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1.
Alexandra Demiri Alexandra Meziti Sokratis Papaspyrou Maria Thessalou-Legaki Konstantinos Ar. Kormas 《Central European Journal of Biology》2009,4(4):558-566
We investigated the diversity of the bacterial 16S rRNA genes occurring on the abdominal setal tufts and in the emptied midgut
of the marine mudshrimp Pestarella tyrrhena (Decapoda: Thalassinidea). There were no dominant phylotypes on the setal tufts. The majority of the phylotypes belonged
to the phylum Bacteroidetes, frequently occurring in the water column. The rest of the phylotypes were related to anoxygenic
photosynthetic α-Proteobacteria and to Actinobacteria. This bacterial profile seems more of a marine assemblage rather than
a specific one suggesting that no specific microbial process can be inferred on the setal tufts. In the emptied midgut, 64
clones were attributed to 16 unique phylotypes with the majority (40.6%) belonging to the γ-Proteobacteria, specifically to
the genus Vibrio, a marine group with known symbionts of decapods. The next most abundant group was the ɛ-Proteobacteria (28.1%), with members
as likely symbionts related to the processes involving redox reactions occurring in the midgut. In addition, phylotypes related
to the Spirochaetes (10.9%) were also present, with relatives capable of symbiosis conducting a nitrite associated metabolism.
Entomoplasmatales, Bacteroidetes and Actinobacteria related phylotypes were also found. These results indicate a specific
bacterial community dominated by putative symbiotic Bacteria within the P. tyrrhena’s midgut. 相似文献
2.
Bacterial,archaeal and eukaryotic diversity in Arctic sediment as revealed by 16S rRNA and 18S rRNA gene clone libraries analysis 总被引:1,自引:0,他引:1
We studied the microbial diversity in the sediment from the Kongsfjorden, Svalbard, Arctic, in the summer of 2005 based on
the analysis of 16S rRNA and 18S rRNA gene clone libraries. The sequences of the cloned 16S rRNA and 18S rRNA gene inserts
were used to determine the species identity or closest relatives by comparison with sequences of known species. Compared to
the other samples acquired in Arctic and Antarctic, which are different from that of ours, the microbial diversity in our
sediment is much higher. The bacterial sequences were grouped into 11 major lineages of the domain Bacteria: Proteobacteria
(include α-, β-, γ-, δ-, and ε-Proteobacteria); Bacteroidetes; Fusobacteria; Firmicutes; Chloroflexi; Chlamydiae; Acidobacteria;
Actinobacteria; Planctomycetes; Verrucomicrobiae and Lentisphaerae. Crenarchaeota were dominant in the archaeal clones containing
inserts. In addition, six groups from eukaryotes including Cercozoa, Fungi, Telonema, Stramenopiles, Alveolata, and Metazoa were identified. Remarkably, the novel group Lentisphaerae was reported in Arctic
sediment at the first time. Our study suggested that Arctic sediment as a unique habitat may contain substantial microbial
diversity and novel species will be discovered. 相似文献
3.
Chunbo Hao Hongxun Zhang Richard Haas Zhihui Bai Baoguo Zhang 《World journal of microbiology & biotechnology》2007,23(1):15-21
A sediment sample (pH 2.5) was collected at an acid mine drainage site in Anhui, China. The present acidophilic microbial
community in the sediment was studied with a 16S rRNA gene clone library. Small-subunit rRNA genes were PCR amplified, cloned
and screened by amplified rDNA restriction analysis (ARDRA). Subsequently, 10 different clones were identified and they were
affiliated with Acidobacteria, β/γ-Proteobacteria, δ-Proteobacteria, Nitrospira, Candidate division TM7, and Low G + C Gram-positives. Phylogenetic analysis of 16S rRNA gene sequences revealed a diversity
of acidophiles in the sediment that were mostly novel. Unexpectedly, 16S rRNA gene sequences affiliated with δ-Proteobacteria were found to constitute more than 60% of clone library. To our knowledge, this is the first occasion that bacteria of δ-Proteobacteria have been found dominant in the acidic habitat. Anaerobic sulfate- or metal reduction is the predominant physiological trait
of bacteria of this subdivision. The high sulfate, ferric iron and the presence of bioavailable carbon in the anaerobic microenvironment
may result in the dominance of bacteria of δ-Proteobacteria. 相似文献
4.
