Nd–Sr isotope and REY geochemistry of metalliferous sediments in a low-temperature off-axis hydrothermal environment (Costa Rica margin)

2012 ◽  
Vol 315-318 ◽  
pp. 132-142 ◽  
Author(s):  
Marc Steinmann ◽  
Sabine Bodeï ◽  
Martine Buatier
Keyword(s):  
Costa Rica ◽  
Low Temperature ◽  
Sr Isotope ◽  
Metalliferous Sediments ◽  
Costa Rica Margin ◽  
Hydrothermal Environment ◽  
Rey Geochemistry

scholarly journals Helarchaeota and co-occurring sulfate-reducing bacteria in subseafloor sediments from the Costa Rica Margin

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Rui Zhao ◽  
Jennifer F. Biddle
Keyword(s):  
Costa Rica ◽  
Metabolic Pathways ◽  
Phylogenetic Analyses ◽  
Sulfate Reducing Bacteria ◽  
Sulfate Reducing ◽  
Hydrocarbon Emission ◽  
Costa Rica Margin ◽  
Reducing Bacteria ◽  
Electron Transfers ◽  
Deep Sediments

AbstractDeep sediments host many archaeal lineages, including the Asgard superphylum which contains lineages predicted to require syntrophic partnerships. Our knowledge about sedimentary archaeal diversity and their metabolic pathways and syntrophic partners is still very limited. We present here new genomes of Helarchaeota and the co-occurring sulfate-reducing bacteria (SRB) recovered from organic-rich sediments off Costa Rica Margin. Phylogenetic analyses revealed three new metagenome-assembled genomes (MAGs) affiliating with Helarchaeota, each of which has three variants of the methyl-CoM reductase-like (MCR-like) complex that may enable them to oxidize short-chain alkanes anaerobically. These Helarchaeota have no multi-heme cytochromes but have Group 3b and Group 3c [NiFe] hydrogenases, and formate dehydrogenase, and therefore have the capacity to transfer the reducing equivalents (in the forms of hydrogen and formate) generated from alkane oxidation to external partners. We also recovered five MAGs of SRB affiliated with the class of Desulfobacteria, two of which showed relative abundances (represented by genome coverages) positively correlated with those of the three Helarchaeota. Genome analysis suggested that these SRB bacteria have the capacity of H2 and formate utilization and could facilitate electron transfers from other organisms by means of these reduced substances. Their co-occurrence and metabolic features suggest that Helarchaeota may metabolize synergistically with some SRB, and together exert an important influence on the carbon cycle by mitigating the hydrocarbon emission from sediments to the overlying ocean.

scholarly journals Using a Ladder of Seeps With Computer Decision Processes to Explore for and Evaluate Cold Seeps on the Costa Rica Active Margin

2021 ◽  
Vol 9 ◽  
Author(s):  
Peter Vrolijk ◽  
Lori Summa ◽  
Benjamin Ayton ◽  
Paraskevi Nomikou ◽  
Andre Hüpers ◽  
...  
Keyword(s):  
Costa Rica ◽  
Chemical Compounds ◽  
Decision Processes ◽  
Mission Planning ◽  
Cold Seeps ◽  
Fluid Sample ◽  
Deep Subsurface ◽  
Costa Rica Margin ◽  
Query Structure ◽  
Scientific Questions

Natural seeps occur at the seafloor as loci of fluid flow where the flux of chemical compounds into the ocean supports unique biologic communities and provides access to proxy samples of deep subsurface processes. Cold seeps accomplish this with minimal heat flux. While individual expertize is applied to locate seeps, such knowledge is nowhere consolidated in the literature, nor are there explicit approaches for identifying specific seep types to address discrete scientific questions. Moreover, autonomous exploration for seeps lacks any clear framework for efficient seep identification and classification. To address these shortcomings, we developed a Ladder of Seeps applied within new decision-assistance algorithms (Spock) to assist in seep exploration on the Costa Rica margin during the R/V Falkor 181210 cruise in December, 2018. This Ladder of Seeps [derived from analogous astrobiology criteria proposed by Neveu et al. (2018)] was used to help guide human and computer decision processes for ROV mission planning. The Ladder of Seeps provides a methodical query structure to identify what information is required to confirm a seep either: 1) supports seafloor life under extreme conditions, 2) supports that community with active seepage (possible fluid sample), or 3) taps fluids that reflect deep, subsurface geologic processes, but the top rung may be modified to address other scientific questions. Moreover, this framework allows us to identify higher likelihood seep targets based on existing incomplete or easily acquired data, including MBES (Multi-beam echo sounder) water column data. The Ladder of Seeps framework is based on information about the instruments used to collect seep information (e.g., are seeps detectable by the instrument with little chance of false positives?) and contextual criteria about the environment in which the data are collected (e.g., temporal variability of seep flux). Finally, the assembled data are considered in light of a Last-Resort interpretation, which is only satisfied once all other plausible data interpretations are excluded by observation. When coupled with decision-making algorithms that incorporate expert opinion with data acquired during the Costa Rica experiment, the Ladder of Seeps proved useful for identifying seeps with deep-sourced fluids, as evidenced by results of geochemistry analyses performed following the expedition.

