Limits...
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.

Show MeSH
Genes for extracellular peptidases and carbohydrate-active enzymes.Carbohydrate-active enzymes (CAZYs) include glycoside hydrolases (GHs), glycosyl transferases (GTs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), auxiliary activities (AAs) and carbohydrate-binding modules (CBMs). The two bar graphs indicate the unique genes (60% amino acids identity) for extracellular peptidases and CAZYs identified in five archaeal groups, and the general function description for extracellular peptidases and carbohydrate-active enzymes is listed in Supplementary Tables 5–7. The gene number has been normalized to the total number of genes recovered from each archaeal group.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4660358&req=5

f1: Genes for extracellular peptidases and carbohydrate-active enzymes.Carbohydrate-active enzymes (CAZYs) include glycoside hydrolases (GHs), glycosyl transferases (GTs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), auxiliary activities (AAs) and carbohydrate-binding modules (CBMs). The two bar graphs indicate the unique genes (60% amino acids identity) for extracellular peptidases and CAZYs identified in five archaeal groups, and the general function description for extracellular peptidases and carbohydrate-active enzymes is listed in Supplementary Tables 5–7. The gene number has been normalized to the total number of genes recovered from each archaeal group.

Mentions: Our data indicate that these deep-sea archaea are metabolically active as aerobic heterotrophs or, in the case of MG-I, mixotrophs. Genes encoding 28 different families of extracellular peptidases for protein degradation were identified. Four of these families were dominant (S08A, M28A, M14A and M22), comprising 70.5%, 72% and 52% of total extracellular peptidase genes in deep-sea MG-I, -II and -III, respectively (Fig. 1, Supplementary Fig. 6a and Supplementary Table 5). Transcripts of these extracellular peptidase genes were among the most abundant in the transcriptomes of MG-II and MG-III in both Guaymas and Cayman plumes (Supplementary Figs 6a and 7). For MG-I, in addition to the S08A and M22 peptidase families, transcripts for M01, S26A and S26B were also detected (Supplementary Table 5), though the most abundant transcripts in the MG-I transcriptome were related to the transport and oxidation of ammonia (Supplementary Fig. 8). Interestingly, the suite of specific extracellular peptidases for which transcripts were detected varied between archaeal groups (Supplementary Fig. 6a), suggesting diverse protein utilization capabilities by MG-I, -II and -III in the deep oceans35.


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)

Genes for extracellular peptidases and carbohydrate-active enzymes.Carbohydrate-active enzymes (CAZYs) include glycoside hydrolases (GHs), glycosyl transferases (GTs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), auxiliary activities (AAs) and carbohydrate-binding modules (CBMs). The two bar graphs indicate the unique genes (60% amino acids identity) for extracellular peptidases and CAZYs identified in five archaeal groups, and the general function description for extracellular peptidases and carbohydrate-active enzymes is listed in Supplementary Tables 5–7. The gene number has been normalized to the total number of genes recovered from each archaeal group.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Genes for extracellular peptidases and carbohydrate-active enzymes.Carbohydrate-active enzymes (CAZYs) include glycoside hydrolases (GHs), glycosyl transferases (GTs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), auxiliary activities (AAs) and carbohydrate-binding modules (CBMs). The two bar graphs indicate the unique genes (60% amino acids identity) for extracellular peptidases and CAZYs identified in five archaeal groups, and the general function description for extracellular peptidases and carbohydrate-active enzymes is listed in Supplementary Tables 5–7. The gene number has been normalized to the total number of genes recovered from each archaeal group.
Mentions: Our data indicate that these deep-sea archaea are metabolically active as aerobic heterotrophs or, in the case of MG-I, mixotrophs. Genes encoding 28 different families of extracellular peptidases for protein degradation were identified. Four of these families were dominant (S08A, M28A, M14A and M22), comprising 70.5%, 72% and 52% of total extracellular peptidase genes in deep-sea MG-I, -II and -III, respectively (Fig. 1, Supplementary Fig. 6a and Supplementary Table 5). Transcripts of these extracellular peptidase genes were among the most abundant in the transcriptomes of MG-II and MG-III in both Guaymas and Cayman plumes (Supplementary Figs 6a and 7). For MG-I, in addition to the S08A and M22 peptidase families, transcripts for M01, S26A and S26B were also detected (Supplementary Table 5), though the most abundant transcripts in the MG-I transcriptome were related to the transport and oxidation of ammonia (Supplementary Fig. 8). Interestingly, the suite of specific extracellular peptidases for which transcripts were detected varied between archaeal groups (Supplementary Fig. 6a), suggesting diverse protein utilization capabilities by MG-I, -II and -III in the deep oceans35.

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