The Physical Environment in Soil Microbiology: An Attempt to Extend Principles of Microbiology to Soil Microorganisms

Hattori, Tsutomu; Hattori, Reiko

doi:10.3109/10408417609102305

Cited by 167 publications

(57 citation statements)

References 63 publications

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“…There was a gradual decrease in similarity as a function of distance along the linear 10-m transect, and there was a roughly linear relationship between the level of similarity between sampling locations and the geographical distance between the locations. These data suggest that at this study site multiple small-scale and ecologically distinct habitats most likely exist in patchy arrangements (9,10) and that each habitat selects for genetically distinct clones. Soil is generally recognized as a spatially heterogeneous habitat in terms of both its composition and its structure (15,32).…”

Section: Resultsmentioning

confidence: 95%

Biogeography of the Purple Nonsulfur Bacterium Rhodopseudomonas palustris

Oda

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Huisman

et al. 2003

Appl Environ Microbiol

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The biogeography of the purple nonsulfur bacterium Rhodopseudomonas palustris on a local scale was investigated. Thirty clones of phototrophic bacteria were isolated from each of five unevenly spaced sampling locations in freshwater marsh sediments along a linear 10-m transect, and a total of 150 clones were characterized by BOX-PCR genomic DNA fingerprinting. Cluster analysis of 150 genomic fingerprints yielded 26 distinct genotypes, and 106 clones constituted four major genotypes that were repeatedly isolated. Representatives of these four major genotypes were tentatively identified as R. palustris based on phylogentic analyses of 16S rRNA gene sequences. The differences in the genomic fingerprint patterns among the four major genotypes were accompanied by differences in phenotypic characteristics. These phenotypic differences included differences in the kinetics of carbon source use, suggesting that there may be functional differences with possible ecological significance among these clonal linages. Morisita-Horn similarity coefficients (C MH ), which were used to compare the numbers of common genotypes found at pairs of sampling locations, showed that there was substantial similarity between locations that were 1 cm apart (C MH , >0.95) but there was almost no similarity between locations that were >9 m apart (C MH , <0.25). These calculations showed there was a gradual decrease in similarity among the five locations as a function of distance and that clones of R. palustris were lognormally distributed along the linear 10-m transect. These data indicate that natural populations of R. palustris are assemblages of genetically distinct ecotypes and that the distribution of each ecotype is patchy.Studies of the spatial distribution of bacteria have demonstrated that populations of the same species found in various ecological habitats have distinctive physiological traits (6,14,24,31). This may be due to the fact that microorganisms are highly mutable (2, 17, 25) and readily acquire traits through adaptive evolution that enable populations to be well suited to persist in a wide array of environments that have different biotic and abiotic characteristics. This is akin to the development of ecotypes within eukaryotic species (8, 13), in which genetic variants possess physiological traits that confer fitness advantages in specific habitats (8). While it is increasingly apparent that ecotypes of prokaryotic species also exist, little is known about their spatial distribution on a local scale.Studies of the population structure and distribution of the host-associated species Escherichia coli have demonstrated that certain clonal types are better adapted than others for colonization of specific hosts. For example, over an 11-month period Caugant et al. (4) found 53 genotypes of E. coli in a single human host. However, only two of these genotypes were persistent over time, and 46% of all the isolates represented a single genotype; the remaining genotypes were apparently transient members of the gastrointestinal flora. T...

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Section: Resultsmentioning

confidence: 95%

Biogeography of the Purple Nonsulfur Bacterium Rhodopseudomonas palustris

Oda

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Huisman

et al. 2003

Appl Environ Microbiol

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“…Models of this type have been employed to describe the dynamics of natural microbial populations in terrestrial 'E-mail: bpboudre@is.dal.ca Q Inter- Research 1999 aquifers, soils and rivers (e.g. Bazin et al 1976, Hattori & Hattori 1976, Hino 1981, Tan & Bond 1995, but this approach has not, to this author's knowledge, been applied to aquatic sediments. The underlying principle behind these models is conservation of mass, and this is achieved by correct balancing of inputs, outputs and accumulations.…”

Section: Introductionmentioning

confidence: 99%

A theoretical investigation of the organic carbon-microbial biomass relation in muddy sediments

Boudreau¹

1999

Aquat. Microb. Ecol.

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A population/diagenetic model is developed to describe the behavior/dynamics of the microbial biomass in aquatic sedirnents. This model is analyzed in order to establish the dominant terms, i.e. processes, in that balance. The result of this analysis shows that production-removal processes, i.e. growth, death, grazing, transformation to inactive or active, etc., are essentially in balance to the best (lowest order) approximation, while all varieties of transport processes, i.e. motility, chemotaxis, bioturbation, burial, etc.. contribute only higher order corrections to this balance. The balance between production-removal processes is shown to imply a linear relation between the size of the microbial biomass and the concentration of organic substrate, as advanced by Rublee (1982; Estuarine comparisons, Academic Press, p. 159-1821, based on empirical evidence.

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“…The radial growth rate can often serve as a qualitative proxy for the underlying biomass growth rate: the two are directly proportional for a fixed-thickness colony that grows only at the edge (44,47). Clearly, other physiological parameters can play a role (33,67), and colony morphology may also be shaped by swarming and chemotaxis, by nutrient availability (56), and by the spatial structure of soil (22). However, measuring growth in liquid is not a feasible general alternative, since liquid supports the growth of fewer species than solid media (53) and many soil bacteria form aggregates when growing in liquid media (e.g., Streptomyces [24]).…”

Section: Figmentioning

confidence: 99%

Distinct Growth Strategies of Soil Bacteria as Revealed by Large-Scale Colony Tracking

Ernebjerg

Kishony

2012

Appl Environ Microbiol

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Our understanding of microbial ecology has been significantly furthered in recent years by advances in sequencing techniques, but comprehensive surveys of the phenotypic characteristics of environmental bacteria remain rare. Such phenotypic data are crucial for understanding the microbial strategies for growth and the diversity of microbial ecosystems. Here, we describe a high-throughput measurement of the growth of thousands of bacterial colonies using an array of flat-bed scanners coupled with automated image analysis. We used this system to investigate the growth properties of members of a microbial community from untreated soil. The system provides high-quality measurements of the number of CFU, colony growth rates, and appearance times, allowing us to directly study the distribution of these properties in mixed environmental samples. We find that soil bacteria display a wide range of growth strategies which can be grouped into several clusters that cannot be reduced to any of the classical dichotomous divisions of soil bacteria, e.g., into copiotophs and oligotrophs. We also find that, at early times, cells are most likely to form colonies when other, nearby colonies are present but not too dense. This maximization of culturability at intermediate plating densities suggests that the previously observed tendency for high density to lead to fewer colonies is partly offset by the induction of colony formation caused by interactions between microbes. These results suggest new types of growth classification of soil bacteria and potential effects of species interactions on colony growth.

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The Physical Environment in Soil Microbiology: An Attempt to Extend Principles of Microbiology to Soil Microorganisms

Cited by 167 publications

References 63 publications

Biogeography of the Purple Nonsulfur Bacterium Rhodopseudomonas palustris

Biogeography of the Purple Nonsulfur Bacterium Rhodopseudomonas palustris

A theoretical investigation of the organic carbon-microbial biomass relation in muddy sediments

Distinct Growth Strategies of Soil Bacteria as Revealed by Large-Scale Colony Tracking

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