Santa Rosalia revisited: Why are there so many species of bacteria?

  title={Santa Rosalia revisited: Why are there so many species of bacteria?},
  author={Daniel E. Dykhuizen},
  journal={Antonie van Leeuwenhoek},
  • D. Dykhuizen
  • Published 2004
  • Environmental Science, Biology
  • Antonie van Leeuwenhoek
The diversity of bacteria in the world is very poorly known. Usually less than one percent of the bacteria from natural communities can be grown in the laboratory. This has caused us to underestimate bacterial diversity and biased our view of bacterial communities. The tools are now available to estimate the number of bacterial species in a community and to estimate the difference between communities. Using what data are available, I have estimated that thirty grams of forest soil contains over… 

Predicting microbial species richness.

It is argued that the methodology provides estimates of microbial richness that are reliable and general, have biologically meaningful SEs, and meet other fundamental statistical standards and can serve as a baseline in microbial diversity studies.

The rare bacterial biosphere.

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  • Biology, Environmental Science
    Annual review of marine science
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In the case of bacteria, the exploration of this rare biosphere has several points of interest and will eventually produce a reasonable estimate of the total number of bacterial taxa in the oceans, which will answer the question of whether "everything is everywhere".

The Rare Bacterial Biosphere

All communities are dominated by a few species that account for most of the biomass and carbon cycling. On the other hand, a large number of species are represented by only a few individuals. In the

Estimating prokaryotic diversity and its limits

It is evident that local and global prokaryotic diversity can be understood through species abundance curves and purely experimental approaches to solving this conundrum will be fruitless.

What are bacterial species?

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  • Biology, Environmental Science
    Annual review of microbiology
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These molecular methods suggest that a typical named species contains many ecotypes, each with the universal attributes of species, which is more like a genus than a species.

Robust estimation of microbial diversity in theory and in practice

It is argued that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions, and recommended is the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.

The generation and maintenance of diversity in microbial communities.

A meta-analysis of bacterial richness estimates from a variety of ecosystems found that nearly all environments contained hundreds to thousands of bacterial taxa, and richness levels increased with the number of individuals in a sample, a pattern consistent with those reported for nonmicrobial taxa.

An ecological perspective on bacterial biodiversity

From recent studies of the distribution of free–living bacterial diversity, a preliminary picture is emerging: bacterial diversity may exhibit regular patterns, and in some cases these patterns may be qualitatively similar to those observed for plants and animals.

Speciation in digital organisms

It is argued that resource limitations are a major factor in the evolutionary origin of complex ecosystems with interacting and persistent species.

Toward a Census of Bacteria in Soil

A statistical model is developed that makes the problem of estimating richness statistically accessible by evaluating the characteristics of samples drawn from simulated communities with parametric community distributions, and shows that generating sufficient sequence data to do so requires less sequencing effort than completely sequencing a bacterial genome.



Homage to Santa Rosalia or Why Are There So Many Kinds of Animals?

The address of the president of a society, founded largely to further the study of evolution, at the close of the year that marks the centenary of Darwin and Wallace's initial presentation of the theory of natural selection.

Comparison of phenotypic diversity and DNA heterogeneity in a population of soil bacteria

This study showed that reassociation of DNA isolated from a collection of bacteria gave a good estimate of the diversity of the collection and that there was good agreement with different phenotypic diversity measures.

Application of phylogenetically based hybridization probes to microbial ecology

Some of the more general themes that are emerging from the application of a molecular-phylogenetic framework to study natural systems are addressed and how these themes serve to structure analytical approaches using nucleic acid probes are addressed.

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  • Biology
    Applied and environmental microbiology
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Deep-subsurface isolates tested seemed to belong to the families Pseudomonadaceae and Neisseriaceae, which might reflect a long period of adaptation to the environmental conditions of the deep subsurface.

Evolution in bacteria: Evidence for a universal substitution rate in cellular genomes

A temporal scale for bacterial evolution is constructed by tying ecological events that took place at known times in the geological past to specific branch points in the genealogical tree relating the 16S ribosomal RNAs of eubacteria, mitochondria, and chloroplasts to specific branches in the bacterial tree.

The Commonness, And Rarity, of Species

The purpose of this paper is to deduce, from a number of examples and from theoretical considerations, some plausible general law as to how abundance or commonness is distributed among species.

The Relation Between the Number of Species and the Number of Individuals in a Random Sample of an Animal Population

Part 1. It is shown that in a large collection of Lepidoptera captured in Malaya the frequency of the number of species represented by different numbers of individuals fitted somewhat closely to a

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A community hybridization technique was applied to determine the similarity and relative diversity of two samples by cross hybridization to determine broad-scale differences in soil microbial community structure, demonstrating that single bacterial species and a mixture of cultivable bacteria were less complex and only 5% similar to whole-community DNA or bacteria directly extracted from the soil.

The Effects of Rare but Promiscuous Genetic Exchange on Evolutionary Divergence in Prokaryotes

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  • Biology, Environmental Science
    The American Naturalist
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I have investigated the determinants of genetic divergence within a metapopulation of bacterial populations, in which each constituent population is adapted to a different ecological niche and

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  • Environmental Science
    The American Naturalist
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These experiments were designed to determine the degree and kind of variability in the structure of the community that one might expect under very similar ecological conditions and show that 95.5% to 98.0% of the specimens composed the same species in the eight communities.