Bacterial Community Diversity in Undisturbed Perhumid Montane Forest Soils in Taiwan 总被引:1,自引:0,他引:1
Yu-Te Lin Yu-Ju Huang Sen-Lin Tang William B. Whitman David C. Coleman Chih-Yu Chiu 《Microbial ecology》2010,59(2):369-378
The diversity and composition of soil bacterial communities in three topographic sites (summit, foot slope, and lakeshore)
from subtropical montane forest ecosystem in Taiwan were examined by using 16S rRNA gene clone library analysis. This locality
is temperate, perhumid, and has low soil acidity (pH < 4), which is an uncommon ecosystem in a monsoonal part of Southeast
Asia. A total of 481 clones were sequenced and placed into ten phylogenetic groups according to their similarities to type
strains of described organisms. Toposequence of the transect was investigated from summit to foot slope and at the lakeshore.
More than 86% of the clones were affiliated with members of the Proteobacteria, Acidobacteria, and Actinobacteria. Within
the Proteobacteria, the β-Proteobacteria was the most abundant, then α-Proteobacteria and γ-Proteobacteria. Based on the Shannon
diversity index (H) analysis, the bacterial community in the foot slope was the most diverse (H = 0.86) and that in summit was the least diverse (H = 0.68). The composition and diversity of soil bacterial communities in the three sites suggested no trend with topographic
change. Less than 20% of the sequences were Acidobacteria-affiliated clones. The low proportion of Acidobacteria observed
may be related to the high soil moisture and anaerobic microhabitats. Moreover, Shannon diversity indices revealed these bacterial
communities to have lower diversity than that of other temperate (H = 0.90) and tropical forest (H = 0.82) ecosystems. The extreme acidity of soil pH and high soil moisture of this forest may explain composition and reduced
the diversity of these soil bacterial communities. 相似文献
5.
Sun jinsheng Guo Fei Geng Xuyun Wei Junli Li Xiang Li Jingjing 《World journal of microbiology & biotechnology》2011,27(2):275-284
Information about seasonal bacterial composition and diversity is of great value for exploitation of marine biological resources
and improvement of ecological environment. Here PCR-amplified restriction fragment length polymorphism (PCR–RFLP) of 16S rRNA
genes was used to evaluate seasonal bacterial diversity and community composition in Bohai Bay. A total of 24 bacterial communities
were sampled from seawater and sediment of three representative sites in a whole seasonal cycle: spring (April), summer (July),
autumn (October), and winter (January). Bacterial Genomic DNA was extracted and PCR-amplified to obtain 16S rDNA fragments
which were cloned to construct 24 16s rDNA libraries. Clones of each library were selected randomly for PCR–RFLP analysis
of rDNA fragments, and eventually 101 genotypes were identified by RFLP fingerprintings. These 101 genotypes were sequenced
and their respective phylotype was identified through the Blast tool of NCBI (similarity 96–100%) and phylogenetic analyses.
Among our phylotypes, 80.2% belonged to the genera α-Proteobacteria, β-proteobacteria,γ-Proteobacteria, δ-Proteobacteria,
ε-proteobacteria, Flavobacteria, Cytophaga-Flavobacteria-Bacteroides, Verrucomicrobia, Firmicutes and Actinobacteria. Sequence
analyses revealed that 47.5% (48) of clone sequences were similar to those of uncultured marine bacteria in the environment.
In addition, bacterial diversity and composition clearly displayed seasonal variety. More genera were discovered in summer
than any other seasons, and some special species appeared only in specific season. 相似文献
6.