scholarly journals “Sifarchaeota” a novel Asgard phylum from Costa Rica sediment capable of polysaccharide degradation and anaerobic methylotrophy

2021 ◽  
Author(s):  
Ibrahim F. Farag ◽  
Rui Zhao ◽  
Jennifer F. Biddle
Keyword(s):  
Costa Rica ◽  
Marine Sediments ◽  
Genomic Analysis ◽  
Close Relation ◽  
Comparative Genomic ◽  
Niche Adaptation ◽  
Genomic Analyses ◽  
Ecological Roles ◽  
Costa Rica Margin ◽  
Metagenome Sequencing

The Asgard superphylum is a deeply branching monophyletic group of Archaea, recently described as some of the closest relatives of the eukaryotic ancestor. The wide application of genomic analyses from metagenome sequencing has established six distinct phyla, whose genomes encode for diverse metabolic capacities and play important biogeochemical and ecological roles in marine sediments. Here, we describe two metagenome-assembled genomes (MAGs) recovered from deep marine sediments off Costa Rica margin, defining a novel lineage phylogenetically married to Thorarchaeota, as such we propose the name “Sifarchaeota” for this phylum. The two “Sifarchaeota” MAGs encode for an anaerobic pathway for methylotrophy enabling the utilization of C1-C3 compounds (methanol and methylamines) to synthesize acetyl CoA. The MAGs showed a remarkable saccharolytic capabilities compared to other Asgard lineages and encoded for diverse classes of carbohydrate active enzymes (CAZymes) targeting different mono-, di- and oligosaccharides. Comparative genomic analysis based on the full metabolic profiles of different Asgard lineages revealed the close relation between “Sifarchaeota” and Odinarchaeota MAGs, which suggested similar metabolic potentials and ecological roles. Furthermore, we identified multiple HGT events from different bacterial donors within “Sifarchaetoa” MAGs, which hypothetically expanded “Sifarchaeota” capacities for substrate utilization, energy production and niche adaptation. Importance The exploration of deep marine sediments has unearthed many new lineages of microbes. The finding of this novel phylum of Asgard archaea is important since understanding the diversity and evolution of Asgard archaea may inform also about the evolution of eukaryotic cells. The comparison of metabolic potentials of the Asgard archaea can help inform about selective pressures the lineages have faced during evolution.

scholarly journals Helarchaeota and Co-occurring Sulfate-Reducing Bacteria in Subseafloor Sediments from the Costa Rica Margin

2021 ◽  
Author(s):  
Rui Zhao ◽  
Jennifer F. Biddle
Keyword(s):  
Costa Rica ◽  
Metabolic Pathways ◽  
Formate Dehydrogenase ◽  
Sulfate Reducing Bacteria ◽  
Sulfate Reducing ◽  
Hydrocarbon Emission ◽  
Costa Rica Margin ◽  
Reducing Bacteria ◽  
Electron Transfers ◽  
Deep Sediments

AbstractDeep sediments host many archaeal lineages, including those of the Asgard superphylum that may depend on/require syntrophic partnerships. Our knowledge about sedimentary archaeal diversity and their metabolic pathways and syntrophic partners is still very limited. We present here new genomes of Helarchaeota and co-occurring sulfate-reducing bacteria (SRB) recovered from organic-rich sediments off Costa Rica Margin. Our molecular analyses revealed three new metagenome-assembled genomes (MAGs) affiliating with Helarchaeota, each of which has three variants of the methyl-CoM reductase-like (MCR-like) complex that may enable them to oxidize short-chain alkanes anaerobically. These Helarchaeota have no multi-heme cytochromes (MHCs) but have Group 3b and Group 3c [NiFe] hydrogenases, and formate dehydrogenase, and therefore could transfer the reducing equivalents generated from alkane oxidation to external partners via the transfer of these substances. We also recovered five MAGs of SRB affiliated with the class of Desulfobacteria, two of which showed relative abundances (represented by genome coverages) positively correlated with those of the three Helarchaeota. Genome analysis suggested that these SRB bacteria have the capacity of H2 and formate utilizations and may facilitate electron transfers from other organisms by means of these reduced substances. Our findings suggest that Helarchaeota may metabolize synergistically with SRB in marine anoxic sediments, and exert an important influence on the carbon cycle by mitigating the hydrocarbon emission from sediments to the overlying ocean.

scholarly journals A hydrothermal seep on the Costa Rica margin: middle ground in a continuum of reducing ecosystems

2012 ◽  
Vol 279 (1738) ◽  
pp. 2580-2588 ◽  
Author(s):  
Lisa A. Levin ◽  
Victoria J. Orphan ◽  
Greg W. Rouse ◽  
Anthony E. Rathburn ◽  
William Ussler ◽  
...  
Keyword(s):  
Costa Rica ◽  
Middle Ground ◽  
Costa Rica Margin
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