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1.
Archaeal 16S rDNA clone libraries were constructed for samples taken at 10, 20 and 30 m depth in a landfill, which corresponded approximately 3, 6 and 9 years operation, respectively. Sequencing and phylogenetic analyses of representative clones showed that all of the rDNAs were closely related to typical methanogens. The distributions of phylotypes in clone libraries were similar to each other. Dominant clones in all the clone libraries were closely related to thermophilic species, such as Methanothermobacter thermautotrophicus, suggesting that the temperatures at these sites were high. This was supported by the results of H2-dependent methanogenic activity tests, showing that the activities of all samples at 55 °C were much higher than those at 25 °C. 相似文献
2.
Endophytic Bacterial Diversity in Rice (Oryza sativa L.) Roots Estimated by 16S rDNA Sequence Analysis 总被引:2,自引:0,他引:2
The endophytic bacterial diversity in the roots of rice (Oryza sativa L.) growing in the agricultural experimental station in Hebei Province, China was analyzed by 16S rDNA cloning, amplified
ribosomal DNA restriction analysis (ARDRA), and sequence homology comparison. To effectively exclude the interference of chloroplast
DNA and mitochondrial DNA of rice, a pair of bacterial PCR primers (799f–1492r) was selected to specifically amplify bacterial
16S rDNA sequences directly from rice root tissues. Among 192 positive clones in the 16S rDNA library of endophytes, 52 OTUs
(Operational Taxonomic Units) were identified based on the similarity of the ARDRA banding profiles. Sequence analysis revealed
diverse phyla of bacteria in the 16S rDNA library, which consisted of alpha, beta, gamma, delta, and epsilon subclasses of
the Proteobacteria, Cytophaga/Flexibacter/Bacteroides (CFB) phylum, low G+C gram-positive bacteria, Deinococcus-Thermus, Acidobacteria, and archaea. The dominant group was Betaproteobacteria (27.08% of the total clones), and the most dominant
genus was Stenotrophomonas. More than 14.58% of the total clones showed high similarity to uncultured bacteria, suggesting that nonculturable bacteria
were detected in rice endophytic bacterial community. To our knowledge, this is the first report that archaea has been identified
as endophytes associated with rice by the culture-independent approach. The results suggest that the diversity of endophytic
bacteria is abundant in rice roots. 相似文献
3.
Comparison and Characterization of Microbial Communities in Sulfide-rich Wastewater with and without Propidium Monoazide Treatment 总被引:2,自引:0,他引:2
A 16S rRNA gene-based culture-independent approach was used to study the bacterial and archaeal communities in a sulfide-rich
wastewater. Propidium Monoazide (PMA) treatment was applied to limit the analysis to the fraction of viable cells in environment.
A total of 104 and 68 clones respective from bacterial clone library and archaeal library were picked and analyzed by restriction
fragment length polymorphism (RFLP). 35 RFLP patterns from bacterial clone library and 10 RFLP patterns from archaeal clone
library were unique and the respective clones were selected for sequencing. BLAST analysis and RFLP analysis showed that the
bacterial clone library mainly consisted of Gammaproteobacteria (73%), Anaerolineae (6%), Bacilli (5%), Deltaproteobacteria (7%), Clostridia (4%), Bacteroidetes (1%), and Chlorobia (1%); Methanomicrobia (99%) and Thermococci (1%) were the only two lineages of the archaeal domains. This study gave a first insight into the overall microbial structure
in a cloth printing and dyeing wastewater treatment plant with high concentration of sulfide and increased knowledge on the
applicability of the PMA treatment in combination with PCR-based molecular techniques to analyze only viable cells in microbial
ecology. 相似文献
4.
Diversity of bacterial community in freshwater of Woopo wetland 总被引:1,自引:0,他引:1
Keun Sik Baik Seong Chan Park Eun Mi Kim Kyung Sook Bae Jae-Hyung Ann Jong-Ok Ka Jongsik Chun Chi Nam Seong 《Journal of microbiology (Seoul, Korea)》2008,46(6):647-655
Diversity of bacterial community in water layer of Woopo wetland was investigated. Cultivable bacterial strains were isolated
by the standard dilution plating technique and culture-independent 16S rRNA gene clones were obtained directly from DNA extracts
of a water sample. Amplified rDNA restriction analysis (ARDRA) was applied onto both of the isolates and 16S rRNA gene clones.