Ma Y Zhang W Xue Y Zhou P Ventosa A Grant WD 《Extremophiles : life under extreme conditions》2004,8(1):45-51
Bacterial diversity associated with Baer Soda Lake in Inner Mongolia of China was investigated using a culture-independent method. Bacterial 16S rRNA gene libraries were generated using bacterial oligonucleotide primers, and 16S rRNA gene sequences of 58 clones were analyzed phylogenetically. The library was dominated by 16S rDNAs of Gram-negative bacteria (24% -Proteobacteria, 31% -Proteobacteria, 33% -Proteobacteria, and 2% -Proteobacteria), with a lower percentage of clones corresponding to Gram-positive bacteria. Forty cloned sequences were similar to that of known bacterial isolates (>97% sequence similarity), represented by the species of the genera Brevundimonas, Comamonas, Alcaligenes, Stenotrophomonas, and Klebsiella. Eighteen cloned sequences showed less affiliation with known taxa (<97% sequence similarity) and may represent novel taxa.Communicated by K. Horikoshi 相似文献
7.
Hongyue Dang Jing Li Mingna Chen Tiegang Li Zhigang Zeng Xuebo Yin 《World journal of microbiology & biotechnology》2009,25(2):179-188
Although the deep-sea sediments harbor diverse and novel bacteria with important ecological and environmental functions, a
comprehensive view of their community characteristics is still lacking, considering the vast area and volume of the deep-sea
sedimentary environments. Sediment bacteria vertical distribution and community structure were studied of the E272 site in
the East Pacific Ocean with the molecular methods of 16S rRNA gene T-RFLP (terminal restriction fragment length polymorphism)
and clone library analyses. Layered distribution of the bacterial assemblages was detected by both methods, indicating that
the shallow sediments (40 cm in depth) harbored a diverse and distinct bacterial composition with fine-scale spatial heterogeneity.
Substantial bacterial diversity was detected and nine major bacterial lineages were obtained, including Acidobacteria, Actinobacteria,
Bacteroidetes, Chloroflexi, Nitrospirae, Planctomycetes, Proteobacteria, and the candidate divisions OP8 and TM6. Three subdivisions of the Proteobacteria presented in our libraries, including the α-, γ- and δ-Proteobacteria. Most of our sequences have low similarity with known bacterial 16S rRNA genes, indicating that these sequences may represent
as-yet-uncultivated novel bacteria. Most of our sequences were related to the GenBank nearest neighboring sequences retrieved
from marine sediments, especially from deep-sea methane seep, gas hydrate or mud volcano environments. Several sequences were
related to the sequences recovered from the deep-sea hydrothermal vent or basalt glasses-bearing sediments, indicating that
our deep-sea sampling site might be influenced to certain degree by the nearby hydrothermal field of the East Pacific Rise
at 13°N.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
8.
Bacterial Community Structure of Sediments of the Bizerte Lagoon (Tunisia), a Southern Mediterranean Coastal Anthropized Lagoon 总被引:2,自引:0,他引:2
Olfa Ben Said Marisol Goñi-Urriza Monia El Bour Patricia Aissa Robert Duran 《Microbial ecology》2010,59(3):445-456
In order to estimate how pollution affects the bacterial community structure and composition of sediments, chemical and molecular
approaches were combined to investigate eight stations around the Bizerte lagoon. Terminal restriction fragment length polymorphism
(T-RFLP) analysis of PCR-amplified 16S rRNA genes revealed that each station was characterized by a specific bacterial community
structure. The combination of this data with those of chemical analysis showed a correlation between the bacterial fingerprint
and the pollutant content, principally with hydrocarbon pollution. The composition of the bacterial community of two contrasted
stations related to the pollution revealed sequences affiliated to α, β, γ, δ, ε subclass of the Proteobacteria, Actinobacteria, and Acidobacteria in both stations although in different extent. Gamma and delta subclass of the Proteobacteria were dominant and represent 70% of clones in the heavy-metal-contaminated station and 47% in the polyaromatic hydrocarbon
(PAH)-contaminated. Nevertheless, most of the sequences found were unaffiliated to cultured bacteria. The adaptation of the
bacterial community mainly to PAH compounds demonstrated here and the fact that these bacterial communities are mainly unknown
suggest that the Bizerte lagoon is an interesting environment to understand the capacity of bacteria to cope with some pollutants. 相似文献
9.
