The Analysis of Natural Microbial Populations by Ribosomal RNA Sequences

Pace, Norman R.; Stahl, David A.; Lane, David; Olsen, Gary J.

doi:10.1007/978-1-4757-0611-6_1

Cited by 879 publications

(555 citation statements)

References 63 publications

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“…One possibility is to identify natural microbial populations by their ribosomal RNA sequences (reviewed by Pace et al 1986). The main use of this technique has been in the phylogenetic placement of species, but it would also be very useful to know, for example, if only three species of bacteria dominate in any water sample.…”

Section: Deep-sea Conditionsmentioning

confidence: 99%

A comparison of the ecology of planktonic bacteria in fresh and salt water

Hobbie

1988

Limnology & Oceanography

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The planktonic bacteria inhabiting fresh and salt waters are not physiologically identical; most marine bacteria, for example, require sodium and some marine forms can thrive at 1,000 atm of pressure in the deep sea. Despite this difference, the conclusion of this review is that the ecology of planktonic bacteria is virtually identical in fresh and salt waters.The differences are small and mostly a matter of relative proportion of various processes. That is, similar bacterial processes occur in fresh and salt waters but in each environment, one process may be more important than another. For example, bacteria in freshwaters are exposed to high amounts of refractory dissolved organic carbon from soil and stream runoff, while many marine bacteria are exposed to relatively more of the labile organic matter from decaying algae. Also, under anaerobic conditions the sulfur cycle will be dominant in the sea while the carbon-methane cycle will be more important in freshwaters. In spite of the presence of relatively high amounts of methane in the sea, there is thus far little evidence that ,a significant amount of methane is being oxidized.Not enough is yet known to determine if there are dilfcrences in the grazing of bacteria in the two systems. Small, flagellated protozoans are very important grazers in freshwater and marine systems but there is some evidence from salt waters that ciliates are also important grazers. Marine ecosystems also contain large animals that can filter out bacteria. Sponges are the dominant suspension feeders on coral reefs, mussels and oysters are dominant in estuarine and marsh systems, and a large appendicularian may filter significant amounts of bacteria through a mucous net. Ecological understanding of the aquatic bacteria has advanced rapidly in the past two decades. One reason is the basic similarity between microbial ecology in fresh and salt waters and the consequent interchangeability of techniques.

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Section: Deep-sea Conditionsmentioning

confidence: 99%

A comparison of the ecology of planktonic bacteria in fresh and salt water

Hobbie

1988

Limnology & Oceanography

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“…Hybridization signals were quantified by PhosphorImaging (Molecular Dynamics, Sunnyvale, CA). In addition to the probes listed above, the following probes were used: S-D-Bact-0338-a-A-18 [4], S-*-Bact-0519-a-A-18 [24], and S-*-Univ-0915-b-A-16 [23].…”

Section: Methodsmentioning

confidence: 99%

A Comparison of the Use of In VitroTranscribed and Native rRNA for the Quantification of Microorganisms in the Environment

McMahon

Raskin

1998

Microbial Ecology

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A B S T R A C TNearly full-length, small subunit (SSU) rRNA was transcribed in vitro from clones of SSU rDNA genes. Comparing the use of in vitro-transcribed and native rRNA indicated that, when in vitrotranscribed rRNA was used as a standard for quantitative hybridizations with oligonucleotide probes, the population was consistently underestimated. The population abundance was expressed as a percentage of specific target SSU rRNA (determined with a specific oligonucleotide probe), relative to the total SSU rRNA (measured with a universal probe). Differences in hybridization signals could be related to specific probe target locations and rRNA denaturation conditions, suggesting that higher order structure is important in quantitative membrane hybridizations. Therefore, in vitro-transcribed rRNA cannot always be used for the absolute quantification of microbial populations, but can be employed as a standard to quantify shifts in population abundance over time, and to compare community structure in various environments.

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“…Final-and is still the most widely used. This rRNA gives information on the phylogenetic identity of the microorganisms (4), and this addresses the first fundamental question of microbial ecology.…”

Section: Microbial Ecology-the Sciencementioning

confidence: 99%