Journal ArticleDOI
Genetic diversity in Sargasso Sea bacterioplankton.
TLDR
The phylogenetically analysed clone libraries of eubacterial 16S ribosomal RNA genes amplified from natural populations of Sargasso Sea picoplankton indicate the presence of a novel microbial group, the SAR 11 cluster, which appears to be a significant component of this oligotrophic bacterioplankton community.Abstract:
BACTERIOPLANKTON are recognized as important agents of biogeochemical change in marine ecosystems, yet relatively little is known about the species that make up these communities. Uncertainties about the genetic structure and diversity of natural bacterioplankton populations stem from the traditional difficulties associated with microbial cultivation techniques. Discrepancies between direct counts and plate counts are typically several orders of magnitude, raising doubts as to whether cultivated marine bacteria are actually representative of dominant planktonic species1–3. We have phylogenetically analysed clone libraries of eubacterial 16S ribosomal RNA genes amplified from natural populations of Sargasso Sea picoplankton by the polymerase chain reaction4. The analysis indicates the presence of a novel microbial group, the SAR 11 cluster, which appears to be a significant component of this oligotrophic bacterioplankton community. A second cluster of lineages related to the oxygenic phototrophs—cyanobacteria, prochlorophytes and chloroplasts—was also observed. However, none of the genes matched the small subunit rRNA sequences of cultivated marine cyanobacteria from similar habitats. The diversity of 16S rRNA genes observed within the clusters suggests that these bacterioplankton may be consortia of independent lineages sharing surprisingly distant common ancestors.read more
Citations
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Assessment of Fungal Diversity in the Environment using Metagenomics: a Decade in Review
Sara Cuadros-Orellana,Laura Rabelo Leite,Ash Smith,Julliane Dutra Medeiros,Fern,a Badotti,Paula Lc Fonseca,Aline Bm Vaz,Guilherme Oliveira,Aristóteles Góes-Neto +9 more
TL;DR: The main advances in the study of fungal diversity are described, statistics of the main metagenomic databases with regard to the representativeness ofFungal phyla are presented, and the future directions in this field are discussed.
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Bacterioplankton community diversity in a series of thermally stratified lakes
TL;DR: The dominant members of the bacterioplankton community in a set of 10 small, thermally stratified lakes in northeastern Indiana were determined by denaturing gradient gel electrophoresis (DGGE) of a polymerase chain reaction amplified fragment of 16S rDNA by analyzing variability in community composition.
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Fourier transform infrared spectroscopy of microalgae as a novel tool for biodiversity studies, species identification, and the assessment of water quality
TL;DR: It is demonstrated that it is possible to accurately identify species and determine the nutritional status of their environment of origin (e.g., N‐source), provided that suitable FTIR spectral libraries are available.
Journal ArticleDOI
Co-occurrence patterns for abundant marine archaeal and bacterial lineages in the deep chlorophyll maximum of coastal California.
TL;DR: This study identifies co-occurrence patterns for marine Archaea and specific bacterial groups in the chlorophyll maximum of the Southern California Bight and shows that abundant microbial OTUs—including the marine Crenarchaeota, SAR11, SAR86 and the Bacteroidetes—co-occur non-randomly.
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Identification of eukaryotic open reading frames in metagenomic cDNA libraries made from environmental samples
Susan Grant,William D. Grant,Don A. Cowan,Brian E. Jones,Yanhe Ma,Antonio Ventosa,Shaun Heaphy +6 more
TL;DR: RNAlater (Ambion) was shown to stabilize RNA in environmental samples for periods of at least 3 months at −20°C, and permits the polyadenylated transcriptome to be isolated from environmental samples with no knowledge of the identity of the microorganisms in the sample or the necessity to culture them.
References
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Randall Keichi Saiki,David H. Gelfand,Susanne Stoffel,Stephen J. Scharf,Russell Higuchi,Glenn Thomas Horn,Kary B. Mullis,Henry A. Erlich +7 more
TL;DR: A thermostable DNA polymerase was used in an in vitro DNA amplification procedure, the polymerase chain reaction, which significantly improves the specificity, yield, sensitivity, and length of products that can be amplified.
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Site-directed mutagenesis by overlap extension using the polymerase chain reaction.
TL;DR: In this paper, complementary oligodeoxyribonucleotide (oligo) primers and the polymerase chain reaction are used to generate two DNA fragments having overlapping ends, and these fragments are combined in a subsequent 'fusion' reaction in which the overlapping ends anneal, allowing the 3' overlap of each strand to serve as a primer for the three' extension of the complementary strand.
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