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Genomics of deep-sea and sub-seafloor microbes.

Siezen RJ, Wilson G - Microb Biotechnol (2009)

View Article: PubMed Central - PubMed

Affiliation: Kluyver Centre for Genomics of Industrial Fermentation; TI Food and Nutrition, 6700AN Wageningen, the Netherlands. r.siezen@cmbi.ru.nl

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The largest metagenome sequencing projects undertaken to date involved surface seawater samples from the Sargasso Sea and the Global Ocean Sampling (GOS) expeditions conducted by Craig Venter and colleagues... This means that there are many more functionalities to be discovered... This surface seawater metagenome sequencing did not take into account the piezophiles (= pressure‐loving) and so it would be reasonable to assume that this is still a large and generally untapped source of potentially useful enzymes and products... The microbes of the very deep differ from those isolated from shallow waters in several aspects... The GOS analysis suggests that near‐surface microorganisms do not need chemotaxis, flagellae or pili to actively swim around in search of food, as they rely mostly on the plentiful O2, CO2 and sunlight for photosynthesis... These properties are characteristic of bacteria with an opportunistic lifestyle and a high degree of gene regulation to respond rapidly to environmental changes when searching for food... A large number of genes are found for synthesis of mono‐ and poly‐unsaturated fatty acids and membrane unsaturation in these deep dwelling microorganisms, as they need to maintain membrane fluidity at low temperature and high pressure... Metagenomics analysis (GS20 pyrosequencing) of ng amounts of DNA extracted from 1–50 m below the seafloor at an Ocean Drilling Program Site (seafloor depth is 1229 m) on the Peru Margin showed that only ∼10% of the sequences had a detectable homology to known sequences... Metagenomics strategies are powerful tools to identify enzymes with novel biocatalytic properties from unculturable members of microbial communities... Both sequence‐based and function‐based screening approaches have been used to identify enzymes with potentially interesting biocatalytic activities from cultured deep‐sea microbes as well as uncultured metagenomes (Table 2)... The adaptive properties of psychrophilic enzymes are high specific activity, relatively low temperature optima and high thermolability... A major challenge will be to develop alternative hosts and their associated vectors for heterologous expression of genes from the diverse phyla existing in the deep‐sea ecosystem... Halophilic enzymes can be applied for non‐aquatic reactions, as they have better thermostability and other unique properties in organic solvents, and could be used in anti‐fouling coating and paint industries, but also for synthesis of optically active substances... Finally, many deep‐sea bacteria can synthesize interesting chemical compounds, such as omega‐3 polyunsaturated fatty acids that are considered useful in reducing the risk of cardiovascular disease, and polyketides which could be used as novel antibiotics.

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The starting point of MetaLook: the world map showing genomics and metagenomics sampling sites. Clicking on a location will provide all genomics and meta data.
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f2: The starting point of MetaLook: the world map showing genomics and metagenomics sampling sites. Clicking on a location will provide all genomics and meta data.

Mentions: Marine microbe researchers are highly organized with respect to storing and sharing their data. The Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) aims to develop global methods for monitoring microbial communities in the ocean and their response to environmental changes. The CAMERA's database (http://camera.calit2.net) includes environmental metagenomic and genomic sequence data, associated environmental parameters (‘metadata’), pre‐computed search results, and software tools to support powerful cross‐analysis of environmental samples (Seshadri et al., 2007) (Fig. 1). The CAMERA includes the Sargasso Sea and GOS expedition data, as well as a vertical profile of marine microbial communities collected at the Hawaii Ocean Time‐Series station ALOHA by Ed DeLong and his research team at MIT. In addition, the MetaLook software has been developed for visualisation, analysis and comparison of marine ecological genomic and metagenomic data with respect to habitat parameters (http://www.megx.net/metalook) (Fig. 2).


Genomics of deep-sea and sub-seafloor microbes.

Siezen RJ, Wilson G - Microb Biotechnol (2009)

The starting point of MetaLook: the world map showing genomics and metagenomics sampling sites. Clicking on a location will provide all genomics and meta data.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3815836&req=5

f2: The starting point of MetaLook: the world map showing genomics and metagenomics sampling sites. Clicking on a location will provide all genomics and meta data.
Mentions: Marine microbe researchers are highly organized with respect to storing and sharing their data. The Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) aims to develop global methods for monitoring microbial communities in the ocean and their response to environmental changes. The CAMERA's database (http://camera.calit2.net) includes environmental metagenomic and genomic sequence data, associated environmental parameters (‘metadata’), pre‐computed search results, and software tools to support powerful cross‐analysis of environmental samples (Seshadri et al., 2007) (Fig. 1). The CAMERA includes the Sargasso Sea and GOS expedition data, as well as a vertical profile of marine microbial communities collected at the Hawaii Ocean Time‐Series station ALOHA by Ed DeLong and his research team at MIT. In addition, the MetaLook software has been developed for visualisation, analysis and comparison of marine ecological genomic and metagenomic data with respect to habitat parameters (http://www.megx.net/metalook) (Fig. 2).

View Article: PubMed Central - PubMed

Affiliation: Kluyver Centre for Genomics of Industrial Fermentation; TI Food and Nutrition, 6700AN Wageningen, the Netherlands. r.siezen@cmbi.ru.nl

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

The largest metagenome sequencing projects undertaken to date involved surface seawater samples from the Sargasso Sea and the Global Ocean Sampling (GOS) expeditions conducted by Craig Venter and colleagues... This means that there are many more functionalities to be discovered... This surface seawater metagenome sequencing did not take into account the piezophiles (= pressure‐loving) and so it would be reasonable to assume that this is still a large and generally untapped source of potentially useful enzymes and products... The microbes of the very deep differ from those isolated from shallow waters in several aspects... The GOS analysis suggests that near‐surface microorganisms do not need chemotaxis, flagellae or pili to actively swim around in search of food, as they rely mostly on the plentiful O2, CO2 and sunlight for photosynthesis... These properties are characteristic of bacteria with an opportunistic lifestyle and a high degree of gene regulation to respond rapidly to environmental changes when searching for food... A large number of genes are found for synthesis of mono‐ and poly‐unsaturated fatty acids and membrane unsaturation in these deep dwelling microorganisms, as they need to maintain membrane fluidity at low temperature and high pressure... Metagenomics analysis (GS20 pyrosequencing) of ng amounts of DNA extracted from 1–50 m below the seafloor at an Ocean Drilling Program Site (seafloor depth is 1229 m) on the Peru Margin showed that only ∼10% of the sequences had a detectable homology to known sequences... Metagenomics strategies are powerful tools to identify enzymes with novel biocatalytic properties from unculturable members of microbial communities... Both sequence‐based and function‐based screening approaches have been used to identify enzymes with potentially interesting biocatalytic activities from cultured deep‐sea microbes as well as uncultured metagenomes (Table 2)... The adaptive properties of psychrophilic enzymes are high specific activity, relatively low temperature optima and high thermolability... A major challenge will be to develop alternative hosts and their associated vectors for heterologous expression of genes from the diverse phyla existing in the deep‐sea ecosystem... Halophilic enzymes can be applied for non‐aquatic reactions, as they have better thermostability and other unique properties in organic solvents, and could be used in anti‐fouling coating and paint industries, but also for synthesis of optically active substances... Finally, many deep‐sea bacteria can synthesize interesting chemical compounds, such as omega‐3 polyunsaturated fatty acids that are considered useful in reducing the risk of cardiovascular disease, and polyketides which could be used as novel antibiotics.

Show MeSH