Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments

ABSTRACTThe South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration, and primary productivity in the global oceans. As a direct result, deep-sea sediments are thin and contain small amounts of labile organic carbon. It was recently shown that the entire SPG sediment column is oxygenated and may be representative of up to a third of the global marine environment. To understand the microbial processes that contribute to the removal of the labile organic matter at the water-sediment interface, a sediment sample was collected and subjected to metagenomic sequencing and analyses. Analysis of nine partially reconstructed environmental genomes, which represent approximately one-third of the microbial community, revealed that the members of the SPG surface sediment microbial community are phylogenetically distinct from surface/upper-ocean organisms. These genomes represent a wide distribution of novel organisms, including deep-branchingAlphaproteobacteria, two novel organisms within theProteobacteria, and new members of theNitrospirae,Nitrospinae, and candidate phylum NC10. These genomes contain evidence for microbially mediated metal (iron/manganese) oxidation and carbon fixation linked to nitrification. Additionally, despite hypothesized energy limitation, members of the SPG microbial community had motility and chemotaxis genes and possessed mechanisms for the degradation of high-molecular-weight organic matter. This study contributes to our understanding of the metabolic potential of microorganisms in deep-sea oligotrophic sediments and their impact on local carbon geochemistry.IMPORTANCEThis research provides insight into the microbial metabolic potential of organisms inhabiting oxygenated deep-sea marine sediments. Current estimates suggest that these environments account for up to a third of the global marine sediment habitat. Nine novel deep-sea microbial genomes were reconstructed from a metagenomic data set and expand the limited number of environmental genomes from deep-sea sediment environments. This research provides phylogeny-linked insight into critical metabolisms, including carbon fixation associated with nitrification, which is assignable to members of the marine group 1Thaumarchaeota,Nitrospinae, andNitrospiraeand neutrophilic metal (iron/manganese) oxidation assignable to a novel proteobacterium.

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Trophic state of benthic deep-sea ecosystems from two different continental margins off Iberia

Biogeosciences ◽

10.5194/bg-10-2945-2013 ◽

2013 ◽

Vol 10 (5) ◽

pp. 2945-2957 ◽

Cited By ~ 10

Author(s):

A. Dell'Anno ◽

A. Pusceddu ◽

C. Corinaldesi ◽

M. Canals ◽

S. Heussner ◽

...

Keyword(s):

Organic Matter ◽

Water Depth ◽

Surface Waters ◽

Deep Sea ◽

Nutritional Value ◽

Trophic State ◽

Phytoplankton Bloom ◽

Continental Margins ◽

Organic C ◽

Deep Sea Sediments

Abstract. The bioavailability of organic matter in benthic deep-sea ecosystems, commonly used to define their trophic state, can greatly influence key ecological processes such as biomass production and nutrient cycling. Here, we assess the trophic state of deep-sea sediments from open slopes and canyons of the Catalan (NW Mediterranean) and Portuguese (NE Atlantic) continental margins, offshore east and west Iberia, respectively, by using a biomimetic approach based on enzymatic digestion of protein and carbohydrate pools. Patterns of sediment trophic state were analyzed in relation to increasing water depth, including repeated samplings over a 3 yr period in the Catalan margin. Two out of the three sampling periods occurred a few months after dense shelf water cascading events. The benthic deep-sea ecosystems investigated in this study were characterized by high amounts of bioavailable organic matter when compared to other deep-sea sediments. Bioavailable organic matter and its nutritional value were significantly higher in the Portuguese margin than in the Catalan margin, thus reflecting differences in primary productivity of surface waters reported for the two regions. Similarly, sediments of the Catalan margin were characterized by significantly higher food quantity and quality in spring, when the phytoplankton bloom occurs in surface waters, than in summer and autumn. Differences in the benthic trophic state of canyons against open slopes were more evident in the Portuguese than in the Catalan margin. In both continental margins, bioavailable organic C concentrations did not vary or increase with increasing water depth. Overall, our findings suggest that the intensity of primary production processes along with the lateral transfer of organic particles, even amplified by episodic events, can have a role in controlling the quantity and distribution of bioavailable organic detritus and its nutritional value along these continental margin ecosystems.

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Copper Porphyrins in Deep-Sea Sediments: A Possible Indicator of Oxidized Terrestrial Organic Matter

Science ◽

10.1126/science.201.4350.49 ◽

1978 ◽

Vol 201 (4350) ◽

pp. 49-51 ◽

Cited By ~ 51

Author(s):

S. E. PALMER ◽

E. W. BAKER

Keyword(s):

Organic Matter ◽

Deep Sea ◽

Terrestrial Organic Matter ◽

Deep Sea Sediments

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Metabolic Diversity within the Globally Abundant Marine Group IIEuryarchaeaOffers Insight into Ecological Patterns

10.1101/349548 ◽

2018 ◽

Author(s):

Benjamin J Tully

Keyword(s):

Organic Matter ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Metabolic Diversity ◽

Metabolic Potential ◽

Surface Ocean ◽

Ecological Patterns ◽

Reference Genomes ◽

Insight Into

AbstractDespite their discovery over 25 years ago, the Marine Group IIEuryarchaea(MGII) have remained a difficult group of organisms to study, lacking cultured isolates and genome references. The MGII have been identified in marine samples from around the world and evidence supports a photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with the remineralization of high molecular weight organic matter. Divided between two clades, the MGII have distinct ecological patterns that are not understood based on the limited number of available genomes. Here, I present the comparative genomic analysis of 250 MGII genomes, providing the most detailed view of these mesophilic archaea to-date. This analysis identified 17 distinct subclades including nine subclades that previously lacked reference genomes. The metabolic potential and distribution of the MGII genera revealed distinct roles in the environment, identifying algal-saccharide-degrading coastal subclades, protein-degrading oligotrophic surface ocean subclades, and mesopelagic subclades lacking proteorhodopsins common in all other subclades. This study redefines the MGII and provides an avenue for understanding the role these organisms play in the cycling of organic matter throughout the water column.

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