A. Meziti K. Ar. Kormas M. -A. Pancucci-Papadopoulou M. Thessalou-Legaki 《Russian Journal of Marine Biology》2007,33(2):84-91
We used sequencing and phylogenetic analysis of PCR-amplified 16S rRNA genes from bacteria that are associated with the esophagus/pharynx,
stomach and intestine of two marine sympatric invertebrates but with different feeding mechanisms, namely the sea urchin Paracentrotus
lividus (grazer) and the ascidian Microcomus sp. (suspension feeder). Amplifiable DNA was retrieved from all sections except the pharynx of the ascidian. Based on the
inferred phylogeny of the retrieved sequences, the sea urchin’s esophagus is mainly characterized mostly by bacteria belonging
to α-, γ-Proteobacteria and Bacteriodetes, most probably originating from the surrounding environment. The stomach revealed
phylotypes that belonged to γ- and δ-Proteobacteria, Verrucomicrobia and Fusobacteria. Since the majority of their closest
relatives are anaerobic species and they could be putative symbionts of the P. lividus stomach, in which anaerobic conditions also prevail. Seven out of eight phylotypes found in the sea urchin’s intestine belonged
to sulfate reducing δ-Proteobacteria, and one to γ-Proteobacteria, with possible nutritional activities, i.e. degradation
of complex organic compounds which is beneficial for the animal. The bacterial phylotypes of the ascidian digestive tract
belonged only to the phyla of Actinobacteria and Proteobacteria. The stomach phylotypes of the ascidian were related to pathogenic
bacteria possibly originating from the water column, while the intestine seemed to harbour putative symbiotic bacteria that
are involved in the degradation of nitrogenous and other organic compounds, thus assisting ascidian nutrition.
The text was submitted by the authors in English. 相似文献
10.
Jong-Shik Kim Robert S. Dungan Soon-Wo Kwon Hang-Yeon Weon 《World journal of microbiology & biotechnology》2006,22(12):1267-1273
The objective of this study was to characterize the bacterial community composition in the bulk soil, rhizosphere soil and root tissue of the tomato plant (Lycopersicum esculentum Mill). 16S ribosomal DNA (rDNA) from the bacterial community was amplified using PCR, and sequence analysis of 16S rDNA clones was subsequently used for bacterial identification and phylogenetic classification. Phylogenetic analysis of clones (total of 68) from the bulk soil, rhizosphere and root tissues showed that about 50% of the bacteria belonged to the α-, β-, γ-, and δ-Proteobacteria or Cytophaga–Flavobacterium–Bacteroides (CFB) phyla, with only one high G+C clone identified. A number of diverse bacteria were identified within Proteobacteria, while 87% of the bacteria belonged to the genus Flavobacterium within the CFB phylum, which is a unique finding for tomato plants. Our results will be of interest to those wanting to identify bacteria that can promote plant growth or resistance to diseases. 相似文献
11.
Abstract
The phylogenetic diversity of the bacterial community associated with leaves of the marine plant Halophila stipulacea in the northern Gulf of Elat was examined by 16S rRNA gene (rDNA) sequence analyses of a clone library. For 59 clones corresponding
to 51 ARDRA (amplified rDNA restriction analysis) groups, the sequence of ∼1 kb was determined, and the fraction of the corresponding
ARDRA groups of the leaf library was calculated. The class Proteobacteria was represented by 62.6% of the clone sequences.
