Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample

Article Abstract:

Marine bacterioplankton diversity was analyzed by utilizing the small-subunit (SSU) ribosomal deoxyribonucleic acids (rDNAs) of bacterial samples from the Oregon coasts. Analysis of the SSU rDNA of bacterial isolates and bacterial SSU rDNAs cloned from a sample of Oregon coastal seawater indicated minimal overlap between the SSU rDNAs of the clones and cultured strains. Furthermore, the bacterial isolates exhibited new SSU rRNA sequences indicating the presence of new microbial species on the basis of SSU rDNA comparisons.

Analysis, Genetic aspects, DNA, Identification and classification, Microbiology, Biological diversity, Biodiversity, Taxonomy (Biology), Microbial populations, Ribosomal proteins

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Phylogenetic diversity of ultraplankton plastid small-subunit rRNA genes recovered in environmental nucleic acid samples from the Pacific and Atlantic coasts of the United States

Article Abstract:

A survey of the diversity of bacterioplankton in Oregon coastal seawater was undertaken using rRNA gene clone libraries, PCR primers, polymorphism analyses, nucleic acid sequencing and oligonucleotide probe hybridizations. Results revealed that 54 of the 116 OCS gene clones were of plastid origin and that clones from the OCS and OM libraries formed at least eight unique lineages within the plastid radiation. The survey confirmed that unidentifiable species are not as common among phytoplankton as they are among bacteria.

Methods, Surveys, Plankton research, Phytoplankton, Plankton populations

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Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR

Article Abstract:

Reannealing of 16S rRNA genes in PCR reactions prevents the formation of gene template-PCR primer hybrids which causes a bias in the estimation of gene abundance in the original template mixture. The final concentration of genes is always 1:1 regardless of the original gene concentration. The formation of the template-primer hybrids increases as the concentration of the PCR products increases. The number of hybrids formed also depends on the number of template molecules present as single strand molecules.

Causes of, Polymerase chain reaction, Errors, Scientific, Scientific errors

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