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1.
High consistency between replicate 454 pyrosequencing analyses of ectomycorrhizal plant root samples
In this methodological study, we compare 454 sequencing and a conventional cloning and Sanger sequencing approach in their
ability to characterize fungal communities PCR amplified from four root systems of the ectomycorrhizal plant Bistorta vivipara. To examine variation introduced by stochastic processes during the laboratory work, we replicated all analyses using two
independently obtained DNA extractions from the same root systems. The ITS1 region was used as DNA barcode and the sequences
were clustered into OTUs as proxies for species using single linkage clustering (BLASTClust) and 97% sequence similarity cut-off. A relatively low overlap in fungal OTUs was observed between the 454 and the clone
library datasets — even among the most abundant OTUs. In a non-metric multidimensional scaling analysis, the samples grouped
more according to methodology compared to plant. Some OTUs frequently detected by 454, most notably those OTUs with taxonomic
affinity to Glomales, were not detected in the Sanger dataset. Likewise, a few OTUs, including Cenococcum sp., only appeared in the clone libraries. Surprisingly, we observed a significant relationship between GC/AT content of
the OTUs and their proportional abundances in the 454 versus the clone library datasets. Reassuringly, a very good consistency
in OTU recovery was observed between replicate runs of both sequencing methods. This indicates that stochastic processes had
little impact when applying the same sequencing technique on replicate samples. 相似文献
2.
The bacterial composition of chlorinated drinking water was analyzed using 16S rRNA gene clone libraries derived from DNA
extracts of 12 samples and compared to clone libraries previously generated using RNA extracts from the same samples. Phylogenetic
analysis of 761 DNA-based clone sequences showed that unclassified bacteria were the most abundant group, representing nearly
62% of all DNA sequences analyzed. Other phylogenetic groups identified included Proteobacteria (20%), Actinobacteria (9%),
Cyanobacteria (4%), and Bacteroidetes (2%). The composition of RNA-based libraries (1122 sequences) was similar to the DNA-based
libraries with a few notable exceptions: Proteobacteria were more dominant in the RNA clone libraries (i.e., 35% RNA; 20%
DNA). Differences in the Proteobacteria composition were also observed; alpha-Proteobacteria was 22 times more abundant in
the RNA-based clones while beta-Proteobacteria was eight times more abundant in the DNA libraries. Nearly twice as many DNA
operational taxonomic units (OTUs) than RNA OTUs were observed at distance 0.03 (101 DNA; 53 RNA). Twenty-four OTUs were shared
between all RNA- and DNA-based libraries (OTU0.03) representing only 18% of the total OTUs, but 81% (1527/1883) of all sequences. Such differences between clone libraries
demonstrate the necessity of generating both RNA- and DNA-derived clone libraries to compare these two different molecular
approaches for community analyses. 相似文献
3.
九龙江河口区nirS型反硝化细菌多样性及系统发育学分析 总被引:2,自引:0,他引:2
【目的】结合16S rRNA基因克隆文库和nirS基因克隆文库的分析,揭示九龙江河口区nirS型反硝化细菌多样性。【方法】选取九龙江河口区一富营养化采样点,分别采集水样及沉积物样品,进行理化因子的测定并提取细菌总DNA。以水样DNA构建16S rRNA基因克隆文库,以沉积物DNA构建nirS基因克隆文库,分析微生物群落结构的多样性并构建系统发育树。【结果】从16S rRNA基因克隆文库中获得86条有效序列,按97%的序列相似性划分为53个OTU,分别属于Proteobacteria门、Planctomycetes门、Bacteroidetes门、Actinobacteria门、Firmicutes门和Chloroflexi门。其中属于Proteobacteria门OTU的克隆子占克隆数的62.9%,是最优势的类群,分属于Alphaproteobacteria、Betaproteobacteria、Gammaproteobacteria和Deltaproteobacteria纲等。从nirS基因克隆文库中获得190条有效序列,翻译为氨基酸序列后,按82%的序列相似性划分为60个OTU,并定位到属的水平。其中Proteobacteria门是最优势的类群,占文库克隆子总数的71.6%,包括Alphaproteobacteria纲(5.8%)、Betaproteobacteria纲(49.0%)和Gammaproteobacteria纲(16.9%)。nirS基因克隆文库中丰度最高的OTU与GenBank中的一株可培养反硝化菌Thauera sp. R-26906具有100%的序列相似性。【结论】九龙江河口区的微生物以及亚硝酸盐还原酶基因(nirS)具有丰富的多样性。大部分NirS序列在GenBank中的最相似序列来源于河口、海湾等相似的环境。 相似文献
4.