Rarefaction curves, coverage rate and diversity indices of ARDRA patterns were calculated. Representative isolates and clones
of all the single isolate/clone phylotype were partially sequenced and analyzed phylogenetically. Sixty-four and 125 phylotypes
were obtained from 203 bacterial isolates and 235 culture-independent 16S rRNA gene clones, respectively. Bacterial isolates
were composed of 4 phyla, of which Firmicutes (49.8%) and Actinobacteria (32.0%) were predominant. Isolates were affiliated with 58 species. Culture-independent 16S rRNA gene clones were composed
of 8 phyla, of which Proteobacteria (62.2%), Actinobacteria (15.5%), and Bacteroidetes (13.7%) were predominant. Diversity of 16S rRNA gene clones originated from cultivation-independent DNA extracts was higher
than that of isolated bacteria. 相似文献
5.
Xu Bo Huang Zun‐xi Wang Xiao‐yan Gao Run‐chi Tang Xiang‐hua Mu Yue‐lin Yang Yun‐Juan Shi Hui Zhu Li‐da 《American journal of primatology》2010,72(8):699-706
The bacterial diversity in fecal samples from the wild pygmy loris was examined with a 16S rDNA clone library and restriction fragment length polymorphism analysis. The clones were classified as Firmicutes (43.1%), Proteobacteria (34.5%), Actinobacteria (5.2%), and Bacteroidetes (17.2%). The 58 different kinds of 16S rDNA sequences were classified into 16 genera and 20 uncultured bacteria. According to phylogenetic analysis, the major genera within the Proteobacteria was Pseudomonas, comprising 13.79% of the analyzed clone sequences. Many of the isolated rDNA sequences did not correspond to known microorganisms, but had high homology to uncultured clones found in human feces. Am. J. Primatol. 72:699–706, 2010. © 2010 Wiley‐Liss, Inc. 相似文献
6.
Tamara Garcia-Armisen Zoi Papalexandratou Hugo Hendryckx Nicholas Camu Gino Vrancken Luc De Vuyst Pierre Cornelis 《Applied microbiology and biotechnology》2010,87(6):2281-2292
Cocoa bean fermentation is a spontaneous process involving a succession of microbial activities, starting with yeasts, followed
by lactic acid bacteria and acetic acid bacteria. So far, all microbiological studies about cocoa bean fermentation were based
on culture-dependent (isolation, cultivation, and identification), or, more recently, culture-independent (PCR-DGGE, or polymerase
chain reaction denaturing gradient gel electrophoresis) methods. Using a metagenomic approach, total DNA was extracted from
heap and box fermentations at different time points and from different locations (Ghana and Brazil, respectively) to generate
a 16 S rDNA clone library that was sequenced. The sequencing data revealed a low bacterial diversity in the fermentation samples
and were in accordance with the results obtained through culture-dependent and a second, culture-independent analysis (PCR-DGGE),
suggesting that almost all bacteria involved in the fermentation process are cultivable. One exception was the identification
by 16 S rDNA library sequencing of Gluconacetobacter species of acetic acid bacteria that were not detected by the two other approaches. The presence of Enterobacteriaceae related to Erwinia/Pantoea/Tatumella, as revealed by 16 S rDNA library sequencing, suggests an impact of these bacteria on fermentation. 相似文献
7.
