perennial ice cover of the lake revealed a diverse array of bacteria and eukarya. Bacterial and eukaryal denaturing gradient gel electrophoresis phylotype profile similarities were low (<59%) between all of the depths compared (five depths spanning 11 m of the ice cover), with the greatest differences occurring between surface and deep ice. The majority of bacterial 16S rRNA gene sequences in the surface ice were related to Actinobacteria (42%) while Gammaproteobacteria (52%) dominated the deep ice community. Comparisons of assemblage composition suggest differences in ice habitability and organismal origin in the upper and lower portions of ice cover. Specifically, the upper ice cover microbiota likely reflect the modern day transport and colonization of biota from the terrestrial landscape, whereas assemblages in the deeper ice are more likely to be persistent remnant biota that originated from the ancient liquid water column of the lake that froze.     

Bacterial diversity,community structure and potential growth rates along an estuarine salinity gradient

Very little is known about growth rates of individual bacterial taxa and how they respond to environmental flux. Here, we characterized bacterial community diversity, structure and the relative abundance of 16S rRNA and 16S rRNA genes (rDNA) using pyrosequencing along the salinity gradient in the Delaware Bay. Indices of diversity, evenness, structure and growth rates of the surface bacterial community significantly varied along the transect, reflecting active mixing between the freshwater and marine ends of the estuary. There was no positive correlation between relative abundances of 16S rRNA and rDNA for the entire bacterial community, suggesting that abundance of bacteria does not necessarily reflect potential growth rate or activity. However, for almost half of the individual taxa, 16S rRNA positively correlated with rDNA, suggesting that activity did follow abundance in these cases. The positive relationship between 16S rRNA and rDNA was less in the whole water community than for free-living taxa, indicating that the two communities differed in activity. The 16S rRNA:rDNA ratios of some typically marine taxa reflected differences in light, nutrient concentrations and other environmental factors along the estuarine gradient. The ratios of individual freshwater taxa declined as salinity increased, whereas the 16S rRNA:rDNA ratios of only some typical marine bacteria increased as salinity increased. These data suggest that physical and other bottom-up factors differentially affect growth rates, but not necessarily abundance of individual taxa in this highly variable environment.     

Bacterial Community Composition in Different Sediments from the Eastern Mediterranean Sea: a Comparison of Four 16S Ribosomal DNA Clone Libraries

The regional variability of sediment bacterial community composition and diversity was studied by comparative analysis of four large 16S ribosomal DNA (rDNA) clone libraries from sediments in different regions of the Eastern Mediterranean Sea (Thermaikos Gulf, Cretan Sea, and South lonian Sea). Amplified rDNA restriction analysis of 664 clones from the libraries indicate that the rDNA richness and evenness was high: for example, a near-1:1 relationship among screened clones and number of unique restriction patterns when up to 190 clones were screened for each library. Phylogenetic analysis of 207 bacterial 16S rDNA sequences from the sediment libraries demonstrated that Gamma-, Delta-, and Alphaproteobacteria, Holophaga/Acidobacteria, Planctomycetales, Actinobacteria, Bacteroidetes, and Verrucomicrobia were represented in all four libraries. A few clones also grouped with the Betaproteobacteria, Nitrospirae, Spirochaetales, Chlamydiae, Firmicutes, and candidate division OPl 1. The abundance of sequences affiliated with Gammaproteobacteria was higher in libraries from shallow sediments in the Thermaikos Gulf (30 m) and the Cretan Sea (100 m) compared to the deeper South Ionian station (2790 m). Most sequences in the four sediment libraries clustered with uncultured 16S rDNA phylotypes from marine habitats, and many of the closest matches were clones from hydrocarbon seeps, benzene-mineralizing consortia, sulfate reducers, sulk oxidizers, and ammonia oxidizers. LIBSHUFF statistics of 16S rDNA gene sequences from the four libraries revealed major differences, indicating either a very high richness in the sediment bacterial communities or considerable variability in bacterial community composition among regions, or both.     