《Fungal Ecology》2015
Metabarcoding data generated using next-generation sequencing (NGS) technologies are overwhelmed with rare taxa and skewed in Operational Taxonomic Unit (OTU) frequencies comprised of few dominant taxa. Low frequency OTUs comprise a rare biosphere of singleton and doubleton OTUs, which may include many artifacts. We present an in-depth analysis of global singletons across sixteen NGS libraries representing different ribosomal RNA gene regions, NGS technologies and chemistries. Our data indicate that many singletons (average of 38 % across gene regions) are likely artifacts or potential artifacts, but a large fraction can be assigned to lower taxonomic levels with very high bootstrap support (∼32 % of sequences to genus with ≥90 % bootstrap cutoff). Further, many singletons clustered into rare OTUs from other datasets highlighting their overlap across datasets or the poor performance of clustering algorithms. These data emphasize a need for caution when discarding rare sequence data en masse: such practices may result in throwing the baby out with the bathwater, and underestimating the biodiversity. Yet, the rare sequences are unlikely to greatly affect ecological metrics. As a result, it may be prudent to err on the side of caution and omit rare OTUs prior to downstream analyses. 相似文献
5.
Zhen-Yu Fan Xiao-Ran Li Dan-Ping Mao Gen-Feng Zhu Sheng-Yue Wang Zhe-Xue Quan 《World journal of microbiology & biotechnology》2009,25(8):1447-1452
PCR-based methods for rRNA gene analysis have been widely used to study diversity of microbiology. However, the analysis would
be difficult when the DNA content in samples is too low to be amplified by conventional PCR. Nested PCR comes up with the
advantage of higher sensitivity. It can detect target DNA at several-fold lower concentrations than conventional PCR. However,
the amplification bias and factors that potentially affect measurement of sample diversity associated with nested PCR method
has received little attention. Here, nested PCR was compared to reconditioning PCR which is based on conventional PCR and
it would reduce the formation of heteroduplex. We investigated the use of both nested and reconditioning PCR methods to construct
clone libraries of 16S rRNA genes from four swimming pool water samples. Abundances of OTUs (operational taxonomic units)
were correlated between the libraries (r
2 = 0.88, P < 0.0005), and some OTUs had equivalent abundances in the two libraries using the Chi-square test. Differences in taxonomic
groups, as well as diversity and richness estimators, were compared by paired t-test and the Wilcoxon test, respectively. There were no significant differences between clone libraries using these two PCR
methods. The results of ∫-Libshuff analysis suggested that nested PCR have no particular biases in revealing OTU diversity
of a bacterial community. Thus, nested PCR produce congruent pictures with reconditioning PCR in the microbial community analysis. 相似文献
6.
Zhao GH Li HM Ryan UM Cong MM Hu B Gao M Ren WX Wang XY Zhang SP Lin Q Zhu XQ Yu SK 《Parasitology international》2012,61(3):497-500
The nuclear ribosomal DNA (rDNA) region spanning 5.8S rDNA and the second internal transcribed spacer (ITS-2) of Baylisascaris schroederi isolated from the Qinling subspecies of giant panda in Shaanxi Province, China were amplified and sequenced. Sequence variations in the two rDNA regions within B. schroederi and among species in the family Ascarididae were examined. The lengths of B. schroederi 5.8S and ITS-2 rDNA sequences were 156 bp and 327 bp, respectively, and no nucleotide variation was found in these two rDNA regions among the 20 B. schroederi samples examined, and these ITS-2 sequences were identical to that of B. schroederi isolated from giant panda in Sichuan province, China. The inter-species differences in 5.8S and ITS-2 rDNA sequences among members of the family Ascarididae were 0-1.3% and 0-17.7%, respectively. Phylogenetic relationships among species in the Ascarididae were re-constructed by Bayesian inference (Bayes), maximum parsimony (MP), and maximum likelihood (ML) analyses, based on combined sequences of 5.8S and ITS-2 rDNA. All B. schroederi samples clustered together and sistered to B. transfuga with high posterior probabilities/bootstrap values, which further confirmed that nematodes isolated from the Qinling subspecies of giant panda in Shaanxi Province, China represent B. schroederi. Because of the large number of ambiguously aligned sequence positions (difficulty of inferring homology by positions), ITS-2 sequence alone is likely unsuitable for phylogenetic analyses at the family level, but the combined 5.8S and ITS-2 rDNA sequences provide alternative genetic markers for the identification of B. schroederi and for phylogenetic analysis of parasites in the family Ascarididae. 相似文献
7.