Ellen Trimarco David Balkwill Mark Davidson T. C. Onstott 《Geomicrobiology journal》2013,30(6):463-473
The extreme environment of South Africa's ultra-deep gold mines offers an opportunity to discover novel microorganisms (e.g., Alkaliphilus transvaalensis), including extremophiles that may provide insight into the origins of life on earth and offer industrial applications because of their thermophilic enzymatic properties. This study employed culture-independent methods to examine the bacterial diversity in water (T = 55° C, pH = 9, Cl? = 1000 ppm and age = 4–53 Ma) emanating from an exploration borehole in a South African Au mine that intersected a quartzite-hosted fault at 3.3 km below land surface. The more adhesive strains of sulfate reducing bacteria were effectively selected and enriched from the planktonic community by forcing water from a flowing borehole through a sand/agar cartridge that was installed within the borehole. The cartridge's agar contained sulfate and lactate that diffused from the agar into the cartridge. DNA was extracted from the sand, after which a bacterial 16S rDNA gene clone library was generated. Analysis of clone sequences indicated that the groundwater bacterial community was quite diverse, including members of the α-, β-, and γ-Proteobacteria (20%), Actinobacteria (6%), Firmicutes (57%), Chloroflexi (3%), and Deinococcus-Thermus (14%) phyla. One of the most frequently detected clone types was associated with Desulfotomaculum (a known SRB). Another predominant clone type was closely related to Meiothermus cerbereus. A proportion of Proteobacteria clones were closely related to Ralstonia, Alishewanella, Hydrogenophaga, or Methylobacterium species. Some of the Firmicutes clones were closely related to Alkaliphilus transvaalensis, which was isolated from a nearby South African Au mine, or to Clostridium thermocellum. Of the total 21 OTUs identified from the cartridge sand, 6 most likely represent novel species of Firmicutes given their dissimilarity to other 16S rDNA sequences in the GenBank database. 相似文献
8.
The introduction of antibiotics to animal feed has contributed to the selection of antibiotic-resistant bacteria in concentrated
animal feeding operations. The aim of this work was to characterize the impact of an aerobic thermophilic biotreatment on
anaerobic antibiotic-resistant bacteria in swine waste. Despite 162- to 6,166-fold reduction in antibiotic-resistant populations
enumerated in the swine waste at 25°C and 37°C, resistant populations remained significant (104 to 105 most probable number per milliliter) in the treated swine waste. Five resistance genes were detected before [tet(LMOS) erm(B)], and six resistance genes were detected after [tet(LMOSY) erm(B)] biotreatment. However, the biotreatment decreased the frequency of detection of resistance genes by 57%. Analysis by
denaturing gradient gel electrophoresis of polymerase chain reaction-amplified 16 S ribosomal DNA (rDNA) fragments showed
that the biotreatment reduced the bacterial diversity of resistant populations enumerated at 37°C. Cloning and sequencing
of the 16 S rDNA of these populations revealed that most clones in the treated swine waste were closely similar to some of
the clones retrieved from the untreated swine waste. This study revealed that the aerobic thermophilic biotreatment developed
in our laboratory does not prevent the introduction of facultatively anaerobic antibiotic-resistant bacteria and their resistance
genes into agricultural ecosystems. Horizontal transfer of ecologically advantageous genes within microbial communities are
likely to prevent thermophilic biotreatments from completely eliminating antibiotic-resistant bacteria and their resistance
genes in animal wastes. 相似文献
9.
新疆野生胀果甘草内生细菌多样性的非培养初步分析 总被引:4,自引:0,他引:4
摘要:【目的】了解新疆野生甘草内生细菌多样性,为开发新的微生物资源奠定基础。【方法】采用改进的CTAB (十六烷基三甲基溴化铵)法提取新疆野生胀果甘草根部总DNA,利用细菌16S rDNA 基因通用引物对甘草总DNA 进行16S rDNA 基因扩增,构建甘草内生细菌16S rDNA基因文库;挑选具有不同酶切图谱的克隆进行测序、比对并构建16S rDNA 基因系统发育树。【结果】构建的甘草内生细菌16S rDNA基因文库中, 150个克隆分属于32个不同的分类单元,Blast结果表明大部分克隆与已知细菌的16S rDNA基因序列相似性较高,分别归属于变形杆菌门(Proteobacteria)的alpha、gamma亚群,厚壁菌门(Firmicutes),放线菌门(Actinobacteria),拟杆菌门(Bacteroidetes)中的鞘脂菌属(Sphingobium),叶杆菌属(Phyllobacterium),生丝单胞菌属(Hyphomonas),土壤杆菌属(Agrobacterium)等14个属, 其中26%的克隆与已知细菌16S rDNA 基因相似性小于96%,可能代表新的分类单元.【结论】甘草内生细菌多样性丰富且存在尚未被认识的新物种。 相似文献
10.