Most sequences originated from members of the γ-subclass (27.3%), affiliated with members of the genera Pseudomonas, Vibrio, Marinomonas, Oceanospirillum, and other marine groups. Affiliation to the α-subclass was determined for 24.2% of the sequences. They were related to the
genera Hyphomonas, Roseobacter, Ruegeria, and Rhizobiaceae. Several α-proteobacterial sequences were distantly related to known sequences. Only 4% of the clone sequences were related
to β-Proteobacteria. Additionally, 7.1% of the sequences possibly belonged to the class Proteobacteria, but branched deeply
from known subclasses. Several sequences were affiliated to members of the orders Verrucomicrobiales and Planctomycetales, the Holophaga/Acidobacterium phylum, and chloroplasts of marine diatoms.
Received: 20 March 1999; Accepted: 13 August 1999; Online Publication: 2 March 2000 相似文献
12.
Cultivable Bacterial Community from South China Sea Sponge as Revealed by DGGE Fingerprinting and 16S rDNA Phylogenetic Analysis 总被引:2,自引:0,他引:2
The cultivable bacterial communities associated with four South China Sea sponges—Stelletta tenuis, Halichondria rugosa, Dysidea avara, and Craniella australiensis in mixed cultures—were investigated by microbial community DNA-based DGGE fingerprinting and 16S rDNA phylogenetic analysis.
Diverse bacteria such as α-, γ-, δ-Proteobacteria, Bacteroidetes, and Firmicutes were cultured, some of which were previously uncultivable bacteria, potential novel strains with less than 95% similarity
to their closest relatives and sponge symbionts growing only in the medium with the addition of sponge extract. According
to 16S rDNA BLAST analysis, most of the bacteria were cultured from sponge for the first time, although similar phyla of bacteria
have been previously recognized. The selective pressure of sponge extract on the cultured bacterial species was suggested,
although the effect of sponge extract on bacterial community in high nutrient medium is not significant. Although α- and γ-Proteobacteria appeared to form the majority of the dominant cultivable bacterial communities of the four sponges, the composition of the
cultivable bacterial community in the mixed culture was different, depending on the medium and sponge species. Greater bacterial
diversity was observed in media C and CS for Stelletta tenuis, in media F and FS for Halichondria rugosa and Craniella australiensis. S. tenuis was found to have the highest cultivable bacterial diversity including α-, γ-, δ-Proteobacteria, Bacteroidetes, and Firmicutes, followed by sponge Dysidea avara without δ-Proteobacteria, sponge Halichondria rugosa with only α-, γ-Proteobacteria and Bacteroidetes, and sponge C. australiensis with only α-, γ-Proteobacteria and Firmicutes. Based on this study, by the strategy of mixed cultivation integrated with microbial community DNA-based DGGE fingerprinting
and phylogenetic analysis, the cultivable bacterial community of sponge could be revealed effectively. 相似文献
13.
乌梁素海富营养化湖区浮游细菌多样性及系统发育分析 总被引:6,自引:0,他引:6
水生生态系统富营养化与细菌群落之间的关系尚不明确。本文通过构建和分析16S rRNA基因片段克隆文库, 以期揭示乌梁素海富营养化水体细菌的多样性及其系统发育关系, 并探讨富营养化与细菌多样性之间的关系。利用Hae III对文库中的87个克隆子进行单酶切, 产生了23种带型, 文库覆盖度达到了73.6%, 反映出文库有较好的代表性。选择每种OTU的一个代表克隆进行测序分析, 基因序列系统发育分析结果表明, 乌梁素海中多数细菌与淡水生态系统中常见的细菌门类相同, 即α-, β-, γ-Proteobacteria, Bacteroidetes, Actinobacteria, 它们分别占总菌数的10.3%、41.4%、4.6%和6.9%, 其中β-Proteobacteria和Bacteroidetes是优势细菌类群。与典型淡水生态系统细菌群落组成不同的是, 乌梁素海中存在约10.3%的轻度嗜盐碱细菌。水体中83.9%的细菌与已培养的细菌的同源性低于97%, 其中58.9%的细菌未能鉴定到属; 其余总菌数16.1%的克隆与具有降解污染物生物活性的已知菌相近。Bacteroidetes、Firmicutes和β-Proteobacteria中的某些类群成为优势菌群可能是对乌梁素海水体富营养化的响应。 相似文献
14.