Sequence variability in the first internal transcribed spacer region within and among Cyclospora species is consistent with polyparasitism 总被引:7,自引:0,他引:7
Olivier C van de Pas S Lepp PW Yoder K Relman DA 《International journal for parasitology》2001,31(13):1475-1487
Cyclospora cayetanensis is a coccidian parasite which causes severe gastroenteritis in humans. Molecular information on this newly emerging pathogen is scarce. Our objectives were to assess genetic variation within and between human-associated C. cayetanensis and baboon-associated Cyclospora papionis by examining the internal transcribed spacer (ITS) region of the ribosomal RNA operon, and to develop an efficient polymerase chain reaction- (PCR)-based method to distinguish C. cayetanensis from other closely related organisms. For these purposes, we studied C. cayetanensis ITS-1 nucleotide variability in 24 human faecal samples from five geographic locations and C. papionis ITS-1 variability in four baboon faecal samples from Tanzania. In addition, a continuous sequence encompassing ITS-1, 5.8S rDNA and ITS-2 was determined from two C. cayetanensis samples. The results indicate that C. cayetanensis and C. papionis have distinct ITS-1 sequences, but identical 5.8S rDNA sequences. ITS-1 is highly variable within and between samples, but variability does not correlate with geographic origin of the samples. Despite this variability, conserved species-specific ITS-1 sequences were identified and a single-round, C. cayetanensis-specific PCR-based assay with a sensitivity of one to ten oocysts was developed. This consistent and remarkable diversity among Cyclospora spp. ITS-1 sequences argues for polyparasitism and simultaneous transmission of multiple strains. 相似文献
8.
The potential for comparing microbial community population structures has been greatly enhanced by developments in next generation sequencing methods that can generate hundreds of thousands to millions of reads in a single run. Conversely, many microbial community comparisons have been published with no more than 1,000 sequences per sample. These studies have presented data on levels of shared operational taxonomic units (OTUs) between communities. Due to lack of coverage, that approach might compromise the conclusions about microbial diversity and the degree of difference between environments. In this study, we present data from recent studies that highlight this problem. Also, we analyzed datasets of 16 rRNA sequences with small and high sequence coverage from different environments to demonstrate that the level of sequencing effort used for analyzing microbial communities biases the results. We randomly sampled pyrosequencing-generated 16S rRNA gene libraries with increasing sequence effort. Sequences were used to calculate Good's coverage, the percentage of shared OTUs, and phylogenetic distance measures. Our data showed that simple counts of presence/absence of taxonomic unities do not reflect the real similarity in membership and structure of the bacterial communities and that community comparisons based on phylogenetic tests provide a way to test statistically significant differences between two or more environments without need an exhaustive sampling effort. 相似文献
9.
目的 对比Sanger和Pyrosequencing测序法分析健康人口腔菌群组成。方法 收集6例健康成人唾液、舌背、黏膜、龈上及龈下菌斑并构建16S rRNA基因文库,分别用Sanger和Pyrosequencing测序法分析。结果 Sanger测序所得已知的序列有5,794条(占6,535总序列数88.7%)、75个属,396个序列划分操作分类单元(operational taxonomic units,OTUs,占总OTUs的61.4%)。Pyrosequencing测序所得已知的序列有10,771条(占11,103总序列数97.0%)、66个属,322个OTUs(占总OTUs的68.0%)。Sanger和Pyrosequencing测序法所得口腔菌群在门、属的水平分布趋势基本一致,但在种的水平分布差异显著。Sanger和Pyrosequencing测序法构建的口腔菌群文库均匀度值分别为0.016和0.007,说明Pyrosequencing分析口腔菌群物种数量分布比Sanger测序方法的文库均匀性稍差,但优势种更显著。结论 Pyrosequencing测序时所构建基因文库能代表口腔菌群的多样性且经济、省时,可以应用于口腔细菌物种的分析。 相似文献
10.