Nacita B. Lantican Ma. Genaleen Q. Diaz J. Jason L. Cantera Francis L. de los ReyesIII Asuncion K. Raymundo 《World journal of microbiology & biotechnology》2011,27(4):859-867
Mt. Makiling Mudspring in Laguna, Philippines is a thermophilic, acidophilic environment that previously has been shown to
harbor novel microorganisms. We assessed the microbial community that exists at this volcanic mudspring using 16S rRNA-based
approaches. DNA was extracted from solfataric soils and sediments taken from Mudspring. The 16S rDNA was PCR amplified using
universal (519F-1392R) and archaeal-specific (23FPL-1391R) primer pairs, cloned, and sequenced. Phylogenetic analysis of the
cloned 16S rDNA showed that eleven clones clustered with, and therefore related to Sulfolobus tokodaii 7 and two clones clustered with S. solfataricu, S. shibatae and S. islandicus. Three clone sequences were related to those found in thermophilic chalcopyrite (CuFeS2), a copper sulfuric ore from bioleaching reactors. One clone had low similarity (95% identity) with uncultured archaeon clone
KOZ184. Fluorescence in situ hybridization (FISH) analysis revealed that about 71% of the microbial community present in the
Mudspring belong to domain Archaea of which 63% were Crenarchaeota and 8% were Euryarchaeota. Seventeen percent (17%) of the
population consisted of bacteria as indicated by the positive hybridization with the BACT338 probe, and the remaining 12%
are unidentified. This study is the first attempt to use molecular techniques in any environment in the Philippines. 相似文献
11.
Cloning and identification of cellulase genes from uncultured microorganisms in pulp sediments from paper mill effluent] 总被引:2,自引:0,他引:2
The metagenomic DNA of pulp sediments from paper mill effluent was extracted and purified. The 16S rDNA was amplified using the purified metagenomic DNA as template and a 16S rDNA library was prepared. Sequence analysis of 16S rDNA clones showed that diverse of uncultured bacteria inhabit in this environment, which can be classified into 4 clusters as Spirochaetes, Proteobacteria, Bacteroidetes and Firmicutes. A metagenomic library containing 10000 clones was constructed into cosmid vector, and the capacity of inserted DNA of which was 3.53 x 10(8) bp. Functional screening of the library resulted in isolation of two independent clones expressing endoglucanase activity, three independent clones expressing exoglucanase activity and two independent clones expressing beta-glucosidase activity. One clone expressing strongest enzyme activity from each activity category was chosen to be further analyzed. Three novel cellulase genes designated as umcel5L, umcel5M and umbgl3D were identified by subcloning, sequencing and expression. The umcel5L encodes an endoglucanase belonging to glycosyl hydrolase family 5, which is most related to an endoglucanase from Bradyrhizobium japonicum at 43% identity and 59% similarity. The umcel5M encodes a cellodextrinase belonging to glycosyl hydrolase family 5, which is most similar to a cellodextrinase from Fibrobacter succinogenes at 48% identity and 69% similarity. The umbgl3D encodes a putative beta-glucosidase belonging to glycosyl hydrolase family 3, which shares highest homology with a beta-glucosidase from Thermotoga maritima at 46% identity and 61% similarity. It is the first time to reveal the bacterial diversity of pulp sediments from paper mill effluent and clone novel cellulase genes from the bacteria by culture-independent method. 相似文献
12.
Detection of Fiber-Digesting Bacteria in the Ceca of Ostrich Using Specific Primer Sets 总被引:1,自引:0,他引:1
The purpose of this study was to detect three fibrolytic bacteria, Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminococcus albus, in the cecal digesta of the ostrich (Struthio camelus) by PCR using a species-specific primer set for each 16S ribosomal RNA gene (16S rDNA). Although amplified DNA fragments
obtained from each primer set had the expected size, the clone library derived from the amplimer contained non-specific sequences.
