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Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea.

Li M, Baker BJ, Anantharaman K, Jain S, Breier JA, Dick GJ - Nat Commun (2015)

Bottom Line: However, little is known about the microorganisms that underpin this key step of the global carbon cycle in the deep oceans.Here we present genomic and transcriptomic evidence that five ubiquitous archaeal groups actively use proteins, carbohydrates, fatty acids and lipids as sources of carbon and energy at depths ranging from 800 to 4,950 m in hydrothermal vent plumes and pelagic background seawater across three different ocean basins.Our results shed light on the ecological and physiological properties of ubiquitous marine archaea and highlight their versatile metabolic strategies in deep oceans that might play a critical role in global carbon cycling.

View Article: PubMed Central - PubMed

Affiliation: Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan 48109, USA.

ABSTRACT
Microbial activity is one of the most important processes to mediate the flux of organic carbon from the ocean surface to the seafloor. However, little is known about the microorganisms that underpin this key step of the global carbon cycle in the deep oceans. Here we present genomic and transcriptomic evidence that five ubiquitous archaeal groups actively use proteins, carbohydrates, fatty acids and lipids as sources of carbon and energy at depths ranging from 800 to 4,950 m in hydrothermal vent plumes and pelagic background seawater across three different ocean basins. Genome-enabled metabolic reconstructions and gene expression patterns show that these marine archaea are motile heterotrophs with extensive mechanisms for scavenging organic matter. Our results shed light on the ecological and physiological properties of ubiquitous marine archaea and highlight their versatile metabolic strategies in deep oceans that might play a critical role in global carbon cycling.

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Proposed transcriptionally active heterotrophic metabolic pathways.Green, blue and red indicate heterotrophic pathways found in MG-I, MG-II and MG-III, respectively.
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f2: Proposed transcriptionally active heterotrophic metabolic pathways.Green, blue and red indicate heterotrophic pathways found in MG-I, MG-II and MG-III, respectively.

Mentions: In contrast to MG-I, -II and -III, the genomic bins of Parvarchaeota and DHVEG-6 contained only one gene related to the S01C family (DegP peptidase) and two genes affiliated with M48B family (HtpX peptidase), and no transcripts of these genes were detected (Supplementary Table 5). These results indicate that (1) MG-I, -II, -III, Parvarchaeota and DHVEG-6 are all capable of degrading and utilizing extracellular proteins; (2) protein degradation is a major metabolic pathway for MG-II and -III while a minor metabolic route for MG-I; and (3) the different archaeal groups each have a different suite of protein degradation genes, suggesting niche differentiation on the basis of substrate (Table 1 and Fig. 2).


Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea.

Li M, Baker BJ, Anantharaman K, Jain S, Breier JA, Dick GJ - Nat Commun (2015)

Proposed transcriptionally active heterotrophic metabolic pathways.Green, blue and red indicate heterotrophic pathways found in MG-I, MG-II and MG-III, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4660358&req=5

f2: Proposed transcriptionally active heterotrophic metabolic pathways.Green, blue and red indicate heterotrophic pathways found in MG-I, MG-II and MG-III, respectively.
Mentions: In contrast to MG-I, -II and -III, the genomic bins of Parvarchaeota and DHVEG-6 contained only one gene related to the S01C family (DegP peptidase) and two genes affiliated with M48B family (HtpX peptidase), and no transcripts of these genes were detected (Supplementary Table 5). These results indicate that (1) MG-I, -II, -III, Parvarchaeota and DHVEG-6 are all capable of degrading and utilizing extracellular proteins; (2) protein degradation is a major metabolic pathway for MG-II and -III while a minor metabolic route for MG-I; and (3) the different archaeal groups each have a different suite of protein degradation genes, suggesting niche differentiation on the basis of substrate (Table 1 and Fig. 2).

Bottom Line: However, little is known about the microorganisms that underpin this key step of the global carbon cycle in the deep oceans.Here we present genomic and transcriptomic evidence that five ubiquitous archaeal groups actively use proteins, carbohydrates, fatty acids and lipids as sources of carbon and energy at depths ranging from 800 to 4,950 m in hydrothermal vent plumes and pelagic background seawater across three different ocean basins.Our results shed light on the ecological and physiological properties of ubiquitous marine archaea and highlight their versatile metabolic strategies in deep oceans that might play a critical role in global carbon cycling.

View Article: PubMed Central - PubMed

Affiliation: Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan 48109, USA.

ABSTRACT
Microbial activity is one of the most important processes to mediate the flux of organic carbon from the ocean surface to the seafloor. However, little is known about the microorganisms that underpin this key step of the global carbon cycle in the deep oceans. Here we present genomic and transcriptomic evidence that five ubiquitous archaeal groups actively use proteins, carbohydrates, fatty acids and lipids as sources of carbon and energy at depths ranging from 800 to 4,950 m in hydrothermal vent plumes and pelagic background seawater across three different ocean basins. Genome-enabled metabolic reconstructions and gene expression patterns show that these marine archaea are motile heterotrophs with extensive mechanisms for scavenging organic matter. Our results shed light on the ecological and physiological properties of ubiquitous marine archaea and highlight their versatile metabolic strategies in deep oceans that might play a critical role in global carbon cycling.

Show MeSH