Monica M. Lins-de-Barros Alexander M. Cardoso Cynthia B. Silveira Joyce L. Lima Maysa M. Clementino Orlando B. Martins Rodolpho M. Albano Ricardo P. Vieira 《Microbial ecology》2013,65(1):205-213
The association of metazoan, protist, and microbial communities with Scleractinian corals forms the basis of the coral holobiont. Coral bleaching events have been occurring around the world, introducing changes in the delicate balance of the holobiont symbiotic interactions. In this study, Archaea, bacteria, and eukaryotic phototrophic plastids of bleached colonies of the Brazilian coral Siderastrea stellata were analyzed for the first time, using 16S rRNA gene libraries. Prokaryotic communities were slightly more diverse in healthy than in bleached corals. However, the eukaryotic phototrophic plastids community was more diverse in bleached corals. Archaea phylogenetic analyses revealed a high percentage of Crenarchaeota sequences, mainly related to Nitrosopumilus maritimus and Cenarchaeum symbiosum. Dramatic changes in bacterial community composition were observed in this bleaching episode. The dominant bacterial group was Alphaproteobacteria followed by Gammaproteobacteria in bleached and Betaproteobacteria in healthy samples. Plastid operational taxonomic units (OTUs) from both coral samples were mainly related to red algae chloroplasts (Florideophycea), but we also observed some OTUs related to green algae chloroplasts (Chlorophyta). There seems to be a strong relationship between the Bacillariophyta phylum and our bleached coral samples as clones related to members of the diatom genera Amphora and Nitzschia were detected. The present study reveals information from a poorly investigated coral species and improves the knowledge of coral microbial community shifts that could occur during bleaching episodes. 相似文献
11.
Phylogenetic diversity of bacterial communities in bovine rumen as affected by diets and microenvironments 总被引:1,自引:0,他引:1
Phylogenetic analysis was conducted to examine ruminal bacteria in two ruminal fractions (adherent fraction vs. liquid fraction)
collected from cattle fed with two different diets: forage alone vs. forage plus concentrate. One hundred forty-four 16S rRNA
gene (rrs) sequences were obtained from clone libraries constructed from the four samples. These rrs sequences were assigned to 116 different operational taxonomic units (OTUs) defined at 0.03 phylogenetic distance. Most of
these OTUs could not be assigned to any known genus. The phylum Firmicutes was represented by approximately 70% of all the sequences. By comparing to the OTUs already documented in the rumen, 52 new
OTUs were identified. UniFrac, SONS, and denaturing gradient gel electrophoresis analyses revealed difference in diversity
between the two fractions and between the two diets. This study showed that rrs sequences recovered from small clone libraries can still help identify novel species-level OTUs. 相似文献
12.
Bacterial diversity in the rumen of Indian Surti buffalo (Bubalus bubalis), assessed by 16S rDNA analysis 总被引:1,自引:0,他引:1
P. R. Pandya K. M. Singh S. Parnerkar A. K. Tripathi H. H. Mehta D. N. Rank R. K. Kothari C. G. Joshi 《Journal of applied genetics》2010,51(3):395-402
Bacterial communities in buffalo rumen were characterized using a culture-independent approach for a pooled sample of rumen
fluid from 3 adult Surti buffaloes. Buffalo rumen is likely to include species of various bacterial phyla, so 16S rDNA sequences
were amplified and cloned from the sample. A total of 191 clones were sequenced and similarities to known 16S rDNA sequences
were examined. About 62.82% sequences (120 clones) had >90% similarity to the 16S rDNA database sequences. Furthermore, about
34.03% of the sequences (65 clones) were 85–89% similar to 16S rDNA database sequences. For the remaining 3.14%, the similarity
was lower than 85%. Phylogenetic analyses were also used to infer the makeup of bacterial communities in the rumen of Surti
buffalo. As a result, we distinguished 42 operational taxonomic units (OTUs) based on unique 16S r DNA sequences: 19 OTUs
affiliated to an unidentified group (45.23% of total OTUs), 11 OTUs of the phylum Firmicutes, also known as the low G+C group
(26.19%), 7 OTUs of theCytophaga-Flexibacter-Bacteroides phylum (16.66%), 4 OTUs of Spirochaetes (9.52%), and 1 OTU of Actinobacteria (2.38%). These include 10 single-clone OTUs,
so Good’s coverage (94.76%) of 16S rRNA libraries indicated that sequences identified in the libraries represent the majority
of bacterial diversity present in rumen. 相似文献
13.