The F. succinogenes-specific primer set recovered a partial 16S rDNA sequence of an uncultivated Fibrobacter with low similarity (<95%) and distantly related phylogenetic positioning to Fibrobacter sequences deposited in the databases, indicating a novel species of Fibrobacter. The sequence was considered to be identical to a clone detected in our previous experiment. Thus, we confirm that the gastrointestinal
tract of the ostrich is one of the habitats of Fibrobacter species. The clone library derived from the R. flavefaciens-specific primer set contained a 16S rDNA sequence with 97% similarity to R. flavefaciens, indicating it could be one of a major fibrolytic bacterium in the ostrich ceca. No R. albus 16S rDNA sequence was found in the clone library of the R. albus-specific primer set. 相似文献
13.
Bacterial community analysis of swine manure treated with autothermal thermophilic aerobic digestion
Due to the enviornmental problems associated with disposal of livestock sludge, many stabilization studies emphasizing on
the sludge volume reduction were performed. However, little is known about the microbial risk present in sludge and its stabilized
products. This study microbiologically explored the effects of anaerobic lagoon fermentation (ALF) and autothermal thermophilic
aerobic digestion (ATAD) on pathogen-related risk of raw swine manure by using culture-independent 16S rDNA cloning and sequencing
methods. In raw swine manure, clones closely related to pathogens such as Dialister pneumosintes, Erysipelothrix rhusiopathiae, Succinivibrioan dextrinosolvens, and Schineria sp. were detected. Meanwhile, in the mesophilic ALF-treated swine manure, bacterial community clones closely related to pathogens
such as Schineria sp. and Succinivibrio dextrinosolvens were still detected. Interestingly, the ATAD treatment resulted in no detection of clones closely related to pathogens in
the stabilized thermophilic bacterial community, with the predominance of novel Clostridia class populations. These findings
support the superiority of ATAD in selectively reducing potential human and animal pathogens compared to ALF, which is a typical
manure stabilization method used in livestock farms. 相似文献
14.
Microbial diversity in hot synthetic compost as revealed by PCR-amplified rRNA sequences from cultivated isolates and extracted DNA 总被引:28,自引:0,他引:28
High-temperature (>/=60 degrees C) synthetic food waste compost was examined by cultivation-dependent and -independent methods to determine predominant microbial populations. Fluorescent direct counts totaled 6.4 (+/-2.5)x10(10) cells gdw(-1) in a freeze-dried 74 degrees C compost sample, while plate counts for thermophilic heterotrophic aerobes averaged 2.6 (+/-1.0)x10(8) CFU gdw(-1). A pre-lysis cell fractionation method was developed to obtain community DNA and a suite of 16S and 18S rDNA-targeted PCR primers was used to examine the presence of Bacteria, Archaea and fungi. Bacterial 16S rDNA, including a domain-specific 1500-bp fragment and a 300-bp fragment specific for Actinobacteria, was amplified by PCR from all compost samples tested. Archaeal rDNA was not amplified in any sample. Fungal 18S rDNA was only amplified from a separate dairy manure compost that reached a peak temperature of 50 degrees C. Amplified rDNA restriction analysis (ARDRA) was used to screen isolated thermophilic bacteria and a clone library of full-length rDNA fragments. ARDRA screening revealed 14 unique patterns among 63 isolates, with one pattern accounting for 31 of the isolates. In the clone library, 52 unique patterns were detected among 70 clones, indicating high diversity of uncultivated bacteria in hot compost. Phylogenetic analysis revealed that the two most abundant isolates belonged in the genera Aneurinibacillus and Brevibacillus, which are not commonly associated with hot compost. With the exception of one Lactobacillus-type sequence, the clone library contained only sequences that clustered within the genus Bacillus. None of the isolates or cloned sequences could be assigned to the group of obligate thermophilic Bacillus spp. represented by B. stearothermophilus, commonly believed to dominate high-temperature compost. Amplified partial fragments from Actinobacteria, spanning the V3 variable region (Neefs et al. (1990) Nucleic Acids Res. 18, 2237-2242), included sequences related to the genera Saccharomonospora, Gordonia, Rhodococcus and Corynebacterium, although none of these organisms were detected among the isolates or full-length cloned rDNA sequences. All of the thermophilic isolates and sequenced rDNA fragments examined in this study were from Gram-positive organisms. 相似文献
15.