分子生物学技术在胃肠道微生态中应用研究进展

哺乳动物胃肠道中栖息着大量的微生物(主要为细菌),它们在营养、生理、免疫等方面对宿主起着有益作用。传统上,胃肠道菌群研究主要依靠培养技术。近来,一些基于16S rRNA(DNA)的分子生物学技术已被广泛应用于胃肠道菌群的研究,这些技术主要有16S rDNA克隆基因文库、16S rDNA指纹技术、定量PCR技术、荧光原位杂交技术及基因芯片技术等。对这些用于胃肠道微生态研究的分子生物学技术作一综述。     

Design and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting

Denaturing gradient gel electrophoresis of PCR-amplified 16S ribosomal DNA (rDNA) fragments has frequently been applied to the fingerprinting of natural bacterial populations (PCR/DGGE). In this study, sequences of bacterial universal primers frequently used in PCR/DGGE were compared with 16S rDNA sequences that represent recently proposed divisions in the domain Bacteria. We found mismatches in 16S rDNA sequences from some groups of bacteria. Inosine residues were then introduced into the bacterial universal primers to reduce amplification biases caused by these mismatches. Using the improved primers, phylotypes affiliated with Verrucomicrobia and candidate division OP11, were detected in DGGE fingerprints of groundwater populations, which have not been detected by PCR/DGGE with conventional universal primers.     

Use of Fe(III) as an Electron Acceptor To Recover Previously Uncultured Hyperthermophiles: Isolation and Characterization of Geothermobacterium ferrireducens gen. nov., sp. nov.

It has recently been recognized that the ability to use Fe(III) as a terminal electron acceptor is a highly conserved characteristic in hyperthermophilic microorganisms. This suggests that it may be possible to recover as-yet-uncultured hyperthermophiles in pure culture if Fe(III) is used as an electron acceptor. As part of a study of the microbial diversity of the Obsidian Pool area in Yellowstone National Park, Wyo., hot sediment samples were used as the inoculum for enrichment cultures in media containing hydrogen as the sole electron donor and poorly crystalline Fe(III) oxide as the electron acceptor. A pure culture was recovered on solidified, Fe(III) oxide medium. The isolate, designated FW-1a, is a hyperthermophilic anaerobe that grows exclusively by coupling hydrogen oxidation to the reduction of poorly crystalline Fe(III) oxide. Organic carbon is not required for growth. Magnetite is the end product of Fe(III) oxide reduction under the culture conditions evaluated. The cells are rod shaped, about 0.5 μm by 1.0 to 1.2 μm, and motile and have a single flagellum. Strain FW-1a grows at circumneutral pH, at freshwater salinities, and at temperatures of between 65 and 100°C with an optimum of 85 to 90°C. To our knowledge this is the highest temperature optimum of any organism in the Bacteria. Analysis of the 16S ribosomal DNA (rDNA) sequence of strain FW-1a places it within the Bacteria, most closely related to abundant but uncultured microorganisms whose 16S rDNA sequences have been previously recovered from Obsidian Pool and a terrestrial hot spring in Iceland. While previous studies inferred that the uncultured microorganisms with these 16S rDNA sequences were sulfate-reducing organisms, the physiology of the strain FW-1a, which does not reduce sulfate, indicates that these organisms are just as likely to be Fe(III) reducers. These results further demonstrate that Fe(III) may be helpful for recovering as-yet-uncultured microorganisms from hydrothermal environments and illustrate that caution must be used in inferring the physiological characteristics of at least some thermophilic microorganisms solely from 16S rDNA sequences. Based on both its 16S rDNA sequence and physiological characteristics, strain FW-1a represents a new genus among the Bacteria. The name Geothermobacterium ferrireducens gen. nov., sp. nov., is proposed (ATCC BAA-426).     

Population diversity in model potable water biofilms receiving chlorine or chloramine residual

Most water utilities use chlorine or chloramine to produce potable water. These disinfecting agents react with water to produce residual oxidants within a water distribution system (WDS) to control bacterial growth. While monochloramine is considered more stable than chlorine, little is known about the effect it has on WDS biofilms. Community structure of 10-week old WDS biofilms exposed to disinfectants was assessed after developing model biofilms from unamended distribution water. Four biofilm types were developed on polycarbonate slides within annular reactors while receiving chlorine, chloramine, or inactivated disinfectant residual. Eubacteria were identified through 16S rDNA sequence analysis. The model WDS biofilm exposed to chloramine mainly contained Mycobacterium and Dechloromonas sequences, while a variety of alpha- and additional beta-proteobacteria dominated the 16S rDNA clone libraries in the other three biofilms. Additionally, bacterial clones distantly related to Legionella were found in one of the biofilms receiving water with inactivated chlorine residual. The biofilm reactor receiving chloraminated water required increasing amounts of disinfectant after 2 weeks to maintain chlorine residual. In contrast, free chlorine residual remained steady in the reactor that received chlorinated water. The differences in bacterial populations of potable water biofilms suggest that disinfecting agents can influence biofilm development. These results also suggest that biofilm communities in distribution systems are capable of changing in response to disinfection practices.     