Linda K. Medlin 《欧洲藻类学杂志》2017,52(1):90-103
A previous study of available diatom sequences tested the value of multiple outgroups in analyses of the 18S ribosomal RNA gene aimed at recovering the three diatom Classes (Coscinodiscophyceae, Mediophyceae, Bacillariophyceae) as monophyletic groups. Of the 34 datasets tested in that study, three recovered these Classes and two of these are explored here in more detail. The major differences between these two datasets were the number of outgroups, the number of nucleotides selected for the analysis and the addition to the dataset of short clone library sequences, primarily from raphid pennate taxa. The addition of short sequences resulted in a smaller dataset in terms of total nucleotides analysed because of the filter selected in the ARB program to generate the final dataset for phylogenetic analysis. The 50% parsimony filter selects a base for the final dataset if that position is parsimony-informative in at least 50% of the sequences chosen for the analysis. Thus, with short sequences, fewer bases are available for selection in the final dataset. A final dataset with fewer nucleotides is produced from the original alignment than from a similar one with no filter applied. If no filter is applied, then a final dataset is produced with all full-length sequences. From these analyses, it was determined that the addition of short clone library sequences recovered sister relationships for certain raphid diatoms that go against conventional wisdom with regard to valve morphology. Thus, the smaller database caused some of the groupings to be unnatural. It was determined that the optimal resolution of the taxa in these datasets resulted from using only full length sequences and selected multiple outgroups. Results obtained from the reduced dataset would be a cause for concern with next generation sequencing in which short amplicons are used to identify taxa. 相似文献
14.
三氯乙烷污染地地下水中Dehalobacter属细菌定量与多样性分析 总被引:2,自引:0,他引:2
[目的]对某公司6个以1,1,1-三氯乙烷(1,1,1-Trichloroethane,1,1,1-TCA)为主要污染物的地下水样品中的降解微生物Dehalobacter spp.(Dhb)进行相对定量和多样性分析.[方法]采用气相色谱法测定6个样品中1,1,1-TCA、1,1-二氯乙烷(1,1-DCA)和氯乙烷(CA)的浓度;通过定量PCR法分别测定6个样品中Dhb占总菌的百分比;以16S rRNA基因通用引物和Dhb特异性引物扩增获得的PCR产物构建了6个样品的Dhb特异性克隆文库,所得序列与GenBank中的最相似序列构建系统发育树.[结果]6个样品中均有1,1-DCA和(或)CA的检出,推测此6处地下水中1,1,1-TCA可能存在生物降解.定量PCR结果表明,6个样品中Dhb丰度差异较大.6个Dhb特异性克隆文库获得41条序列,序列比对结果表明,与它们最相似的已知分类地位的序列全部属于Dhb属.这些序列按99%的相似性被划分成7个可操作性分类单元(OTU).其中24条序列属于OTU1,该OTU的序列与已知能阵解1,1,1-TCA的Dehalobacter sp.str.TCA1的16S rRNA基因序列相似性达98%;文库中的3个OTU与GenBank中16S rRNA基因序列同源性最高仅为95%-96%.[结论]该污染场地地下水中存在多样性较丰富的降解微生物Dehalobacter属细菌,它们可能与现场的1,1,1-TCA生物降解有关. 相似文献
15.
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
16.
Impact of sequence processing and taxonomic classification approaches on eukaryotic community structure from environmental samples with emphasis on diatoms
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Kristin Hardge Stefan Neuhaus Estelle S. Kilias Christian Wolf Katja Metfies Stephan Frickenhaus 《Molecular ecology resources》2018,18(2):204-216
Next‐generation sequencing is a common method for analysing microbial community diversity and composition. Configuring an appropriate sequence processing strategy within the variety of tools and methods is a nontrivial task and can considerably influence the resulting community characteristics. We analysed the V4 region of 18S rRNA gene sequences of marine samples by 454‐pyrosequencing. Along this process, we generated several data sets with QIIME, mothur, and a custom‐made pipeline based on DNAStar and the phylogenetic tree‐based PhyloAssigner. For all processing strategies, default parameter settings and punctual variations were used. Our results revealed strong differences in total number of operational taxonomic units (OTUs), indicating that sequence preprocessing and clustering had a major impact on protist diversity estimates. However, diversity estimates of the abundant biosphere (abundance of ≥1%) were reproducible for all conducted processing pipeline versions. A qualitative comparison of diatom genera emphasized strong differences between the pipelines in which phylogenetic placement of sequences came closest to light microscopy‐based diatom identification. We conclude that diversity studies using different sequence processing strategies are comparable if the focus is on higher taxonomic levels, and if abundance thresholds are used to filter out OTUs of the rare biosphere. 相似文献
17.