Four strains of obligately thermophilic Bacilli capable of growing with carbon monoxide as a sole carbon and energy source were isolated from settling ponds of a sugar factory. Most of them could be identified as strains of Bacillus schlegelii on the basis of cell wall composition, DNA homology menaquinone and DNA base content. Growth with CO was very fast (t
d
=3 h) and was optimal at 65°C. No growth occurred below 50°C. As with the mesophilic carboxydotrophs, hydrogen plus carbon dioxide could also serve as autotrophic substrates. Growth of the isolates with CO depended on the presence of molybdenum in the growth medium. This suggested CO oxidase in the newly isolated Bacilli being a molybdenum hydroxylase similar to the enzymes from the mesophilic carboxydotrophs. Some data characterizing the CO-oxidizing activity in extracts of the thermophilic isolates are also provided.This paper is respectively dedicated to Professor Dr. H. G. Schlegel on the occasion of his 60th birthday 相似文献
16.
Thermus kawarayensis sp. nov., a new member of the genus Thermus, isolated from Japanese hot springs
A long-rod-shaped thermophilic microorganism, strain KW11, was isolated from a hot springs located in the Kawarayu, Gunma, Japan. Cloning and preliminary sequence analysis of 16S rDNA showed that this isolate belongs to the genus Thermus. The cells were 10–20 m long, about 0.8 m in diameter, and produced no pigment in contrast with most of the Thermus species previously reported. KW11 was an aerobic heterotroph and grew at temperatures ranging from 40–73°C, with optimal growth occurring at 68°C. The pH range for growth was from 5.8–8.9, with optimal growth around pH 7. KW11 was sensitive to ampicillin, penicillin G, kanamycin, and streptomycin. The G+C content of DNA was 69 mol%. The main fatty acids were 16:0 (52.9%), iso-15:0 (22.1%), and iso-17:0 (15.6%). The 16S rDNA sequence of KW11 showed 96.0, 95.8, and 95.4% similarity with the sequences of T. aquaticus, T. igniterrae, and T. thermophilus, respectively, and less than 95% with other Thermus species. The physiological differences and phylogenetic evidence indicated that strain KW11 represents T. kawarayensis, a novel species of the genus Thermus. The type strain is isolate KW11T (JCM12314, DSM16200). 相似文献
17.
Hanajima D Fukumoto Y Yasuda T Suzuki K Maeda K Morioka R 《Journal of applied microbiology》2011,111(6):1416-1425
Aims: This study aimed to characterize microbial community dynamics in aerated cow manure slurry at different aeration intensities. Methods and Results: Batch aerobic treatments were set up in 5‐l jar fermentor, each containing 3 l of manure slurry; the slurries were subjected to low, medium and high (50, 150 and 250 ml min?1, respectively) aeration for 9 days. Microbial community composition was determined using terminal restriction fragment length polymorphism and a clone library targeting 16S rRNA genes. High and medium aeration accelerated organic carbon degradation in parallel with the degree of aeration intensity; however, 90% of the initial total organic carbon was retained during low‐aeration treatment. During the active stages of organic carbon decomposition, clones belonging to the class Bacilli accumulated. Moreover, Bacilli accumulation occurred earlier under high aeration than under medium aeration. Conclusions: Organic matter degradation was mainly governed by a common microbial assemblage consisting of many lineages belonging to the class Bacilli. The timing of community development differed depending on aeration intensity. Significance and Impact of the Study: This study reports on changes in several environmentally important parameters and the principal microbial assemblage during the pollution‐reducing phase of cattle manure aeration treatment. 相似文献
18.