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
15.
【目的】为了解东太平洋中国多金属结核勘探合同区西区2个站位(WBC1305和WBC1316A)深海沉积物细菌群多样性。【方法】直接提取环境样品总基因组,通过PCR和TA克隆策略构建了2个站位6个层次16S r RNA基因文库,对2个站位沉积物表层泥样中细菌多样性和群落结构特征进行分析,并通过构建系统发育树,进行系统发育学分析。【结果】2个站位6个文库共获得有效克隆533个,其中472个克隆包括α-变形菌纲、β-变形菌纲、γ-变形菌纲、δ-变形菌纲、浮霉菌门、酸杆菌门、硝化螺旋菌门、放线菌门、绿弯菌门、厚壁菌门、拟杆菌门、迷踪菌门、芽单胞菌门、Hydrogenedentes、Chlorobi和Nitrospinae16个细菌类群,而另外61个克隆为不可分类细菌类群。【结论】结果表明γ-变形菌纲和厚壁菌门分别是WBC1305和WBC1316A站位的优势种群;WBC1316A站位细菌群落结构更加丰富和复杂。 相似文献
16.
Arvind Kumar Gupta Ashraf Yusuf Rangrez Pankaj Verma Anil Chatterji Yogesh S. Shouche 《Indian journal of microbiology》2009,49(2):169-187
Microbial communities in coastal subsurface sediments play an important role in biogeochemical cycles. In this study microbial
communities in tidal subsurface sediments of Balramgari in the state of Orissa, India were investigated using a culture independent
approach. Two 16S rDNA cloned libraries were prepared from the closely located (100 m along the coast) subsurface sediment
samples. Library I sediment samples had higher organic carbon content but lower sand percentage in comparison to Library II.
A total of 310 clone sequences were used for DOTUR analysis which revealed 51 unique phylotypes or operational taxonomic units
(OTUs) for both libraries. The OTUs were affiliated with 13 major lineages of domain bacteria including Proteobacteria (α, β, δ and λ), Acidobacteria, Actinobacteria, Cyanobacteria, Chloroflexi, Firmicutes, Verrucomicrobia, Bacteroidetes, Gemmatimonadetes and TM7. We encountered few pathogenic bacteria such as Aeromonas hydrophila and Ochrobactrum intermedium, in sediment from Library I. ∫-LIBSHUFF comparison depicts that the two libraries were significantly different communities.
Most of the OTUs from both libraries possessed ≥85% to <97% similarity to RDP database sequences depicting the putative presence
of new species, genera and phylum. This work revealed the complex and unique bacterial diversity from coastal habitat of Balramgari
and shows that, in coastal habitat a variability of physical and chemical parameter has a prominent impact on the microbial
community structure. 相似文献
17.
Daniela Bulgari Paola Casati Lorenzo Brusetti Fabio Quaglino Milena Brasca Daniele Daffonchio Piero Attilio Bianco 《Journal of microbiology (Seoul, Korea)》2009,47(4):393-401
Diversity of bacterial endophytes associated with grapevine leaf tissues was analyzed by cultivation and cultivation-independent
methods. In order to identify bacterial endophytes directly from metagenome, a protocol for bacteria enrichment and DNA extraction
was optimized. Sequence analysis of 16S rRNA gene libraries underscored five diverse Operational Taxonomic Units (OTUs), showing
best sequence matches with γ-Proteobacteria, family Enterobacteriaceae, with a dominance of the genus Pantoea. Bacteria isolation through cultivation revealed the presence of six OTUs, showing best sequence matches with Actinobacteria,
genus Curtobacterium, and with Firmicutes genera Bacillus and Enterococcus. Length Heterogeneity-PCR (LH-PCR) electrophoretic peaks from single bacterial clones were used to setup a database representing
the bacterial endophytes identified in association with grapevine tissues. Analysis of healthy and phytoplasma-infected grapevine
plants showed that LH-PCR could be a useful complementary tool for examining the diversity of bacterial endophytes especially
for diversity survey on a large number of samples. 相似文献
18.