Nucleotide sequences of 5.8S rRNA gene and rDNA internal transcribed spacers ITS-1 and ITS-2 were determined in diploid wheat Triticum urartu. It was shown that 5.8S rRNA gene of this wheat species consists of 163 base pairs and GC-content is 59.5%. When comparing 5.8S rRNA sequences in diploid wheat, rice and lupine and also 5.8S rRNA in hexaploid wheat and horse beans a high evolutional conservatism of its structure was revealed. The size of ITS-1 and ITS-2 in Tr. urartu is 219 and 225 base pairs long correspondingly. While comparing structures of similar rDNA regions of Tr. urartu, rice and maize a high level of homology was found only between nucleotides adjoining genes of high molecular rRNAs. In ITS-1 of Tr. urartu an insertion of 5'-GACGACGACATTGTCCGTC-3' was found, which is absent in maize and rice. 相似文献
18.
Morphologically similar microbial communities that often form on the walls of geographically distinct limestone caves have not yet been comparatively studied. Here, we analysed phylotype distribution in yellow microbial community samples obtained from the walls of distinct caves located in Spain, Czech Republic and Slovenia. To infer the level of similarity in microbial community membership, we analysed inserts of 474 16S rRNA gene clones and compared those using statistical tools. The results show that the microbial communities under investigation are composed solely of Bacteria. The obtained phylotypes formed three distinct groups of operational taxonomic units (OTUs). About 60% of obtained sequences formed three core OTUs common to all three sampling sites. These were affiliated with actinobacterial Pseudonocardinae (30-50% of sequences in individual sampling site libraries), but also with gammaproteobacterial Chromatiales (6-25%) and Xanthomonadales (0.5-2.0%). Another 7% of sequences were common to two sampling sites and formed eight OTUs, while the remaining 35% were site specific and corresponded mostly to OTUs containing single sequences. The same pattern was observed when these data were compared with sequence data available from similar studies. This comparison showed that distinct limestone caves support microbial communities composed mostly of phylotypes common to all sampling sites. 相似文献
19.
Nikhil Ram-Mohan Aharon Oren R. Thane Papke 《Extremophiles : life under extreme conditions》2016,20(5):747-757
Stability of microbial communities can impact the ability of dispersed cells to colonize a new habitat. Saturated brines and their halophile communities are presumed to be steady state systems due to limited environmental perturbations. In this study, the bacteriorhodopsin-containing fraction of the haloarchaeal community from Eilat salt crystallizer ponds was sampled five times over 3 years. Analyses revealed the existence of a constant core as several OTUs were found repeatedly over the length of the study: OTUs comprising 52 % of the total cloned and sequenced PCR amplicons were found in every sample, and OTUs comprising 89 % of the total sequences were found in more than one, and often more than two samples. LIBSHUFF and UNIFRAC analyses showed statistical similarity between samples and Spearman’s coefficient denoted significant correlations between OTU pairs, indicating non-random patterns in abundance and co-occurrence of detected OTUs. Further, changes in the detected OTUs were statistically linked to deviations in salinity. We interpret these results as indicating the existence of an ever-present core bacteriorhodopsin-containing Eilat crystallizer community that fluctuates in population densities, which are controlled by salinity rather than the extinction of some OTUs and their replacement through immigration and colonization. 相似文献
20.
Seung-Yoon Oh Jonathan J. Fong Myung Soo Park Limseok Chang Young Woon Lim 《Journal of microbiology (Seoul, Korea)》2014,52(6):465-472
Fungal spores are widespread and common in the atmosphere. In this study, we use a metagenomic approach to study the fungal diversity in six total air samples collected from April to May 2012 in Seoul, Korea. This springtime period is important in Korea because of the peak in fungal spore concentration and Asian dust storms, although the year of this study (2012) was unique in that were no major Asian dust events. Clustering sequences for operational taxonomic unit (OTU) identification recovered 1,266 unique OTUs in the combined dataset, with between 223?96 OTUs present in individual samples. OTUs from three fungal phyla were identified. For Ascomycota, Davidiella (anamorph: Cladosporium) was the most common genus in all samples, often accounting for more than 50% of all sequences in a sample. Other common Ascomycota genera identified were Alternaria, Didymella, Khuskia, Geosmitha, Penicillium, and Aspergillus. While several Basidiomycota genera were observed, Chytridiomycota OTUs were only present in one sample. Consistency was observed within sampling days, but there was a large shift in species composition from Ascomycota dominant to Basidiomycota dominant in the middle of the sampling period. This marked change may have been caused by meteorological events. A potential set of 40 allergyinducing genera were identified, accounting for a large proportion of the diversity present (22.5?7.2%). Our study identifies high fungal diversity and potentially high levels of fungal allergens in springtime air of Korea, and provides a good baseline for future comparisons with Asian dust storms. 相似文献