Unbiased analyses of ITS folding motifs in a taxonomically confusing lineage: Anagnostidinema visiae sp. nov. (cyanobacteria)

Cyanobacteria are diverse prokaryotic, photosynthetic organisms present in nearly every known ecosystem. Recent investigations around the world have recovered vast amounts of novel biodiversity in seldom sampled habitats. One phylogenetically significant character, the secondary folding structures of the 16S–23S ITS rDNA region, has allowed an unprecedented capacity to erect new species. However, two questions arise: Is this feature as informative as is proposed, and how do we best employ these features? Submerged sinkholes with oxygen-poor, sulfur-rich ground water in Lake Huron (USA) contain microbial mats dominated by both oxygenic and anoxygenic cyanobacteria. We sought to document some of this unique cyanobacterial diversity. Using culture-based investigations, we recovered 45 strains, of which 23 were analyzed employing 16S–23S rDNA sequences, ITS folding patterns, ecology, and morphology. With scant morphological discontinuities and nebulous 16S rDNA gene sequence divergence, ITS folding patterns were effective at articulating cryptic biodiversity. However, we would have missed these features had we not folded all the available motifs from the strains, including those with highly similar 16S rDNA gene sequences. If we had relied solely on morphological or 16S rDNA gene data, then we might well have missed the diversity of Anagnostidinema. Thus, in order to avoid conformation basis, which is potentially common when employing ITS structures, we advocate clustering strains based on ITS rDNA region patterns independently and comparing them back to 16S rDNA gene phylogenies. Using a total evidence approach, we erected a new taxon according to the International Code of Nomenclature for Algae, Fungi, and Plants: Anagnostidinema visiae.     

Development of a real-time PCR method for the detection of fossil 16S rDNA fragments of phototrophic sulfur bacteria in the sediments of Lake Cadagno

Lake Cadagno is a crenogenic meromictic lake situated in the southern range of the Swiss Alps characterized by a compact chemocline that has been the object of many ecological studies. The population dynamics of phototrophic sulfur bacteria in the chemocline has been monitored since 1994 with molecular methods such as 16S rRNA gene clone library analysis. To reconstruct paleo-microbial community dynamics, we developed a quantitative real-time PCR methodology for specific detection of 16S rRNA gene sequences of purple and green sulfur bacteria populations from sediment samples. We detected fossil 16S rDNA of nine populations of phototrophic sulfur bacteria down to 9-m sediment depth, corresponding to about 9500 years of the lake's biogeological history. These results provide the first evidence for the presence of 16S rDNA of anoxygenic phototrophic bacteria in Holocene sediments of an alpine meromictic lake and indicate that the water column stratification and the bacterial plume were already present in Lake Cadagno thousands of years ago. The finding of Chlorobium clathratiforme remains in all the samples analyzed shows that this population, identified in the water column only in 2001, was already a part of the lake's biota in the past.     

东北太平洋深海沉积物细菌多样性

采用两种方法提取中国结核合同区东区沉积物不同层次总DNA,通过克隆测序构建了含有79个克隆子的细菌16S rRNA基因文库,分析了该海域沉积物中细菌的多样性.79个克隆在系统发育树中形成了11个大分支,包括Gamma proteobacteria(22.8%),Alpha proteobacteria(16.5%),Planctomycetacia(7.6%),Delta proteobacteria(6.3%), Nitrospira(6.3%),Actinobacteria(6.3%),Beta proteobacteria(5%),Acidobacteria(5.1%),Sphingobacteria(3.8%),Firmicutes(2.5%),Other bacteria(17.7%),其中Gamma proteobacteria在总文库中所占比例最高,该分支细菌在0～2cm、4～6cm层也是优势菌种.Gamma proteobacteria中假单胞菌(Pseudomonas)为优势属(22.2%).各个层次中所含细菌类群有所不同,Alpha proteobacteria、Gamma proteobacteria、Delta proteobacteria 、Planctomycetacia、Nitrospira 、Actinobacteria和Acidobacteria为三层样品共有类群.