A diverse bacterial community in an anoxic quinoline-degrading bioreactor determined by using pyrosequencing and clone library analysis 总被引:2,自引:0,他引:2
Zhang X Yue S Zhong H Hua W Chen R Cao Y Zhao L 《Applied microbiology and biotechnology》2011,91(2):425-434
There is a concern of whether the structure and diversity of a microbial community can be effectively revealed by short-length
pyrosequencing reads. In this study, we performed a microbial community analysis on a sample from a high-efficiency denitrifying
quinoline-degrading bioreactor and compared the results generated by pyrosequencing with those generated by clone library
technology. By both technologies, 16S rRNA gene analysis indicated that the bacteria in the sample were closely related to,
for example, Proteobacteria, Actinobacteria, and Bacteroidetes. The sequences belonging to Rhodococcus were the most predominant, and Pseudomonas, Sphingomonas, Acidovorax, and Zoogloea were also abundant. Both methods revealed a similar overall bacterial community structure. However, the 622 pyrosequencing
reads of the hypervariable V3 region of the 16S rRNA gene revealed much higher bacterial diversity than the 130 sequences
from the full-length 16S rRNA gene clone library. The 92 operational taxonomic unit (OTUs) detected using pyrosequencing belonged
to 45 families, whereas the 37 OTUs found in the clone library belonged to 25 families. Most sequences obtained from the clone
library had equivalents in the pyrosequencing reads. However, 64 OTUs detected by pyrosequencing were not represented in the
clone library. Our results demonstrate that pyrosequencing of the V3 region of the 16S rRNA gene is not only a powerful tool
for discovering low-abundance bacterial populations but is also reliable for dissecting the bacterial community structure
in a wastewater environment. 相似文献
19.
Yongqin Liu Tandong Yao Nianzhi Jiao Shichang Kang Sijun Huang Qiang Li Kejuan Wang Xiaobo Liu 《Extremophiles : life under extreme conditions》2009,13(1):89-99
Culturable bacteria in the glacial meltwater in the ablation zones of glacier at high altitude (6,350 m) on Mt Everest were
isolated and identified by 16S rRNA amplification and sequencing. The obtained sequences revealed the presence of members
of α, β, and γ-Proteobacteria, Actinobacteria, and Firmicutes, with the Actinobacteria dominant in the studied habitat. All
16S rRNA sequences were similar to previously determined sequences, ranging from 97 to 99% identical values. The strains isolated
from meltwater were distinctly different from those recovered from a cryoconite hole and under glacier habitat. The majority
of the isolates’ nearest neighbors were from the permafrost, dust, soil, plant, and aqueous environments. The Biolog bioassay
and growth test under different temperatures suggested that the culturable bacteria in glacial meltwater could be divided
into three categories in terms of their survival strategies: Group I sensitive to temperature change but versatile in utilization of carbon substrates (capable of utilization of about 70% of
the Biolog carbon substrates); Group II tolerant to variable temperature and less capable of carbon utilization (less than half of the Biolog carbon species can
be used); Group III slow in growth and weak in carbon utilization (only a few Biolog carbon substrates can be used). 相似文献
20.
To elucidate the bacterial diversity in biofilms formed on a condenser tube from a nuclear power plant, 16S rRNA gene sequences were examined using a PCR-cloning-sequencing approach. Twelve operational taxonomic units were retrieved in the clone library, and the estimated species richness was low (13.2). Most of the clones (94.7%) were affiliated with α-Proteobacteria; Planctomycetes and γ-Proteobacteria were much rarer. Interestingly, except for one clone belonging to Pseudoalteromonas, most of the sequences displayed sequence similarities <97% of those of the closest type strains. Based on 16S rRNA phylogenetic analysis, most bacteria were assigned to novel taxa above the species level. The low species richness and unusual bacterial composition may be attributable to selective pressure from chlorine in the cooling water. To prevent or control bacterial biofilms in cooling circuits, additional studies of the physiology and ecology of these species will be essential. 相似文献