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Bacterial genomes: habitat specificity and uncharted organisms.

Dini-Andreote F, Andreote FD, Araújo WL, Trevors JT, van Elsas JD - Microb. Ecol. (2012)

Bottom Line: The capability and speed in generating genomic data have increased profoundly since the release of the draft human genome in 2000.Here, we propose that scientists should be concerned with attaining an improved equal representation of most of the bacterial tree of life organisms, at the genomic level.Not only will such efforts contribute to our overall understanding of the microbial diversity extant in ecosystems as well as the structuring of the extant genomes, but they will also facilitate the development of better methods for (meta)genome annotation.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil.

ABSTRACT
The capability and speed in generating genomic data have increased profoundly since the release of the draft human genome in 2000. Additionally, sequencing costs have continued to plummet as the next generation of highly efficient sequencing technologies (next-generation sequencing) became available and commercial facilities promote market competition. However, new challenges have emerged as researchers attempt to efficiently process the massive amounts of sequence data being generated. First, the described genome sequences are unequally distributed among the branches of bacterial life and, second, bacterial pan-genomes are often not considered when setting aims for sequencing projects. Here, we propose that scientists should be concerned with attaining an improved equal representation of most of the bacterial tree of life organisms, at the genomic level. Moreover, they should take into account the natural variation that is often observed within bacterial species and the role of the often changing surrounding environment and natural selection pressures, which is central to bacterial speciation and genome evolution. Not only will such efforts contribute to our overall understanding of the microbial diversity extant in ecosystems as well as the structuring of the extant genomes, but they will also facilitate the development of better methods for (meta)genome annotation.

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a Range of bacterial genome sizes in various habitats delimited by quartile 25 and 75 values. Numbers in parentheses indicate the amount of analysed genomes. Data were extracted from the Genomes OnLine Database (GOLD) [4] in September 2011. b Proposed model for microbial genome evolution and habitat-specific speciation
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Fig1: a Range of bacterial genome sizes in various habitats delimited by quartile 25 and 75 values. Numbers in parentheses indicate the amount of analysed genomes. Data were extracted from the Genomes OnLine Database (GOLD) [4] in September 2011. b Proposed model for microbial genome evolution and habitat-specific speciation

Mentions: Recent advances in meta(genome) data processing have provided knowledge on factors that modulate microbial speciation and genome evolution. The link is remarkable between the functional complexity of microbial genomes and the habitats where organisms survive and reproduce. Recently, Raes et al. [17] described an effective model to determine the effective genome size in metagenomics data. Intrinsic to this model is the concept that each habitat harbours a specific range of genome sizes which stand in relation to the prevailing factors in the habitat (Fig. 1a). The concept has been used as a metric parameter to infer community diversity and complexity [2], in which longer average genome lengths correlate with a more complex and dynamic habitats. The hypothesis is that bacteria with larger genomes can easier cope with such conditions as they encode a larger metabolic and stress tolerance potential [18]. In fact, the evolution of microbial species is affected by the environmental pressures acting over time (Fig. 1b). A clear example of this is the massive genome reduction in bacteria that adapts to a mutualistic/symbiotic lifestyle [cf. 20], resulting in tiny, gene-dense genomes [5]. It remains to be seen whether habitat-specific patterns can be distinguished among different genomes within the species. Certainly, the concept of habitat-specific genomes highlights the role of surrounding environment acting at the core of genome speciation and the evolution of microbial species. The collection of contextual (meta)data, encompassing physical–chemical parameters and allocating the source of a sequence in terms of space and time, surely will allow a better interpretation of unknown genes and species, as well as gaining new insights into the known fraction [28].Figure 1


Bacterial genomes: habitat specificity and uncharted organisms.

Dini-Andreote F, Andreote FD, Araújo WL, Trevors JT, van Elsas JD - Microb. Ecol. (2012)

a Range of bacterial genome sizes in various habitats delimited by quartile 25 and 75 values. Numbers in parentheses indicate the amount of analysed genomes. Data were extracted from the Genomes OnLine Database (GOLD) [4] in September 2011. b Proposed model for microbial genome evolution and habitat-specific speciation
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3375415&req=5

Fig1: a Range of bacterial genome sizes in various habitats delimited by quartile 25 and 75 values. Numbers in parentheses indicate the amount of analysed genomes. Data were extracted from the Genomes OnLine Database (GOLD) [4] in September 2011. b Proposed model for microbial genome evolution and habitat-specific speciation
Mentions: Recent advances in meta(genome) data processing have provided knowledge on factors that modulate microbial speciation and genome evolution. The link is remarkable between the functional complexity of microbial genomes and the habitats where organisms survive and reproduce. Recently, Raes et al. [17] described an effective model to determine the effective genome size in metagenomics data. Intrinsic to this model is the concept that each habitat harbours a specific range of genome sizes which stand in relation to the prevailing factors in the habitat (Fig. 1a). The concept has been used as a metric parameter to infer community diversity and complexity [2], in which longer average genome lengths correlate with a more complex and dynamic habitats. The hypothesis is that bacteria with larger genomes can easier cope with such conditions as they encode a larger metabolic and stress tolerance potential [18]. In fact, the evolution of microbial species is affected by the environmental pressures acting over time (Fig. 1b). A clear example of this is the massive genome reduction in bacteria that adapts to a mutualistic/symbiotic lifestyle [cf. 20], resulting in tiny, gene-dense genomes [5]. It remains to be seen whether habitat-specific patterns can be distinguished among different genomes within the species. Certainly, the concept of habitat-specific genomes highlights the role of surrounding environment acting at the core of genome speciation and the evolution of microbial species. The collection of contextual (meta)data, encompassing physical–chemical parameters and allocating the source of a sequence in terms of space and time, surely will allow a better interpretation of unknown genes and species, as well as gaining new insights into the known fraction [28].Figure 1

Bottom Line: The capability and speed in generating genomic data have increased profoundly since the release of the draft human genome in 2000.Here, we propose that scientists should be concerned with attaining an improved equal representation of most of the bacterial tree of life organisms, at the genomic level.Not only will such efforts contribute to our overall understanding of the microbial diversity extant in ecosystems as well as the structuring of the extant genomes, but they will also facilitate the development of better methods for (meta)genome annotation.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil.

ABSTRACT
The capability and speed in generating genomic data have increased profoundly since the release of the draft human genome in 2000. Additionally, sequencing costs have continued to plummet as the next generation of highly efficient sequencing technologies (next-generation sequencing) became available and commercial facilities promote market competition. However, new challenges have emerged as researchers attempt to efficiently process the massive amounts of sequence data being generated. First, the described genome sequences are unequally distributed among the branches of bacterial life and, second, bacterial pan-genomes are often not considered when setting aims for sequencing projects. Here, we propose that scientists should be concerned with attaining an improved equal representation of most of the bacterial tree of life organisms, at the genomic level. Moreover, they should take into account the natural variation that is often observed within bacterial species and the role of the often changing surrounding environment and natural selection pressures, which is central to bacterial speciation and genome evolution. Not only will such efforts contribute to our overall understanding of the microbial diversity extant in ecosystems as well as the structuring of the extant genomes, but they will also facilitate the development of better methods for (meta)genome annotation.

Show MeSH