Fecal microbial diversity in a strict vegetarian as determined by molecular analysis and cultivation
Fecal microbial diversity in a strictly vegetarian woman was determined by the 16S rDNA library method, terminal restriction fragment length polymorphism (T-RFLP) analysis and a culture-based method. The 16S rDNA library was generated from extracted fecal DNA, using bacteria-specific primers. Randomly selected clones were partially sequenced. T-RFLP analysis was performed using amplified 16S rDNA. The lengths of T-RF were analyzed after digestion by HhaI and MspI. The cultivated bacterial isolates were used for partial sequencing of 16S rDNA. Among 183 clones obtained, approximately 29% of the clones belonged to 13 known species. About 71% of the remaining clones were novel "phylotypes" (at least 98% similarity of clone sequence). A total of 55 species or phylotypes were identified among the 16S rDNA library, while the cultivated isolates included 22 species or phylotypes. In addition, many new phylotypes were detected from the 16S rDNA library. The 16S rDNA library and isolates commonly included the Bacteroides group, Bifidobacterium group, and Clostridium rRNA clusters IV, XIVa, XVI and XVIII. T-RFLP analysis revealed the major composition of the vegetarian gut microbiota were Clostridium rRNA subcluster XIVa and Clostridium rRNA cluster XVIII. The dominant feature of this strictly vegetarian gut microbiota was the detection of many Clostridium rRNA subcluster XIVa and C. ramosum (Clostridium rRNA cluster XVIII). 相似文献
19.
Huirong Li Yong Yu Wei Luo Yinxin Zeng Bo Chen 《Extremophiles : life under extreme conditions》2009,13(2):233-246
In order to assess bacterial diversity within four surface sediment samples (0–5 cm) collected from the Pacific Arctic Ocean,
16S ribosomal DNA clone library analysis was performed. Near full length 16S rDNA sequences were obtained for 463 clones from
four libraries and 13 distinct major lineages of Bacteria were identified (α, β, γ, δ and ε-Proteobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, Firmicutes, Planctomycetes, Spirochetes, and Verrucomicrobia). α, γ, and δ-Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria were common phylogenetic groups from all the sediments. The γ-Proteobacteria were the dominant
bacterial lineage, representing near or over 50% of the clones. Over 35% of γ-Proteobacteria clones of four clone library
were closely related to cultured bacterial isolates with similarity values ranging from 94 to 100%. The community composition
was different among sampling sites, which potentially was related to geochemical differences. 相似文献
20.
Culturability and In Situ Abundance of Pelagic Bacteria from the North Sea 总被引:8,自引:13,他引:8
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Heike Eilers Jakob Pernthaler Frank Oliver Glckner Rudolf Amann 《Applied microbiology》2000,66(7):3044-3051
The culturability of abundant members of the domain Bacteria in North Sea bacterioplankton was investigated by a combination of various cultivation strategies and cultivation-independent 16S rRNA-based techniques. We retrieved 16S rRNA gene (rDNA) clones from environmental DNAs and determined the in situ abundance of different groups and genera by fluorescence in situ hybridization (FISH). A culture collection of 145 strains was established by plating on oligotrophic medium. Isolates were screened by FISH, amplified ribosomal DNA restriction analysis (ARDRA), and sequencing of representative 16S rDNAs. The majority of isolates were members of the genera Pseudoalteromonas, Alteromonas, and Vibrio. Despite being readily culturable, they constituted only a minor fraction of the bacterioplankton community. They were not detected in the 16S rDNA library, and FISH indicated rare (<1% of total cell counts) occurrence as large, rRNA-rich, particle-associated bacteria. Conversely, abundant members of the Cytophaga-Flavobacteria and gamma proteobacterial SAR86 clusters, identified by FISH as 17 to 30% and up to 10% of total cells in the North Sea bacterioplankton, respectively, were cultured rarely or not at all. Whereas SAR86-affiliated clones dominated the 16S rDNA library (44 of 53 clones), no clone affiliated to the Cytophaga-Flavobacterum cluster was retrieved. The only readily culturable abundant group of marine bacteria was related to the genus Roseobacter. The group made up 10% of the total cells in the summer, and the corresponding sequences were also present in our clone library. Rarefaction analysis of the ARDRA patterns of all of the isolates suggested that the total culturable diversity by our method was high and still not covered by the numbers of isolated strains but was almost saturated for the gamma proteobacteria. This predicts a limit to the isolation of unculturable marine bacteria, particularly the gamma-proteobacterial SAR86 cluster, as long as no new techniques for isolation are available and thus contrasts with more optimistic accounts of the culturability of marine bacterioplankton. 相似文献